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:c.762G>T

CA902401

Gene: RPE65 (HGNC:6121)
Condition: RPE65-related recessive retinopathy (MONDO:0100368)
Inheritance Mode: Autosomal recessive inheritance
UUID: da68b3a7-7141-49bf-9316-0019694da3a8
Approved on: 2024-12-12
Published on: 2024-12-12

HGVS expressions

NM_000329.3:c.762G>T
NC_000001.11:g.68439287C>A
CM000663.2:g.68439287C>A
NC_000001.10:g.68904970C>A
CM000663.1:g.68904970C>A
NC_000001.9:g.68677558C>A
NG_008472.1:g.15673G>T
NG_008472.2:g.15673G>T
ENST00000262340.6:c.762G>T
ENST00000262340.5:c.762G>T
NM_000329.2:c.762G>T
More

Likely Pathogenic

Met criteria codes 4
PP4_Moderate PP3_Moderate PM2_Supporting PM3

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
The NM_000329.3(RPE65):c.762G>T (p.Glu254Asp) variant is a missense variant in RPE65 causing a substitution of glutamic acid with aspartic acid at position 254. This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.774, which is above the ClinGen LCA/eoRD VCEP threshold of ≥0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate). This variant has been reported in at least 3 unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant (1 point, PM3, PMID: 35129589). At least one proband harboring this variant exhibits a phenotype including clinical diagnosis of LCA (0.5 pt) and significant, documented improvement of FST or other measure of dark-adapted vision after treatment with Luxturna or other RPE65 gene therapy. (8.5 points, PMID: 38295874, PP4_Moderate). 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: PM2_Supporting, PP3_Moderate, PP4_Moderate, PM3 (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP4_Moderate
At least one proband harboring this variant exhibits a phenotype including clinical diagnosis of LCA (0.5 pt) and significant, documented improvement of FST or other measure of dark-adapted vision after treatment with Luxturna or other RPE65 gene therapy. (8.5 points, PMID: 38295874, PP4_Moderate).
PP3_Moderate
The computational predictor REVEL gives a score of 0.774, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM3
This variant has been reported in at least 3 unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant (1 point, PM3, PMID: 35129589).
Curation History
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