Exomiser Analysis Results for Mu03

Analysis Settings

Settings used for this analysis:

---
vcf: "/home/sieny/Gemini_Data/SHFam/AllSH.vcf"
ped: "/home/sieny/Gemini_Data/SHFam/sfam.ped"
proband: "Mu03"
hpoIds:
- "HP:0001112"
modeOfInheritance: "AUTOSOMAL_RECESSIVE"
analysisMode: "PASS_ONLY"
frequencySources:
- "THOUSAND_GENOMES"
- "ESP_AFRICAN_AMERICAN"
- "ESP_EUROPEAN_AMERICAN"
- "ESP_ALL"
- "EXAC_AFRICAN_INC_AFRICAN_AMERICAN"
- "EXAC_AMERICAN"
- "EXAC_EAST_ASIAN"
- "EXAC_SOUTH_ASIAN"
- "EXAC_FINNISH"
- "EXAC_NON_FINNISH_EUROPEAN"
- "EXAC_OTHER"
pathogenicitySources:
- "POLYPHEN"
- "MUTATION_TASTER"
- "SIFT"
analysisSteps:
- priorityType: "HIPHIVE_PRIORITY"
- minPriorityScore: 0.501
  priorityType: "HIPHIVE_PRIORITY"
- {}
- decoratedFilter:
    maxFreq: 1.0
- decoratedFilter:
    keepNonPathogenic: true
- modeOfInheritance: "AUTOSOMAL_RECESSIVE"
- priorityType: "OMIM_PRIORITY"
---
outputPassVariantsOnly: false
outputPrefix: "/home/sieny/Gemini_Data/SHFam/leber-hiphive-genome-PASS_ONLY"
outputFormats:
- "HTML"
- "VCF"
- "TSV_GENE"
- "TSV_VARIANT"
numGenes: 0

Filtering Summary

Filter Report Passed filter Failed filter
Gene priority score
    Genes filtered for minimum HIPHIVE_PRIORITY score of 0.501
112 0
Regulatory feature 340 0
Frequency
    Variants filtered for maximum allele frequency of 1.00%
340 0
Pathogenicity
    Retained all non-pathogenic variants of all types. Scoring was applied, but the filter passed all variants.
340 0
Inheritance
    Genes filtered for compatibility with AUTOSOMAL_RECESSIVE inheritance.
112 0

Variant Type Distribution

Variant Type Ab01 Mu03 Sh02
FRAMESHIFT_ELONGATION 0 0 0
FRAMESHIFT_TRUNCATION 0 1 0
FRAMESHIFT_VARIANT 0 0 0
INTERNAL_FEATURE_ELONGATION 0 0 0
FEATURE_TRUNCATION 0 0 0
MNV 1 7 1
STOP_GAINED 1 1 1
STOP_LOST 0 0 0
START_LOST 0 0 0
SPLICE_ACCEPTOR_VARIANT 0 0 0
SPLICE_DONOR_VARIANT 0 0 0
MISSENSE_VARIANT 5 20 11
INFRAME_INSERTION 0 0 0
DISRUPTIVE_INFRAME_INSERTION 0 0 0
INFRAME_DELETION 0 0 0
DISRUPTIVE_INFRAME_DELETION 0 0 0
FIVE_PRIME_UTR_TRUNCATION 0 0 0
THREE_PRIME_UTR_TRUNCATION 0 0 0
SPLICE_REGION_VARIANT 3 5 4
STOP_RETAINED_VARIANT 0 0 0
INITIATOR_CODON_VARIANT 0 0 0
SYNONYMOUS_VARIANT 6 7 7
CODING_TRANSCRIPT_INTRON_VARIANT 88 175 82
NON_CODING_TRANSCRIPT_EXON_VARIANT 1 0 0
NON_CODING_TRANSCRIPT_INTRON_VARIANT 1 0 0
THREE_PRIME_UTR_EXON_VARIANT 2 1 4
FIVE_PRIME_UTR_INTRON_VARIANT 1 3 1
THREE_PRIME_UTR_INTRON_VARIANT 0 0 0
UPSTREAM_GENE_VARIANT 0 1 0
DOWNSTREAM_GENE_VARIANT 0 0 0
INTERGENIC_VARIANT 3 5 7

Prioritised Genes

Exomiser Score: 0.818

Phenotype Score: 0.584

Variant Score: 0.950

Phenotype matches:
Phenotypic similarity 0.584 to Leber Congenital Amaurosis associated with AIPL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0012795, Abnormality of the optic disc
Phenotypic similarity 0.416 to mouse mutant involving AIPL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001326, retinal degeneration
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:604393 Cone-rod dystrophy - autosomal recessive
ORPHA:1872 Cone Rod Dystrophy
ORPHA:65 Leber Congenital Amaurosis
Top ranked variants:

Exomiser Score: 0.644

Phenotype Score: 0.518

Variant Score: 0.925

Phenotype matches:
Phenotypic similarity 0.518 to Camurati-Engelmann Disease associated with TGFB1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Known diseases:
OMIM:131300 Camurati-Engelmann disease - autosomal dominant
OMIM:219700 Cystic fibrosis lung disease, modifier of (susceptibility)
ORPHA:1328 Camurati-Engelmann Disease
ORPHA:586 Cystic Fibrosis
Top ranked variants:
MISSENSE chr19:g.41858769T>G [.:0/1:.] rs945084245 (variation viewer)
Variant score: 1.000 CONTRIBUTING VARIANT
Transcripts:
TGFB1:uc002oqh.2:c.181A>C:p.(Ser61Arg)
TGFB1:uc002oqi.3:c.-30+1662T>G:p.(=)
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.017 (B)
Mutation Taster: 1.000 (P)
SIFT: 0.053 (D)
Frequency Data:
No frequency data
NON_FS_SUBSTITUTION chr19:g.41858747ACCT>CCCC [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.595

Phenotype Score: 0.520

Variant Score: 0.900

Phenotype matches:
Phenotypic similarity 0.520 to Infantile Onset Spinocerebellar Ataxia associated with TWNK.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:271245 Mitochondrial DNA depletion syndrome 7 - autosomal recessive
OMIM:609286 Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 3 - autosomal dominant
OMIM:616138 Perrault syndrome 5 - autosomal recessive
ORPHA:1186 Infantile Onset Spinocerebellar Ataxia
Top ranked variants:
SPLICING chr10:g.102750621CGT>TGC [0/1:1/1:1/1] rs386747051 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.590

Phenotype Score: 0.518

Variant Score: 0.900

Phenotype matches:
Phenotypic similarity 0.518 to Birdshot Chorioretinopathy associated with HLA-A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
ORPHA:179 Birdshot Chorioretinopathy
Top ranked variants:

Exomiser Score: 0.566

Phenotype Score: 0.510

Variant Score: 0.899

Phenotype matches:
Phenotypic similarity 0.510 to Acrocallosal syndrome associated with KIF7.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Known diseases:
OMIM:200990 Acrocallosal syndrome - autosomal dominant/recessive
OMIM:607131 ?Al-Gazali-Bakalinova syndrome (unconfirmed)
OMIM:614120 ?Hydrolethalus syndrome 2 (unconfirmed)
ORPHA:166024 Multiple Epiphyseal Dysplasia, Al-Gazali Type
ORPHA:36 Acrocallosal Syndrome
Top ranked variants:
MISSENSE chr15:g.90191914T>G [.:0/1:.]
Variant score: 1.000 CONTRIBUTING VARIANT
Transcripts:
KIF7:uc002bof.2:c.1015A>C:p.(Thr339Pro)
KIF7:uc002bog.2:c.646A>C:p.(Thr216Pro)
Pathogenicity Data:
Best Score: 0.999874
Polyphen2: 0.856 (P)
Mutation Taster: 1.000 (P)
SIFT: 0.003 (D)
Frequency Data:
No frequency data
MISSENSE chr15:g.90176163G>C [.:0/1:.] rs764218371 (variation viewer)
Variant score: 0.798 CONTRIBUTING VARIANT
Transcripts:
KIF7:uc002bof.2:c.2783C>G:p.(Ala928Gly)
KIF7:uc010upw.1:c.1241C>G:p.(Ala414Gly)
Pathogenicity Data:
Best Score: 0.202
Polyphen2: 0.018 (B)
SIFT: 0.202 (T)
Frequency Data:
No frequency data

Exomiser Score: 0.490

Phenotype Score: 0.501

Variant Score: 0.875

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
SPLICING chr1:g.204413297CGG>TGA [.:.:0/1] rs386638669 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
NON_FS_SUBSTITUTION chr1:g.204399061AGGG>GGGA [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
SPLICING chr1:g.204413297CGG>TGA [.:0/1:.] rs386638669 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
SYNONYMOUS chr1:g.204403689C>T [.:0/1:0/1] rs114076026 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.0394%
ExAC AMR: 0.0088%

Exomiser Score: 0.460

Phenotype Score: 0.512

Variant Score: 0.850

Phenotype matches:
Phenotypic similarity 0.512 to Neonatal Adrenoleukodystrophy associated with PEX6.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:614862 Peroxisome biogenesis disorder 4A - autosomal recessive
OMIM:614863 Peroxisome biogenesis disorder 4B - autosomal recessive
OMIM:616617 Heimler syndrome 2 - unknown
ORPHA:44 Neonatal Adrenoleukodystrophy
ORPHA:772 Infantile Refsum Disease
ORPHA:912 Zellweger Syndrome
Top ranked variants:
NON_FS_SUBSTITUTION chr6:g.42932200GGC>TGT [.:1/1:.] rs386700658 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.043

Phenotype Score: 0.539

Variant Score: 0.500

Phenotype matches:
Phenotypic similarity 0.539 to Retinitis pigmentosa 71 associated with IFT172.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Phenotypic similarity 0.464 to zebrafish mutant involving HGNC:30391.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - ZP:0001272, abnormal(ly) physical object quality midbrain neural keel
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
Known diseases:
OMIM:615630 Short-rib thoracic dysplasia 10 with or without polydactyly - autosomal recessive
OMIM:616394 Retinitis pigmentosa 71 - autosomal recessive
ORPHA:110 Bardet-Biedl Syndrome
ORPHA:474 Jeune Syndrome
ORPHA:791 Retinitis Pigmentosa
Top ranked variants:
MISSENSE chr2:g.27707975A>C [.:0/1:.]
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.998 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.000 (D)
Frequency Data:
No frequency data
INTRONIC chr2:g.27669365G>GT [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr2:g.27708078T>A [.:0/1:0/1] rs55759707 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7987%

Exomiser Score: 0.041

Phenotype Score: 0.533

Variant Score: 0.500

Phenotype matches:
Phenotypic similarity 0.533 to mouse mutant involving SPTBN4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001330, abnormal optic nerve morphology
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
MISSENSE chr19:g.41062930T>G [.:0/1:.]
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.985 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.001 (D)
Frequency Data:
No frequency data
INTRONIC chr19:g.41008446T>G [.:0/1:.] rs879143736 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.41071531A>C [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.41071540T>C [.:0/1:.] rs779102882 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC SAS: 0.0121%
INTRONIC chr19:g.41071548ACCCA>CCCCC [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.036

Phenotype Score: 0.520

Variant Score: 0.500

Phenotype matches:
Phenotypic similarity 0.520 to Muscle-Eye-Brain Disease associated with LARGE1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Phenotypic similarity 0.468 to mouse mutant involving LARGE1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0002699, abnormal vitreous body morphology
Known diseases:
OMIM:608840 Muscular dystrophy-dystroglycanopathy - autosomal recessive
OMIM:613154 Muscular dystrophy-dystroglycanopathy - autosomal recessive
ORPHA:588 Muscle-Eye-Brain Disease
Top ranked variants:
MISSENSE chr22:g.33670469A>G [.:0/1:.] rs954461878 (variation viewer)
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.917 (P)
Mutation Taster: 1.000 (P)
SIFT: 0.105 (T)
Frequency Data:
No frequency data
INTRONIC chr22:g.33670704A>G [0/1:0/1:.] rs16992039 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.3395%

Exomiser Score: 0.036

Phenotype Score: 0.520

Variant Score: 0.500

Phenotype matches:
Phenotypic similarity 0.520 to ?Phosphoenolpyruvate carboxykinase-1, cytosolic, deficiency associated with PCK1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:261680 ?Phosphoenolpyruvate carboxykinase-1, cytosolic, deficiency (unconfirmed)
Top ranked variants:
MISSENSE chr20:g.56138185A>G [.:0/1:.] rs983640947 (variation viewer)
Variant score: 1.000 CONTRIBUTING VARIANT
Transcripts:
PCK1:uc002xyn.4:c.712A>G:p.(Asn238Asp)
PCK1:uc010zzm.2:c.11-1040A>G:p.(=)
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 1.000 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.000 (D)
Frequency Data:
No frequency data
INTERGENIC chr20:g.56131387ACG>CTT [0/1:0/1:0/1] rs796790348 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PCK1:uc010zzm.2::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.036

Phenotype Score: 0.520

Variant Score: 0.499

Phenotype matches:
Phenotypic similarity 0.520 to Peroxisomal Acyl-Coa Oxidase Deficiency associated with ACOX1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:264470 Peroxisomal acyl-CoA oxidase deficiency - autosomal recessive
ORPHA:2971 Peroxisomal Acyl-Coa Oxidase Deficiency
Top ranked variants:
MISSENSE chr17:g.73947032G>C [0/1:0/1:0/1] rs143994351 (variation viewer)
Pathogenicity Data:
Best Score: 0.999858
Polyphen2: 0.002 (B)
Mutation Taster: 1.000 (P)
SIFT: 1.000 (T)
Frequency Data:
ESP EA: 0.0116%
ESP All: 0.0077%
ExAC NFE: 0.0031%
INTRONIC chr17:g.73942957G>GT [.:0/1:0/1] rs373022785 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.035

Phenotype Score: 0.520

Variant Score: 0.497

Phenotype matches:
Phenotypic similarity 0.520 to Sclerosteosis associated with LRP4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:212780 Cenani-Lenz syndactyly syndrome - autosomal recessive
OMIM:614305 Sclerosteosis 2 - autosomal dominant/recessive
OMIM:616304 ?Myasthenic syndrome, congenital, 17 (unconfirmed)
ORPHA:3152 Sclerosteosis
Top ranked variants:
MISSENSE chr11:g.46890172C>G [.:.:0/1] rs192480207 (variation viewer)
Variant score: 0.994 CONTRIBUTING VARIANT
Transcripts:
LRP4:uc001ndn.4:c.4930G>C:p.(Asp1644His)
LRP4:uc001ndl.3:n.198-4453C>G:
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.976 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.001 (D)
Frequency Data:
1000Genomes: 0.0399%
ExAC AFR: 0.0096%
INTRONIC chr11:g.46890760C>T [.:.:0/1] rs181569888 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
LRP4:uc001ndn.4:c.4693-77G>A:p.(=)
LRP4:uc001ndl.3:n.198-3865C>T:
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0399%

Exomiser Score: 0.032

Phenotype Score: 0.545

Variant Score: 0.460

Phenotype matches:
Phenotypic similarity 0.545 to Combined oxidative phosphorylation deficiency 3 associated with TSFM.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001138, Optic neuropathy
Phenotypic similarity 0.424 to mouse mutant involving TSFM.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001325, abnormal retina morphology
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:610505 Combined oxidative phosphorylation deficiency 3 - autosomal recessive
Top ranked variants:
MISSENSE chr12:g.58177056A>G [.:0/1:.] rs746165219 (variation viewer)
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.995 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.004 (D)
Frequency Data:
ExAC AFR: 0.0099%
ExAC FIN: 0.4635%
ExAC NFE: 0.0121%
ExAC OTH: 0.1149%
INTRONIC chr12:g.58186606C>T [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.030

Phenotype Score: 0.501

Variant Score: 0.500

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:607341 Focal cortical dysplasia, type II, somatic - unknown
Top ranked variants:
MISSENSE chr1:g.11190630C>T [.:.:0/1] rs779045714 (variation viewer)
Variant score: 1.000 CONTRIBUTING VARIANT
Transcripts:
MTOR:uc001asc.3:c.184G>A:p.(Glu62Lys)
MTOR:uc001asd.3:c.5569G>A:p.(Glu1857Lys)
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 0.066 (B)
Mutation Taster: 1.000 (P)
SIFT: 0.142 (T)
Frequency Data:
ExAC NFE: 0.0030%
INTRONIC chr1:g.11169272GG>AC [.:0/1:0/1] rs368788090 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.029

Phenotype Score: 0.501

Variant Score: 0.498

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
MISSENSE chr3:g.45785126G>T [0/1:.:0/1] rs558613899 (variation viewer)
Pathogenicity Data:
Best Score: 0.99999
Polyphen2: 0.009 (B)
Mutation Taster: 1.000 (P)
SIFT: 0.403 (T)
Frequency Data:
ExAC AMR: 0.0086%
ExAC SAS: 0.0061%
ExAC NFE: 0.0255%
INTRONIC chr3:g.45731039T>G [.:0/1:.] rs899833371 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr3:g.45772742TTC>CTT [0/1:.:0/1] rs796640653 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr3:g.45776875C>CT [0/1:.:.] rs35082575 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr3:g.45780391A>G [.:0/1:.] rs140198501 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2196%
ESP AA: 0.7269%
ESP EA: 0.0233%
ESP All: 0.2615%
ExAC AFR: 0.8221%
ExAC AMR: 0.0703%
ExAC SAS: 0.0193%
ExAC NFE: 0.0199%
ExAC OTH: 0.2257%

Exomiser Score: 0.028

Phenotype Score: 0.501

Variant Score: 0.493

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
MISSENSE chr8:g.28928257T>C [.:0/1:.] rs1033955710 (variation viewer)
Variant score: 0.985 CONTRIBUTING VARIANT
Transcripts:
KIF13B:uc003xhh.4:c.5245A>G:p.(Lys1749Glu)
KIF13B:uc011laz.2:c.802A>G:p.(Lys268Glu)
Pathogenicity Data:
Best Score: 0.985037
Polyphen2: 0.780 (P)
Mutation Taster: 0.985 (P)
SIFT: 0.020 (D)
Frequency Data:
No frequency data
INTRONIC chr8:g.29023426T>C [.:0/1:.] rs2291453 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.027

Phenotype Score: 0.505

Variant Score: 0.484

Phenotype matches:
Phenotypic similarity 0.505 to Blau Syndrome associated with NOD2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0100654, Retrobulbar optic neuritis
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:186580 Blau syndrome - autosomal dominant
OMIM:266600 Inflammatory bowel disease 1, Crohn disease (susceptibility)
ORPHA:90340 Blau Syndrome
Top ranked variants:
MISSENSE chr16:g.50750810A>G [0/1:0/1:0/1] rs104895467 (variation viewer)
Pathogenicity Data:
Best Score: 0.999912
Polyphen2: 0.977 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.029 (D)
Frequency Data:
1000Genomes: 0.0399%
ESP EA: 0.1163%
ESP All: 0.0769%
ExAC AFR: 0.0096%
ExAC AMR: 0.0777%
ExAC NFE: 0.2068%

Exomiser Score: 0.026

Phenotype Score: 0.520

Variant Score: 0.464

Phenotype matches:
Phenotypic similarity 0.520 to Adams-Oliver syndrome 2 associated with DOCK6.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
Known diseases:
OMIM:614219 Adams-Oliver syndrome 2 - autosomal recessive
ORPHA:974 Adams-Oliver Syndrome
Top ranked variants:
MISSENSE chr19:g.11332560G>A [0/1:.:.] rs145081732 (variation viewer)
Variant score: 0.928 CONTRIBUTING VARIANT
Transcripts:
DOCK6:uc002mqs.5:c.3517C>T:p.(Arg1173Trp)
DOCK6:uc010xlq.3:c.1534C>T:p.(Arg512Trp)
Pathogenicity Data:
Best Score: 0.002
Polyphen2: 0.586 (P)
SIFT: 0.002 (D)
Frequency Data:
1000Genomes: 0.1597%
ESP AA: 0.2388%
ESP EA: 0.2842%
ESP All: 0.2691%
ExAC AFR: 0.2267%
ExAC AMR: 0.1210%
ExAC SAS: 0.4179%
ExAC FIN: 0.0302%
ExAC NFE: 0.2941%
ExAC OTH: 0.3341%
INTRONIC chr19:g.11325898C>A [.:0/1:.]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
DOCK6:uc002mqs.5:c.4106+165G>T:p.(=)
DOCK6:uc010xlq.3:c.2123+165G>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.11312556C>G [0/1:.:.] rs373843420 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0200%
ESP EA: 0.1346%
ESP All: 0.0917%
ExAC SAS: 0.0671%
ExAC FIN: 0.1106%
ExAC NFE: 0.3634%
ExAC OTH: 0.4673%
INTRONIC chr19:g.11348295A>G [.:0/1:.] rs748384369 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.11363677C>T [0/1:0/1:0/1] rs371589719 (variation viewer)
Variant score: 0.000
Transcripts:
DOCK6:uc002mqs.5:c.133-43G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ESP EA: 0.0120%
ESP All: 0.0081%
ExAC NFE: 0.0039%

Exomiser Score: 0.022

Phenotype Score: 0.501

Variant Score: 0.469

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
MISSENSE chr16:g.2086730T>G [.:0/1:.] rs771530557 (variation viewer)
Pathogenicity Data:
Best Score: 1.0
Polyphen2: 1.000 (D)
Mutation Taster: 1.000 (P)
SIFT: 0.000 (D)
Frequency Data:
ExAC AFR: 0.0797%
ExAC FIN: 0.3782%
ExAC NFE: 0.0573%
INTRONIC chr16:g.2087462T>G [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.020

Phenotype Score: 0.506

Variant Score: 0.450

Phenotype matches:
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
SPLICING chr17:g.36892431AGGGA>GGGGG [.:0/1:.]
Variant score: 0.900 CONTRIBUTING VARIANT
Transcripts:
PCGF2:uc002hqp.1:c.577-12_577-8delTCCCTinsCCCCC:p.?
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr17:g.36906047A>C [.:0/1:.] rs892144622 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PCGF2:uc002hqp.1::
PCGF2:uc021twi.1::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.018

Phenotype Score: 0.520

Variant Score: 0.425

Phenotype matches:
Phenotypic similarity 0.520 to Lacticacidemia due to PDX1 deficiency associated with PDHX.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:245349 Lacticacidemia due to PDX1 deficiency - autosomal recessive
Top ranked variants:
NON_FS_SUBSTITUTION chr11:g.34938265CGGCC>TGGCT [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr11:g.34982146TTC>GTA [0/1:.:0/1] rs71481472 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
NON_FS_SUBSTITUTION chr11:g.34938265CGGCC>TGGCT [.:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.018

Phenotype Score: 0.501

Variant Score: 0.445

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
SPLICING chr3:g.195012987C>T [0/1:.:0/1] rs184360297 (variation viewer)
Variant score: 0.890 CONTRIBUTING VARIANT
Transcripts:
ACAP2:uc003fun.4:c.1953+7G>A:p.?
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0200%
ESP AA: 0.0227%
ESP EA: 0.0233%
ESP All: 0.0231%
ExAC AFR: 0.0388%
ExAC SAS: 0.0083%
ExAC FIN: 0.0454%
ExAC NFE: 0.0783%
SYNONYMOUS chr3:g.195063302G>C [.:0/1:0/1] rs141814202 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
ACAP2:uc003fun.4:c.426C>G:p.(=)
ACAP2:uc003fuo.3:c.426C>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1198%
ExAC AFR: 0.2214%
ExAC AMR: 0.0173%
INTRONIC chr3:g.195133474GT>ATAAC [.:.:0/1] rs796511317 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr3:g.195133474GT>ATAAC [0/1:.:.] rs796511317 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.018

Phenotype Score: 0.584

Variant Score: 0.351

Phenotype matches:
Phenotypic similarity 0.584 to Leber Congenital Amaurosis associated with CEP290.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0012795, Abnormality of the optic disc
Phenotypic similarity 0.416 to mouse mutant involving CEP290.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001326, retinal degeneration
Phenotypic similarity 0.428 to zebrafish mutant involving HGNC:29021.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - ZP:0007138, abnormal(ly) decreased process quality sensory epithelium regeneration
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:610188 Joubert syndrome 5 - autosomal recessive
OMIM:610189 Senior-Loken syndrome 6 - autosomal recessive
OMIM:611134 Meckel syndrome 4 - autosomal recessive
OMIM:611755 Leber congenital amaurosis 10 - autosomal recessive
OMIM:615991 ?Bardet-Biedl syndrome 14 (unconfirmed)
ORPHA:110 Bardet-Biedl Syndrome
ORPHA:2318 Joubert Syndrome With Oculorenal Defect
ORPHA:3156 Senior-Loken Syndrome
ORPHA:564 Meckel Syndrome
ORPHA:65 Leber Congenital Amaurosis
Top ranked variants:
MISSENSE chr12:g.88481706T>C [.:.:0/1]
Variant score: 0.702 CONTRIBUTING VARIANT
Transcripts:
CEP290:uc001taq.3:c.1225A>G:p.(Met409Val)
CEP290:uc001tar.3:c.4045A>G:p.(Met1349Val)
Pathogenicity Data:
Best Score: 0.298
Polyphen2: 0.001 (B)
SIFT: 0.298 (T)
Frequency Data:
No frequency data
INTRONIC chr12:g.88452566A>G [0/1:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.016

Phenotype Score: 0.533

Variant Score: 0.394

Phenotype matches:
Phenotypic similarity 0.533 to mouse mutant involving FAM104A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
MISSENSE chr17:g.71228379G>C [.:0/1:0/1] rs180917408 (variation viewer)
Pathogenicity Data:
Best Score: 0.108
Polyphen2: 0.359 (B)
SIFT: 0.108 (T)
Frequency Data:
1000Genomes: 0.2396%
ESP AA: 0.2075%
ESP EA: 0.5527%
ESP All: 0.4361%
ExAC AFR: 0.1847%
ExAC AMR: 0.1883%
ExAC SAS: 0.1299%
ExAC FIN: 0.0317%
ExAC NFE: 0.6182%
ExAC OTH: 0.6173%
INTRONIC chr17:g.71223424GA>G [.:0/1:.] rs71154980 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
FAM104A:uc002jji.4:c.222-22del:p.(=)
FAM104A:uc002jjj.4:c.222-22del:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.014

Phenotype Score: 0.508

Variant Score: 0.409

Phenotype matches:
Phenotypic similarity 0.508 to Vici Syndrome associated with EPG5.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Known diseases:
OMIM:242840 Vici syndrome - autosomal recessive
ORPHA:1493 Vici Syndrome
Top ranked variants:
MISSENSE chr18:g.43440297T>G [.:0/1:.] rs767940928 (variation viewer)
Pathogenicity Data:
Best Score: 0.168
Polyphen2: 0.133 (B)
SIFT: 0.168 (T)
Frequency Data:
ExAC FIN: 0.1138%
ExAC NFE: 0.0091%
ExAC OTH: 0.1174%
INTRONIC chr18:g.43450722G>A [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.43450749A>T [.:0/1:.] rs766734082 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.0838%
ExAC AMR: 0.1272%
ExAC SAS: 0.0521%
ExAC FIN: 0.5224%
ExAC NFE: 0.1285%

Exomiser Score: 0.012

Phenotype Score: 0.501

Variant Score: 0.402

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:601455 Charcot-Marie-Tooth disease, type 4D - autosomal recessive
Top ranked variants:
INTRONIC chr8:g.134269190G>A [0/1:0/1:0/1] rs115154322 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.9585%

Exomiser Score: 0.010

Phenotype Score: 0.507

Variant Score: 0.369

Phenotype matches:
Phenotypic similarity 0.507 to Osteopetrosis, autosomal recessive 7 associated with TNFRSF11A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0007807, Optic nerve compression
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:174810 Osteolysis, familial expansile - autosomal dominant
OMIM:602080 Paget disease of bone 2, early-onset (susceptibility)
OMIM:612301 Osteopetrosis, autosomal recessive 7 - autosomal recessive
Top ranked variants:
SPLICING chr18:g.60025474C>T [.:0/1:.] rs751564829 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.3051%
ExAC AMR: 0.7423%
ExAC EAS: 0.5122%
ExAC SAS: 0.2870%
ExAC FIN: 0.8449%
ExAC NFE: 0.1193%
ExAC OTH: 0.1901%
INTRONIC chr18:g.60015314T>A [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.60015322T>G [.:0/1:.] rs112651184 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.005

Phenotype Score: 0.501

Variant Score: 0.300

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
MISSENSE chr2:g.233990568A>C [.:0/1:.]
Variant score: 0.600 CONTRIBUTING VARIANT
Transcripts:
INPP5D:uc010zmo.2:c.463A>C:p.(Thr155Pro)
INPP5D:uc010zmp.2:c.460A>C:p.(Thr154Pro)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr2:g.234103863C>AG [0/1:.:.] rs368422568 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
INPP5D:uc010zmo.2:c.2510-182delCinsAG:p.(=)
INPP5D:uc010zmp.2:c.2507-182delCinsAG:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.003

Phenotype Score: 0.520

Variant Score: 0.224

Phenotype matches:
Phenotypic similarity 0.520 to Filippi syndrome associated with CKAP2L.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Known diseases:
OMIM:272440 Filippi syndrome - autosomal recessive
Top ranked variants:
MISSENSE chr2:g.113522157T>C [.:0/1:0/1] rs374624935 (variation viewer)
Pathogenicity Data:
Best Score: 0.543
SIFT: 0.543 (T)
Frequency Data:
1000Genomes: 0.0599%
ExAC AFR: 0.1475%
ExAC AMR: 0.0087%
INTRONIC chr2:g.113504172C>T [.:0/1:0/1] rs201606987 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0399%
ExAC AFR: 0.0909%
ExAC AMR: 0.0174%

Exomiser Score: 0.002

Phenotype Score: 0.287

Variant Score: 0.468

Phenotype matches:
Phenotypic similarity 0.575 to Spinocerebellar ataxia 1 associated with ATXN1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Known diseases - observed variants incompatible with mode of inheritance:
OMIM:164400 Spinocerebellar ataxia 1 - autosomal dominant
Top ranked variants:
MISSENSE chr6:g.16327915A>C [.:.:0/1] rs11969612 (variation viewer)
Pathogenicity Data:
Best Score: 0.065
Polyphen2: 0.227 (B)
SIFT: 0.065 (T)
Frequency Data:
No frequency data
INTRONIC chr6:g.16326458TG>T [.:.:0/1] rs148903266 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.6190%
ncRNA_INTRONIC chr6:g.16753451G>A [0/1:.:.] rs771052177 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC SAS: 0.0131%

Exomiser Score: 0.001

Phenotype Score: 0.629

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Phenotypic similarity 0.533 to mouse mutant involving ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:605039 Bohring-Opitz syndrome - autosomal dominant/recessive
OMIM:614286 Myelodysplastic syndrome, somatic - somatic
ORPHA:97297 Bohring-Opitz Syndrome
Top ranked variants:
SYNONYMOUS chr20:g.31022450T>G [.:0/1:.] rs756882312 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AMR: 0.0135%
ExAC EAS: 0.0193%
ExAC SAS: 0.0219%
ExAC FIN: 0.0527%
ExAC NFE: 0.0071%
ExAC OTH: 0.3279%
SYNONYMOUS chr20:g.31022459T>G [.:0/1:.] rs779376742 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC EAS: 0.0179%
ExAC FIN: 0.0246%
ExAC NFE: 0.0022%

FAS

Exomiser Score: 0.001

Phenotype Score: 0.262

Variant Score: 0.409

Phenotype matches:
Phenotypic similarity 0.524 to BehçEt Disease associated with FAS.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0100654, Retrobulbar optic neuritis
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
Known diseases - observed variants incompatible with mode of inheritance:
OMIM:601859 Autoimmune lymphoproliferative syndrome, type IA - autosomal dominant
ORPHA:117 BehçEt Disease
ORPHA:3437 Vogt-Koyanagi-Harada Disease
ORPHA:85408 Rheumatoid Factor-Negative Juvenile Idiopathic Arthritis
ORPHA:85410 Oligoarticular Juvenile Idiopathic Arthritis
Top ranked variants:
SPLICING chr10:g.90762788T>A [0/1:0/1:0/1] rs113022949 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1997%
ExAC AFR: 0.5194%
ExAC AMR: 0.0348%
ExAC SAS: 0.0061%
ExAC NFE: 0.0030%
INTRONIC chr10:g.90767424G>T [0/1:.:.] rs200239064 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
ESP AA: 0.1816%
ESP EA: 0.0465%
ESP All: 0.0923%
ExAC AFR: 0.2396%
ExAC AMR: 0.0550%
ExAC NFE: 0.0299%
ExAC OTH: 0.1139%
ncRNA_EXONIC chr10:g.90774250G>A [0/1:.:.] rs190852915 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0998%
ESP AA: 0.1280%
ESP EA: 0.0242%
ESP All: 0.0575%
ExAC AFR: 0.4046%
ExAC AMR: 0.0995%
ExAC NFE: 0.0417%
ExAC OTH: 0.1645%

Exomiser Score: 0.001

Phenotype Score: 0.586

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.586 to Warsaw breakage syndrome associated with DDX11.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000588, Optic nerve coloboma
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:613398 Warsaw breakage syndrome - autosomal recessive
Top ranked variants:

Exomiser Score: 0.001

Phenotype Score: 0.586

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.586 to Mitochondrial complex I deficiency associated with NDUFS4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Phenotypic similarity 0.498 to mouse mutant involving NDUFS4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001059, optic nerve atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:252010 Mitochondrial complex I deficiency - autosomal recessive
OMIM:256000 Leigh syndrome - autosomal recessive
ORPHA:2609 Isolated Complex I Deficiency
Top ranked variants:
INTRONIC chr5:g.52899166C>CT [.:.:1/1]
Variant score: 0.000
Transcripts:
NDUFS4:uc003jpe.2:c.99-116_99-115insT:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.001

Phenotype Score: 0.586

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.586 to Mitochondrial complex I deficiency associated with TMEM126B.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:252010 Mitochondrial complex I deficiency - autosomal recessive
ORPHA:2609 Isolated Complex I Deficiency
Top ranked variants:
INTRONIC chr11:g.85346850C>T [.:0/1:.] rs760711401 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr11:g.85346855C>T [.:0/1:.] rs371251945 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

CRX

Exomiser Score: 0.001

Phenotype Score: 0.584

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.584 to Leber Congenital Amaurosis associated with CRX.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0012795, Abnormality of the optic disc
Phenotypic similarity 0.475 to mouse mutant involving CRX.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0002864, abnormal ocular fundus morphology
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Known diseases:
OMIM:120970 Cone-rod retinal dystrophy-2 - autosomal dominant
OMIM:613829 Leber congenital amaurosis 7 - autosomal recessive
ORPHA:1872 Cone Rod Dystrophy
ORPHA:65 Leber Congenital Amaurosis
ORPHA:791 Retinitis Pigmentosa
Top ranked variants:
INTERGENIC chr19:g.48321616TC>T [.:.:0/1]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
CRX:uc010elm.2::
CRX:uc021uwp.1::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr19:g.48321631T>TC [.:.:0/1]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
CRX:uc010elm.2::
CRX:uc021uwp.1::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr19:g.48321634CCCA>TCCC [.:.:0/1]
Variant score: 0.000
Transcripts:
CRX:uc010elm.2::
CRX:uc021uwp.1::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr19:g.48321645C>A [0/1:.:0/1] rs113740908 (variation viewer)
Variant score: 0.000
Transcripts:
CRX:uc010elm.2::
CRX:uc021uwp.1::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.001

Phenotype Score: 0.584

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.584 to Leber Congenital Amaurosis associated with GUCY2D.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0012795, Abnormality of the optic disc
Phenotypic similarity 0.395 to mouse mutant involving GUCY2D.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001326, retinal degeneration
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:204000 Leber congenital amaurosis 1 - autosomal recessive
OMIM:601777 Cone-rod dystrophy 6 - autosomal dominant
ORPHA:1872 Cone Rod Dystrophy
ORPHA:65 Leber Congenital Amaurosis
Top ranked variants:
INTRONIC chr17:g.7919229T>C [.:0/1:.] rs759075619 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
GUCY2D:uc002gjt.2:c.3044-16T>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC NFE: 0.0024%
SYNONYMOUS chr17:g.7919303C>T [0/1:0/1:0/1] rs749621660 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
GUCY2D:uc002gjt.2:c.3102C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AMR: 0.0256%
ExAC NFE: 0.0020%

Exomiser Score: 0.001

Phenotype Score: 0.584

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.584 to Leber Congenital Amaurosis associated with IQCB1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0012795, Abnormality of the optic disc
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:609254 Senior-Loken syndrome 5 - autosomal recessive
ORPHA:3156 Senior-Loken Syndrome
ORPHA:65 Leber Congenital Amaurosis
Top ranked variants:
INTRONIC chr3:g.121500479TACACACACACACAC>T [0/1:.:.] rs149985093 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr3:g.121527883A>T [.:0/1:.] rs753472834 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.0654%
ExAC AMR: 0.0284%
ExAC SAS: 0.0310%
ExAC FIN: 0.5499%
ExAC NFE: 0.0530%

Exomiser Score: 0.001

Phenotype Score: 0.531

Variant Score: 0.036

Phenotype matches:
Phenotypic similarity 0.471 to Multiple Epiphyseal Dysplasia, Beighton Type associated with COL2A1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0007973, Retinal dysplasia
Phenotypic similarity 0.531 to mouse mutant involving COL2A1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0005195, abnormal posterior eye segment morphology
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:108300 Stickler syndrome, type I - autosomal dominant
OMIM:132450 Epiphyseal dysplasia, multiple, with myopia and deafness - autosomal dominant
OMIM:150600 Legg-Calve-Perthes disease - unknown
OMIM:151210 Platyspondylic skeletal dysplasia, Torrance type - autosomal dominant
OMIM:156550 Kniest dysplasia - autosomal dominant
OMIM:183900 SED congenita - autosomal dominant
OMIM:184250 SMED Strudwick type - autosomal dominant
OMIM:200610 Achondrogenesis, type II or hypochondrogenesis - autosomal dominant
OMIM:215150 Otospondylomegaepiphyseal dysplasia - autosomal recessive
OMIM:271700 Spondyloperipheral dysplasia - autosomal dominant
OMIM:604864 Osteoarthritis with mild chondrodysplasia - autosomal dominant
OMIM:608805 Avascular necrosis of the femoral head - autosomal dominant
OMIM:609162 Czech dysplasia - autosomal dominant
OMIM:609508 Stickler sydrome, type I, nonsyndromic ocular - autosomal dominant
OMIM:616583 Spondyloepiphyseal dysplasia, Stanescu type - autosomal dominant
ORPHA:166011 Multiple Epiphyseal Dysplasia, Beighton Type
ORPHA:1856 Spondyloperipheral Dysplasia-Short Ulna Syndrome
ORPHA:2380 Legg-Calvé-Perthes Disease
ORPHA:485 Kniest Dysplasia
ORPHA:85166 Platyspondylic Dysplasia, Torrance Type
ORPHA:85198 Dysspondyloenchondromatosis
ORPHA:90653 Stickler Syndrome Type 1
ORPHA:93296 Achondrogenesis Type 2
ORPHA:93315 Spondylometaphyseal Dysplasia, 'corner Fracture' Type
ORPHA:93316 Spondylometaphyseal Dysplasia, Schmidt Type
ORPHA:93346 Spondyloepimetaphyseal Dysplasia Congenita, Strudwick Type
ORPHA:94068 Spondyloepiphyseal Dysplasia Congenita
Top ranked variants:
MISSENSE chr12:g.48369250C>T [.:0/1:0/1] rs147569641 (variation viewer)
Pathogenicity Data:
Best Score: 0.928
Polyphen2: 0.001 (B)
SIFT: 0.928 (T)
Frequency Data:
1000Genomes: 0.0200%
ESP EA: 0.0465%
ESP All: 0.0308%
ExAC AMR: 0.0173%
ExAC SAS: 0.0061%
ExAC NFE: 0.0961%
INTRONIC chr12:g.48369944A>C [.:0/1:.] rs906963357 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48376409G>C [0/1:.:.] rs866690960 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48376447A>G [0/1:0/1:0/1] rs3829737 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48376618C>T [0/1:.:.] rs867065694 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48379961ATCA>CTCG [0/1:0/1:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48380030GA>AG [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48392362C>G [0/1:.:.] rs867951729 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.48397921C>T [0/1:.:.] rs866653353 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.001

Phenotype Score: 0.550

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.550 to Homozygous Familial Hypercholesterolemia associated with LDLRAP1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001138, Optic neuropathy
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:603813 Hypercholesterolemia, familial, autosomal recessive - autosomal recessive
ORPHA:391665 Homozygous Familial Hypercholesterolemia
Top ranked variants:
INTRONIC chr1:g.25883564G>A [0/1:.:.] rs868055126 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
LDLRAP1:uc001bkl.4:c.345-80G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.25891465C>T [.:.:0/1] rs544099040 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1597%
INTRONIC chr1:g.25891540C>T [0/1:.:.] rs113373071 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7188%
INTRONIC chr1:g.25891772A>C [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.25893242TG>CA [.:0/1:.] rs35137241 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.540

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.540 to Microcephaly and chorioretinopathy, autosomal recessive, 1 associated with TUBGCP6.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:251270 Microcephaly and chorioretinopathy, autosomal recessive, 1 - autosomal recessive
ORPHA:2518 Autosomal Recessive Chorioretinopathy-Microcephaly Syndrome
Top ranked variants:
INTRONIC chr22:g.50682064G>A [.:1/1:1/1] rs57495517 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.535

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.535 to Retinitis pigmentosa 43 associated with PDE6A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Phenotypic similarity 0.505 to mouse mutant involving PDE6A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0002864, abnormal ocular fundus morphology
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:613810 Retinitis pigmentosa 43 - autosomal recessive
ORPHA:791 Retinitis Pigmentosa
Top ranked variants:
INTRONIC chr5:g.149245593C>T [.:0/1:.] rs910837415 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PDE6A:uc003lrg.4:c.2358+140G>A:p.(=)
PDE6A:uc021yfs.1:c.2115+140G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149301411GC>AA [0/1:.:0/1] rs386693505 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149311668GTCCG>TTCCA [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149311749T>C [.:0/1:.] rs879169124 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149311831G>T [.:0/1:.] rs370382512 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149311840G>A [.:0/1:.] rs374128227 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149311862G>T [.:0/1:.] rs61743000 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149311872A>T [.:0/1:.] rs77037326 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149312037C>T [.:0/1:.] rs77906196 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149312067T>C [.:0/1:.] rs75204652 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149312076CATT>C [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.149312088G>A [.:0/1:.] rs113884923 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.534

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.534 to Peroxisome biogenesis disorder 2A associated with PEX5.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001093, Optic nerve dysplasia
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:202370 Peroxisome biogenesis disorder 2B - autosomal recessive
OMIM:214110 Peroxisome biogenesis disorder 2A - unknown
OMIM:616716 Rhizomelic chondrodysplasia punctata, type 5 - unknown
ORPHA:44 Neonatal Adrenoleukodystrophy
ORPHA:772 Infantile Refsum Disease
ORPHA:912 Zellweger Syndrome
Top ranked variants:
INTRONIC chr12:g.7344465A>G [.:.:0/1] rs114296508 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7188%
INTRONIC chr12:g.7344470A>T [.:.:0/1] rs114737848 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7188%
INTRONIC chr12:g.7362204G>T [0/1:0/1:0/1] rs10734685 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.7362236G>T [.:0/1:.] rs7977141 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.2241%
ExAC AMR: 0.0771%
ExAC NFE: 0.0786%

Exomiser Score: 0.000

Phenotype Score: 0.533

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.533 to Retinitis pigmentosa 36 associated with PRCD.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000543, Optic disc pallor
Known diseases:
OMIM:610599 Retinitis pigmentosa 36 - autosomal recessive
ORPHA:791 Retinitis Pigmentosa
Top ranked variants:
INTRONIC chr17:g.74524651TT>GG [.:0/1:0/1] rs376307503 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PRCD:uc002jrw.1:c.-819+736_-819+737delTTinsGG:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.74536333CGGG>GGGT [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.74536333CGGGG>GGGGC [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.533

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.453 to Congenital Stationary Night Blindness associated with GRM6.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0008002, Abnormality of macular pigmentation
Phenotypic similarity 0.533 to mouse mutant involving GRM6.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Phenotypic similarity 0.458 to zebrafish mutant involving HGNC:4598.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - ZP:0002885, abnormal(ly) has fewer parts of type pronephric duct motile cilium towards pronephric duct inner dynein arm
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
Known diseases:
OMIM:257270 Night blindness, congenital stationary - autosomal recessive
ORPHA:215 Congenital Stationary Night Blindness
Top ranked variants:
INTRONIC chr5:g.178419154GC>T [0/1:.:.]
Variant score: 0.000
Transcripts:
GRM6:uc003mjr.3:c.505-71_505-70delGCinsA:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.178419154GC>T [.:.:0/1]
Variant score: 0.000
Transcripts:
GRM6:uc003mjr.3:c.505-71_505-70delGCinsA:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.528

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.528 to Leukoencephalopathy with ataxia associated with CLCN2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001138, Optic neuropathy
Phenotypic similarity 0.404 to mouse mutant involving CLCN2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001326, retinal degeneration
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:607628 Epilepsy, idiopathic generalized, susceptibility to, 11 (susceptibility)
OMIM:615651 Leukoencephalopathy with ataxia - autosomal recessive
Top ranked variants:
UTR3 chr3:g.184064346T>C [0/1:.:1/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.524

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.524 to BehçEt Disease associated with ERAP1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0100654, Retrobulbar optic neuritis
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
ORPHA:117 BehçEt Disease
Top ranked variants:
SYNONYMOUS chr5:g.96117414A>G [0/1:.:1/1] rs766710538 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AMR: 0.0174%
ExAC NFE: 0.0060%

Exomiser Score: 0.000

Phenotype Score: 0.524

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.524 to BehçEt Disease associated with TLR4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0100654, Retrobulbar optic neuritis
Phenotypic similarity 0.406 to mouse mutant involving TLR4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0003727, abnormal retinal layer morphology
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
ORPHA:117 BehçEt Disease
Top ranked variants:
INTRONIC chr9:g.120466929CA>C [0/1:1/1:1/1] rs5900307 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.287

Variant Score: 0.266

Phenotype matches:
Phenotypic similarity 0.574 to Cherubism associated with SH3BP2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0200057, Marcus Gunn pupil
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases - observed variants incompatible with mode of inheritance:
OMIM:118400 Cherubism - autosomal dominant
ORPHA:184 Cherubism
Top ranked variants:
MISSENSE chr4:g.2828835C>T [.:0/1:.] rs116666035 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2196%
ExAC AFR: 0.5801%
ExAC AMR: 0.6079%
ExAC EAS: 0.1506%
ExAC SAS: 0.0121%
ExAC NFE: 0.1587%
INTRONIC chr4:g.2814255C>G [.:0/1:.] rs531609511 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2196%
INTRONIC chr4:g.2826997C>T [.:0/1:.] rs189595794 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2196%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to AICA-ribosiduria due to ATIC deficiency associated with ATIC.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.501 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.501 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:608688 AICA-ribosiduria due to ATIC deficiency - autosomal recessive
ORPHA:250977 Aica-Ribosiduria
Top ranked variants:
INTRONIC chr2:g.216182769AC>TT [.:0/1:0/1] rs386655016 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr2:g.216184361TG>T [.:0/1:0/1] rs750430695 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC NFE: 0.0015%
INTRONIC chr2:g.216211690G>A [0/1:.:.] rs770440688 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC EAS: 0.0117%
ExAC NFE: 0.0015%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Peters Plus Syndrome associated with B3GLCT.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
Known diseases:
OMIM:261540 Peters-plus syndrome - autosomal recessive
ORPHA:709 Peters Plus Syndrome
Top ranked variants:
INTRONIC chr13:g.31789169CT>C [0/1:.:.] rs398022187 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
B3GLCT:uc010aaz.3:c.71-18del:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr13:g.31821105C>T [.:0/1:.] rs367837499 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
B3GLCT:uc010aaz.3:c.271-55C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to PEHO syndrome associated with CCDC88A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Phenotypic similarity 0.416 to mouse mutant involving CCDC88A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0002792, abnormal retinal vasculature morphology
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:260565 PEHO syndrome - autosomal recessive
Top ranked variants:

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Polyarteritis nodosa, childhood-onset associated with CECR1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:182410 ?Sneddon syndrome (unconfirmed)
OMIM:615688 Polyarteritis nodosa, childhood-onset - autosomal recessive
Top ranked variants:
INTRONIC chr22:g.17673719GA>G [.:1/1:.] rs35262317 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Albers-SchöNberg Osteopetrosis associated with CLCN7.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Phenotypic similarity 0.485 to mouse mutant involving CLCN7.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006219, optic nerve degeneration
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Known diseases:
OMIM:166600 Osteopetrosis, autosomal dominant 2 - autosomal dominant
OMIM:611490 Osteopetrosis, autosomal recessive 4 - autosomal recessive
ORPHA:53 Albers-SchöNberg Osteopetrosis
ORPHA:667 Autosomal Recessive Malignant Osteopetrosis
Top ranked variants:
INTRONIC chr16:g.1503947T>C [.:0/1:.] rs769937312 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
CLCN7:uc002clv.3:c.1154-52A>G:p.(=)
CLCN7:uc002clw.3:c.1082-52A>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC EAS: 0.0264%
ExAC FIN: 0.2653%
ExAC NFE: 0.0029%
INTRONIC chr16:g.1524016T>G [.:0/1:.]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
CLCN7:uc002clv.3:c.141+819A>C:p.(=)
CLCN7:uc002clw.3:c.141+819A>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr16:g.1524245A>G [0/1:.:0/1] rs140228719 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1597%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Leukoencephalopathy with vanishing white matter associated with EIF2B5.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:603896 Leukoencephalopathy with vanishing white matter - autosomal recessive
Top ranked variants:
INTRONIC chr3:g.183862635A>C [.:0/1:.] rs761724411 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
EIF2B5:uc003fmp.3:c.2107-37A>C:p.(=)
EIF2B5:uc003fmq.3:c.1270-37A>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC FIN: 0.0173%
ExAC NFE: 0.0099%
ExAC OTH: 0.1205%
INTRONIC chr3:g.183862638T>C [.:0/1:.] rs765174109 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
EIF2B5:uc003fmp.3:c.2107-34T>C:p.(=)
EIF2B5:uc003fmq.3:c.1270-34T>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AMR: 0.0194%
ExAC FIN: 0.0173%
ExAC NFE: 0.0182%
ExAC OTH: 0.1211%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Xeroderma Pigmentosum associated with ERCC2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Known diseases:
OMIM:278730 Xeroderma pigmentosum, group D - autosomal recessive
OMIM:601675 Trichothiodystrophy 1, photosensitive - autosomal recessive
OMIM:610756 Cerebrooculofacioskeletal syndrome 2 - autosomal recessive
ORPHA:1466 Cofs Syndrome
ORPHA:220295 Xeroderma Pigmentosum-Cockayne Syndrome Complex
ORPHA:910 Xeroderma Pigmentosum
Top ranked variants:
INTRONIC chr19:g.45855979CT>C [0/1:0/1:.] rs774486982 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ESP EA: 0.0242%
ESP All: 0.0160%
ExAC AMR: 0.0433%
ExAC NFE: 0.0271%
INTRONIC chr19:g.45859051A>C [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.45860640A>G [.:0/1:.] rs753798158 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC FIN: 0.0360%
ExAC NFE: 0.0046%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Peho Syndrome associated with KIF1A.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:610357 Spastic paraplegia 30, autosomal recessive - autosomal recessive
OMIM:614213 Neuropathy, hereditary sensory, type IIC - autosomal recessive
OMIM:614255 Mental retardation, autosomal dominant 9 - autosomal dominant
ORPHA:2836 Peho Syndrome
ORPHA:970 Hereditary Sensory And Autonomic Neuropathy Type 2
Top ranked variants:
INTRONIC chr2:g.241674222T>C [0/1:0/1:.] rs3755533 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr2:g.241702865A>C [.:0/1:.] rs1032791208 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr2:g.241725730T>G [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

MUT

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Vitamin B12-Unresponsive Methylmalonic Acidemia Type Mut- associated with MUT.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:251000 Methylmalonic aciduria, mut - autosomal recessive
ORPHA:289916 Vitamin B12-Unresponsive Methylmalonic Acidemia Type Mut0
ORPHA:79312 Vitamin B12-Unresponsive Methylmalonic Acidemia Type Mut-
Top ranked variants:
INTRONIC chr6:g.49416352T>C [.:1/1:.] rs192166377 (variation viewer)
Variant score: 0.000
Transcripts:
MUT:uc003ozg.4:c.1444+177A>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1997%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 associated with NALCN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:615419 Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 - autosomal recessive
OMIM:616266 Congenital contractures of the limbs and face, hypotonia, and developmental delay - autosomal dominant
ORPHA:1146 Digitotalar Dysmorphism
ORPHA:1147 Sheldon-Hall Syndrome
ORPHA:2053 Freeman-Sheldon Syndrome
Top ranked variants:
INTRONIC chr13:g.101727071CAG>C [0/1:1/1:.] rs112963196 (variation viewer)
Variant score: 0.000
Transcripts:
NALCN:uc001vox.1:c.3955-60_3955-59del:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Arthrogryposis With Oculomotor Limitation And Electroretinal Anomalies associated with PIEZO2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Known diseases:
OMIM:108145 Arthrogryposis, distal, type 5 - autosomal dominant
OMIM:114300 Arthrogryposis, distal, type 3 - autosomal dominant
OMIM:248700 ?Marden-Walker syndrome (unconfirmed)
ORPHA:1154 Arthrogryposis With Oculomotor Limitation And Electroretinal Anomalies
ORPHA:376 Gordon Syndrome
Top ranked variants:
INTRONIC chr18:g.10726142GG>CA [.:.:0/1] rs370235704 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PIEZO2:uc002kos.2:c.4855+5262_4855+5263delCCinsTG:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.10742744G>C [0/1:.:.] rs554637450 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PIEZO2:uc002kos.2:c.4440-131C>G:p.(=)
PIEZO2:uc002kot.1:c.153-131C>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.10726142GG>CA [0/1:.:.] rs370235704 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.10789388A>G [.:0/1:0/1]
Variant score: 0.000
Transcripts:
PIEZO2:uc002kos.2:c.1883-25T>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.10797178C>T [.:0/1:.] rs113036785 (variation viewer)
Variant score: 0.000
Transcripts:
PIEZO2:uc002kos.2:c.1527+194G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Muscle-Eye-Brain Disease associated with POMT1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:236670 Muscular dystrophy-dystroglycanopathy - autosomal recessive
OMIM:609308 Muscular dystrophy-dystroglycanopathy - autosomal recessive
OMIM:613155 Muscular dystrophy-dystroglycanopathy - autosomal recessive
ORPHA:588 Muscle-Eye-Brain Disease
Top ranked variants:
INTRONIC chr9:g.134381874C>T [0/1:0/1:0/1] rs144305611 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
ESP AA: 0.2270%
ESP EA: 0.0349%
ESP All: 0.1000%
ExAC AFR: 0.2220%
ExAC AMR: 0.0086%
ExAC FIN: 0.0151%
ExAC NFE: 0.0450%
ExAC OTH: 0.1101%
INTRONIC chr9:g.134394396C>T [0/1:.:0/1] rs191519212 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
ExAC AFR: 0.2281%
ExAC AMR: 0.0088%
ExAC NFE: 0.0048%
ExAC OTH: 0.1174%
SYNONYMOUS chr9:g.134397594C>T [0/1:0/1:0/1] rs140553130 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
ExAC AFR: 0.2220%
ExAC AMR: 0.0086%
ExAC OTH: 0.1104%

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Developmental And Speech Delay Due To Sox5 Deficiency associated with SOX5.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
Known diseases:
ORPHA:313892 Developmental And Speech Delay Due To Sox5 Deficiency
Top ranked variants:
INTRONIC chr12:g.24102647T>C [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.24102655T>C [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Osteopetrosis, autosomal recessive 1 associated with TCIRG1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:259700 Osteopetrosis, autosomal recessive 1 - autosomal recessive
ORPHA:667 Autosomal Recessive Malignant Osteopetrosis
Top ranked variants:
INTRONIC chr11:g.67814473C>T [0/1:.:.] rs116497880 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TCIRG1:uc001one.3:c.1166-427C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr11:g.67817739C>T [.:0/1:.] rs372043757 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TCIRG1:uc001one.3:c.2236+18C>T:p.(=)
TCIRG1:uc009ysd.3:n.223+18C>T:
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.1094%
ExAC SAS: 0.0061%
ExAC NFE: 0.0015%

XPC

Exomiser Score: 0.000

Phenotype Score: 0.520

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.520 to Xeroderma Pigmentosum associated with XPC.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Known diseases:
OMIM:278720 Xeroderma pigmentosum, group C - autosomal recessive
ORPHA:910 Xeroderma Pigmentosum
Top ranked variants:
INTRONIC chr3:g.14190242T>G [.:0/1:.] rs771531637 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AFR: 0.2282%
ExAC AMR: 0.0261%
ExAC EAS: 0.0352%
ExAC SAS: 0.0183%
ExAC FIN: 0.2650%
ExAC NFE: 0.0889%
INTRONIC chr3:g.14208603C>T [0/1:0/1:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.515

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.515 to mouse mutant involving MAPK8IP3.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0009770, abnormal optic chiasm morphology
Phenotypic similarity 0.179 to zebrafish mutant involving HGNC:6884.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - ZP:0009323, abnormal(ly) overlap with ceratohyal cartilage towards ceratohyal cartilage
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:

Exomiser Score: 0.000

Phenotype Score: 0.513

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.513 to mouse mutant involving MYO10.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr5:g.16667065C>G [0/1:.:.] rs33273 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr5:g.16763549G>A [.:0/1:.] rs140203547 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
MYO10:uc003jft.4:c.1494+41C>T:p.(=)
MYO10:uc010itx.3:c.363+41C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2396%
ESP AA: 0.2125%
ESP EA: 0.8137%
ESP All: 0.6251%
ExAC AFR: 0.1124%
ExAC AMR: 0.7012%
ExAC SAS: 0.0974%
ExAC FIN: 0.1362%
ExAC NFE: 0.6055%
ExAC OTH: 0.4464%
INTRONIC chr5:g.16699517G>A [0/1:0/1:.] rs143791002 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1597%
ExAC AFR: 0.7216%
ExAC AMR: 0.0262%
ExAC OTH: 0.1142%
INTRONIC chr5:g.16699795C>G [0/1:0/1:0/1] rs148561336 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1997%
ExAC AFR: 0.9631%
ExAC AMR: 0.0441%
INTRONIC chr5:g.16702051T>C [0/1:.:.] rs137951670 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1997%
INTRONIC chr5:g.16877875T>C [0/1:.:.] rs141774917 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2596%
INTRONIC chr5:g.16902700G>A [.:.:0/1] rs202222314 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0200%
INTRONIC chr5:g.16902814T>G [.:0/1:.] rs545305570 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%

Exomiser Score: 0.000

Phenotype Score: 0.512

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.512 to Neonatal Adrenoleukodystrophy associated with PEX14.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:614887 Peroxisome biogenesis disorder 13A - autosomal recessive
ORPHA:44 Neonatal Adrenoleukodystrophy
ORPHA:772 Infantile Refsum Disease
ORPHA:912 Zellweger Syndrome
Top ranked variants:
MISSENSE chr1:g.10683142G>A [0/1:0/1:0/1] rs145888212 (variation viewer)
Pathogenicity Data:
Best Score: 0.001
Polyphen2: 0.001 (B)
SIFT: 1.000 (T)
Frequency Data:
ESP AA: 0.1135%
ESP EA: 0.0116%
ESP All: 0.0461%
ExAC AFR: 0.0509%
ExAC SAS: 0.0129%
ExAC NFE: 0.0093%
UPSTREAM chr1:g.10534797C>T [.:0/1:.] rs141469820 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PEX14:uc001arl.3::
PEX14:uc001ark.3::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.3195%

Exomiser Score: 0.000

Phenotype Score: 0.512

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.512 to Autosomal Recessive Chorioretinopathy-Microcephaly Syndrome associated with TUBGCP4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:616335 Microcephaly and chorioretinopathy, autosomal recessive, 3 - autosomal recessive
ORPHA:2518 Autosomal Recessive Chorioretinopathy-Microcephaly Syndrome
Top ranked variants:
UTR5 chr15:g.43663437C>A [.:.:0/1] rs544065838 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TUBGCP4:uc001zrn.3:c.-116C>A:p.(=)
TUBGCP4:uc001zro.3:c.-116C>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
INTRONIC chr15:g.43687166G>A [0/1:.:0/1] rs189815876 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1198%
INTRONIC chr15:g.43687711G>GT [.:0/1:.] rs199601830 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.6789%
INTRONIC chr15:g.43689589T>C [.:0/1:.] rs879129753 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.512

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.512 to Spinocrebellar ataxia, autosomal recessive 12 associated with WWOX.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:133239 Esophageal squamous cell carcinoma, somatic - autosomal dominant
OMIM:614322 Spinocrebellar ataxia, autosomal recessive 12 - autosomal recessive
OMIM:616211 Epileptic encephalopathy, early infantile, 28 - autosomal recessive
ORPHA:251510 46,Xy Partial Gonadal Dysgenesis
ORPHA:99977 Squamous Cell Carcinoma Of Esophagus
Top ranked variants:
INTRONIC chr16:g.78142308G>TT [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr16:g.78724929C>A [0/1:0/1:.] rs546493978 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0399%
INTRONIC chr16:g.78142308G>TT [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr16:g.78724941A>G [0/1:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

T

Exomiser Score: 0.000

Phenotype Score: 0.512

Variant Score: 0.000

Phenotype matches:
Proximity score 0.512 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.512 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:182940 Neural tube defects, susceptibility to (susceptibility)
OMIM:615709 Sacral agenesis with vertebral anomalies - autosomal recessive
Top ranked variants:
chr14:g.22573825T>AA [.:0/1:0/1]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
chr14:g.22933004C>T [.:.:0/1] rs118083570 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.5391%

Exomiser Score: 0.000

Phenotype Score: 0.512

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.512 to mouse mutant involving NCALD.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Proximity score 0.500 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:

Exomiser Score: 0.000

Phenotype Score: 0.511

Variant Score: 0.000

Phenotype matches:
Proximity score 0.511 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.511 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:203290 Albinism, oculocutaneous, type III - autosomal recessive
OMIM:612271 Skin/hair/eye pigmentation, variation in, 11 (Melanesian blond hair) (non-disease)
ORPHA:79433 Oculocutaneous Albinism Type 3
Top ranked variants:
INTRONIC chr9:g.12698321G>A [.:.:0/1] rs16929364 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TYRP1:uc003zkv.4:c.709-130G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.8387%
INTRONIC chr9:g.12708192G>T [.:.:0/1] rs147966025 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TYRP1:uc003zkv.4:c.1408+49G>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1997%
ExAC AFR: 0.2092%
ExAC AMR: 0.0091%
ExAC NFE: 0.0016%

Exomiser Score: 0.000

Phenotype Score: 0.511

Variant Score: 0.000

Phenotype matches:
Proximity score 0.511 in interactome to OCA2 and phenotypic similarity 0.629 to Oculocutaneous Albinism Type 2 associated with OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.511 in interactome to OCA2 and phenotypic similarity 0.332 to mouse mutant of OCA2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006159, ocular albinism
Known diseases:
OMIM:605899 Glycine encephalopathy - autosomal recessive
Top ranked variants:
SYNONYMOUS chr9:g.6550882C>A [0/1:.:0/1] rs145407593 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
GLDC:uc003zkc.3:c.2490G>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1398%
ESP AA: 0.2951%
ESP EA: 0.0116%
ESP All: 0.1076%
ExAC AFR: 0.3940%
ExAC OTH: 0.1101%
INTRONIC chr9:g.6565336A>C [.:0/1:.]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
GLDC:uc003zkc.3:c.1926+18T>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6588292C>A [0/1:.:0/1] rs78601535 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1707+109G>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.3994%
INTRONIC chr9:g.6592121CGCA>TGCG [0/1:0/1:0/1]
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1482+19_1482+22delTGCGinsCGCA:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594704CAAGC>AAAGA [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594714AGC>CGA [.:0/1:.]
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+298_1261+300delGCTinsTCG:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594738A>C [.:0/1:.] rs62568999 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+276T>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0200%
INTRONIC chr9:g.6594743G>A [.:0/1:.] rs796310772 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+271C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594748C>G [.:0/1:.] rs559338670 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+266G>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594768C>A [.:0/1:.] rs62569001 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+246G>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594774A>AC [.:1/1:.] rs796101365 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+239_1261+240insG:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6594802T>C [.:0/1:.]
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.1261+212A>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
SYNONYMOUS chr9:g.6606627G>A [0/1:.:0/1] rs12006003 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.678C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.3994%
ESP AA: 0.9305%
ESP EA: 0.0349%
ESP All: 0.3383%
ExAC AFR: 0.9706%
ExAC AMR: 0.1209%
ExAC NFE: 0.0345%
ExAC OTH: 0.2203%
INTRONIC chr9:g.6620398T>G [.:0/1:.] rs112624547 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.335-79A>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0399%
INTRONIC chr9:g.6639262C>T [.:0/1:.] rs191493033 (variation viewer)
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.334+5352G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr9:g.6639274A>T [0/1:.:.]
Variant score: 0.000
Transcripts:
GLDC:uc003zkc.3:c.334+5340T>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

DCC

Exomiser Score: 0.000

Phenotype Score: 0.507

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.507 to mouse mutant involving DCC.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0001330, abnormal optic nerve morphology
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:114500 Colorectal cancer, somatic - unknown
OMIM:157600 Mirror movements 1 - autosomal dominant
Top ranked variants:
INTRONIC chr18:g.50319204T>C [.:0/1:.] rs62083271 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
DCC:uc002lfe.2:c.412+40460T>C:p.(=)
DCC:uc010xdr.1:c.-170+40460T>C:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.50741728G>GA [0/1:.:.] rs142466329 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr18:g.50923500TCA>ACG [.:0/1:.] rs386803350 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.506

Variant Score: 0.000

Phenotype matches:
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
INTRONIC chr17:g.30267579TA>T [0/1:0/1:0/1] rs533433146 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
SUZ12:uc002hgs.2:c.386+75del:p.(=)
SUZ12:uc002hgt.2:c.386+75del:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr17:g.30330032A>T [.:0/1:.] rs201248045 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
SUZ12:uc002hgs.2::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.30300131T>A [0/1:0/1:0/1] rs187589526 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.4792%
ExAC AFR: 0.3185%
ExAC AMR: 0.0508%
ExAC EAS: 0.0343%
ExAC SAS: 0.0083%
ExAC NFE: 0.0202%
ExAC OTH: 0.3745%
INTRONIC chr17:g.30321563TTTTT>GTTTG [0/1:0/1:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr17:g.30330314T>G [0/1:0/1:0/1] rs112531463 (variation viewer)
Variant score: 0.000
Transcripts:
SUZ12:uc002hgs.2::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.4792%

Exomiser Score: 0.000

Phenotype Score: 0.506

Variant Score: 0.000

Phenotype matches:
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
INTRONIC chr12:g.19626314TATTTATTTATTT>AATTAATTAATTA [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr12:g.19671152C>T [.:0/1:.] rs200892830 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.506

Variant Score: 0.000

Phenotype matches:
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.506 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
chr4:g.47637G>A [0/1:0/1:.] rs898262850 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr4:g.737083T>G [.:0/1:.] rs1043663557 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.000

Phenotype matches:
Proximity score 0.505 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr22:g.29750621G>A [0/1:0/1:0/1] rs779421119 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC EAS: 0.0116%
ExAC NFE: 0.0060%
INTRONIC chr22:g.29763028T>C [.:0/1:0/1] rs547897076 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0200%

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.499 to Retinitis Pigmentosa associated with PDE6B.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Phenotypic similarity 0.504 to mouse mutant involving PDE6B.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0002864, abnormal ocular fundus morphology
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:163500 Night blindness, congenital stationary, autosomal dominant 2 - autosomal dominant
OMIM:613801 Retinitis pigmentosa-40 - autosomal recessive
ORPHA:215 Congenital Stationary Night Blindness
ORPHA:791 Retinitis Pigmentosa
Top ranked variants:
INTRONIC chr4:g.657806G>A [0/1:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr4:g.666216G>A [.:.:0/1] rs116716537 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
PDE6B:uc011buz.2::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.4193%
ESP AA: 0.5780%
ESP EA: 0.0629%
ESP All: 0.2190%

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.323 to Hermansky-Pudlak syndrome 7 associated with DTNBP1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001107, Ocular albinism
Phenotypic similarity 0.440 to mouse mutant involving DTNBP1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0005098, abnormal optic choroid morphology
Proximity score 0.504 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:614076 Hermansky-Pudlak syndrome 7 - autosomal recessive
Top ranked variants:
INTRONIC chr6:g.15637776A>G [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr6:g.15662932T>G [.:0/1:.] rs935265026 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:
Proximity score 0.504 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr19:g.50296166C>T [0/1:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.50296443C>T [.:.:0/1] rs114685663 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7788%
INTRONIC chr19:g.50296493C>T [.:.:0/1] rs141184809 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.5990%
INTRONIC chr19:g.50306736T>C [.:0/1:0/1] rs149238034 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.5591%

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:
Proximity score 0.504 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.504 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
INTRONIC chr1:g.23407755T>G [.:0/1:.] rs879189668 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
KDM1A:uc001bgi.2:c.2099-184T>G:p.(=)
KDM1A:uc001bgj.2:c.2171-184T>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTERGENIC chr1:g.23415707G>A [.:0/1:.] rs528497836 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
KDM1A:uc001bgi.2::
KDM1A:uc001bgl.3::
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0200%

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Phenotype matches:
Proximity score 0.503 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr17:g.33923558A>G [.:0/1:.] rs1050618745 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.33923563A>G [.:0/1:.] rs889255169 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.33997950G>A [.:0/1:0/1] rs115641617 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1797%
ESP AA: 0.9986%
ESP EA: 0.0116%
ESP All: 0.3460%
ExAC AFR: 0.9425%
ExAC AMR: 0.0347%
ExAC NFE: 0.0075%
ExAC OTH: 0.1106%

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Phenotype matches:
Proximity score 0.503 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
SYNONYMOUS chr11:g.970233C>T [0/1:0/1:.] rs747946542 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
AP2A2:uc001lss.3:c.201C>T:p.(=)
AP2A2:uc001lst.2:c.201C>T:p.(=)
AP2A2:uc009yco.2:n.414C>T:
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC SAS: 0.0061%
ExAC NFE: 0.0120%
ExAC OTH: 0.5556%
INTRONIC chr11:g.992776C>A [.:0/1:.] rs143278363 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.4992%

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.503 to Lymphangioleiomyomatosis associated with TSC2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000648, Optic atrophy
Proximity score 0.500 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:606690 Lymphangioleiomyomatosis, somatic - unknown
OMIM:607341 ?Focal cortical dysplasia, type II, somatic (unconfirmed)
OMIM:613254 Tuberous sclerosis-2 - autosomal dominant
ORPHA:538 Lymphangioleiomyomatosis
ORPHA:805 Tuberous Sclerosis Complex
Top ranked variants:
INTRONIC chr16:g.2098222T>G [.:0/1:.] rs749329928 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TSC2:uc002con.3:c.-30+156T>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC AMR: 0.7812%
ExAC EAS: 0.2283%
ExAC SAS: 0.0982%
ExAC NFE: 0.0912%
UTR3 chr16:g.2138670TAA>T [0/1:.:0/1] rs993209148 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
TSC2:uc002con.3:c.*61_*62del:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Phenotype matches:
Proximity score 0.503 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:612936 Spastic paraplegia 50, autosomal recessive - autosomal recessive
Top ranked variants:
INTRONIC chr7:g.99703848C>G [.:0/1:0/1] rs202052188 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0599%
ExAC AFR: 0.2923%
ExAC AMR: 0.0261%
ExAC NFE: 0.0015%

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Phenotype matches:
Proximity score 0.503 in interactome to AP1S2 and phenotypic similarity 0.629 to Fried Syndrome associated with AP1S2.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr1:g.67000126C>T [0/1:0/1:.] rs75408192 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
SGIP1:uc001dcr.3:c.10+75C>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7388%
INTRONIC chr1:g.67154730CA>C [.:0/1:.] rs35898963 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.67101497C>A [0/1:.:0/1] rs1408851 (variation viewer)
Variant score: 0.000
Transcripts:
SGIP1:uc001dcr.3:c.100-130C>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.5591%
INTRONIC chr1:g.67109487C>T [0/1:.:0/1] rs114694782 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.5192%

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.503 to mouse mutant involving KIAA1324.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0002699, abnormal vitreous body morphology
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.629 to Bohring-Opitz syndrome associated with ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Proximity score 0.500 in interactome to ASXL1 and phenotypic similarity 0.533 to mouse mutant of ASXL1.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
No known disease
Top ranked variants:
INTRONIC chr1:g.109730404T>C [0/1:0/1:0/1] rs149238694 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.7388%
INTRONIC chr1:g.109731967G>A [.:0/1:0/1] rs1037349857 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.109732367T>C [0/1:0/1:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.502

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.502 to mouse mutant involving OPN4.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - MP:0006243, impaired pupillary reflex
Proximity score 0.500 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
INTRONIC chr10:g.88418125T>G [.:0/1:.] rs878972191 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr10:g.88418134T>G [.:0/1:.] rs1013557596 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr10:g.88421164A>C [.:0/1:.] rs777530949 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC SAS: 0.0216%
ExAC FIN: 0.2569%
ExAC NFE: 0.0108%
ExAC OTH: 0.1188%
INTRONIC chr10:g.88421171A>C [.:0/1:.] rs770292897 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC EAS: 0.0250%
ExAC SAS: 0.0081%
ExAC FIN: 0.3396%
ExAC NFE: 0.0228%

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
Known diseases:
OMIM:611369 Lethal congenital contractural syndrome 3 - autosomal recessive
Top ranked variants:
INTRONIC chr19:g.3661112A>G [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr19:g.3661125A>C [.:0/1:.] rs780729188 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
ExAC FIN: 0.1520%
ExAC NFE: 0.0047%
INTRONIC chr19:g.3661136A>C [.:0/1:.] rs917605288 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr1:g.38332057T>TTCTCTCTC [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.38332078T>A [.:.:0/1] rs4653333 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.38332057T>TTCTCTCTC [.:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.38334317TC>AA [.:.:0/1] rs386630429 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.38397824CGCAC>G [.:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.38397833GGGTT>ACA [.:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr1:g.151209292C>T [.:.:0/1] rs201876385 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr1:g.151220261G>A [.:0/1:0/1] rs151063600 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1797%
ESP AA: 0.5780%
ESP EA: 0.0943%
ESP All: 0.2409%

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr11:g.17111227C>T [0/1:.:0/1] rs149159222 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
INTRONIC chr11:g.17131918T>G [.:0/1:.] rs191337971 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr11:g.17144079T>A [0/1:.:.] rs116951398 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.3395%

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Phenotypic similarity 0.442 to zebrafish mutant involving HGNC:1769.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - ZP:0005877, abnormal(ly) mislocalised keratinocyte
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr16:g.29872282T>G [.:0/1:.] rs986415233 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr16:g.29872293T>G [.:0/1:.] rs908248648 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr15:g.56258809A>T [0/1:1/1:.] rs6493829 (variation viewer)
Variant score: 0.000
Transcripts:
NEDD4:uc002adl.3:c.46-65T>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
INTRONIC chr10:g.94594414GTA>ATATT [.:0/1:0/1]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
EXOC6:uc010qnr.2:c.38-56_38-54delGTAinsATATT:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr17:g.58018413A>C [.:0/1:.] rs955100199 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.58024854T>G [.:0/1:.] rs956924368 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.58024865T>G [.:0/1:.] rs992720286 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr7:g.77814720A>G [.:.:0/1] rs75421672 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.2196%
INTRONIC chr7:g.77975042G>T [0/1:0/1:.] rs113234399 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.6390%

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
INTRONIC chr2:g.9419411GACAC>AACAT [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr2:g.9463141G>A [0/1:.:0/1] rs145276372 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
ASAP2:uc002qzh.2:c.471-109G>A:p.(=)
ASAP2:uc002qzi.2:c.471-109G>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.5990%
INTRONIC chr2:g.9419411GACAC>AACAT [0/1:.:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
INTRONIC chr7:g.944922C>CA [.:0/1:.] rs112479370 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr7:g.944929C>G [.:0/1:0/1] rs28533260 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr7:g.944934ACAG>GC [.:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr7:g.944945CGG>GGGGAC [.:.:0/1]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr7:g.1009149C>A [0/1:.:.] rs181956039 (variation viewer)
Variant score: 0.000
Transcripts:
ADAP1:uc010ksc.3:c.-135+3668G>T:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.1597%

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to PTEN and phenotypic similarity 0.629 to Bannayan-Riley-Ruvalcaba Syndrome associated with PTEN.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0000587, Abnormality of the optic nerve
No known disease
Top ranked variants:
INTRONIC chr15:g.39881034A>G [.:0/1:.]
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
THBS1:uc001zkh.3:c.1646-126A>G:p.(=)
THBS1:uc010bbi.3:c.-65A>G:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr15:g.39886277C>A [0/1:0/1:.] rs775296490 (variation viewer)
Variant score: 0.000 CONTRIBUTING VARIANT
Transcripts:
THBS1:uc001zkh.3:c.3268-23C>A:p.(=)
THBS1:uc010bbi.3:c.1684-23C>A:p.(=)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr15:g.39887535T>C [.:0/1:.] rs376193323 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
1000Genomes: 0.0799%
ExAC AFR: 0.4145%
ExAC AMR: 0.0374%
ExAC NFE: 0.0046%

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to Familial Infantile Myoclonic Epilepsy associated with TBC1D24.
Best Phenotype Matches:
HP:0001112, Leber optic atrophy - HP:0001112, Leber optic atrophy
No known disease
Top ranked variants:
INTRONIC chr17:g.57719366T>G [.:0/1:.] rs9899439 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.57719366TT>G [.:0/1:.]
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data
INTRONIC chr17:g.57719366T>G [0/1:.:0/1] rs9899439 (variation viewer)
Pathogenicity Data:
No pathogenicity data
Frequency Data:
No frequency data

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Phenotype matches:
Proximity score 0.501 in interactome to TBC1D24 and phenotypic similarity 1.000 to