The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000329.3(RPE65):c.430T>G (p.Tyr144Asp)

CA226550

98868 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 5e6acb29-c2f8-443c-a4e2-a70d61308b32
Approved on: 2024-07-23
Published on: 2024-07-23

HGVS expressions

NM_000329.3:c.430T>G
NM_000329.3(RPE65):c.430T>G (p.Tyr144Asp)
NC_000001.11:g.68444596A>C
CM000663.2:g.68444596A>C
NC_000001.10:g.68910279A>C
CM000663.1:g.68910279A>C
NC_000001.9:g.68682867A>C
NG_008472.1:g.10364T>G
NG_008472.2:g.10364T>G
ENST00000262340.6:c.430T>G
ENST00000262340.5:c.430T>G
NM_000329.2:c.430T>G

Likely Pathogenic

Met criteria codes 5
PP4 PM3 PS3_Supporting PM2_Supporting PP3_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Leber Congenital Amaurosis/early onset Retinal Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RPE65 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP
NM_000329.3(RPE65):c.430T>G is a missense variant predicted to replace tyrosine with aspartic acid at position 144. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant has been reported in at least 2 apparently unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant (1 pt, PMID: 19117922, PMID: 11462243, PMID: 28127548, PM3). At least one proband harboring this variant exhibits a phenotype including diagnosis of Leber congenital amaurosis (0.5 pts), reduced visual acuity (1 pt), macular atrophic changes (0.5 pts), abnormal electroretinogram responses, visual field constriction (1 pt), retinal vessel attenuation (0.5 pts), and retinal pigment epithelium depigmentation and granularity in the fundus (0.5 pts), which together are specific for RPE65-related recessive retinopathy (total 4 pts, PMID: 19117922, PP4). The computational predictor REVEL gives a score of 0.977, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate). The variant exhibited no detectable enzymatic activity in a retinoid isomerase assay relative to the wild-type control, which is lower than the ClinGen LCA / eoRD VCEP PS3_Supporting threshold of <10% activity, indicating that it triggers a severe defect in protein function (PMID: 16828753, PS3_Supporting). In summary, this variant meets the criteria to be classified as likely pathogenic for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA / eoRD VCEP: PS3_Supporting, PM2_Supporting, PM3, PP3_Moderate, and PP4. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP4
At least one proband harboring this variant exhibits a phenotype including diagnosis of Leber congenital amaurosis (0.5 pts), reduced visual acuity (1 pt), macular atrophic changes (0.5 pts), abnormal ERG, visual field constriction (1 pt), vessel attenuation (0.5 pts), and RPE depigmentation and granularity in the fundus (0.5 pts), which together are specific for RPE65-related recessive retinopathy (total 4 pts, PMID: 19117922, PP4).
PM3
This variant has been reported in at least 2 apparently unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant (1 pt, PMID: 19117922, PMID: 11462243, PMID: 28127548, PM3).
PS3_Supporting
The variant exhibited no detectable enzymatic activity in a retinoid isomerase assay relative to the wild-type control, which is lower than the ClinGen LCA / eoRD VCEP PS3_Supporting threshold of <10% activity, indicating that it triggers a severe defect in protein function (PMID: 16828753, PS3_Supporting).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.977, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
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