The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000329.3(RPE65):c.1244C>T (p.Ala415Val)

CA16617183

421620 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: f548066b-0b8f-4134-a015-ff673e1f1743

HGVS expressions

NM_000329.3:c.1244C>T
NM_000329.3(RPE65):c.1244C>T (p.Ala415Val)
NC_000001.11:g.68431376G>A
CM000663.2:g.68431376G>A
NC_000001.10:g.68897059G>A
CM000663.1:g.68897059G>A
NC_000001.9:g.68669647G>A
NG_008472.1:g.23584C>T
NG_008472.2:g.23584C>T
ENST00000262340.6:c.1244C>T
ENST00000262340.5:c.1244C>T
NM_000329.2:c.1244C>T

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP4_Moderate PP3_Moderate PM3_Supporting

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.1244C>T is a missense variant causing substitution of alanine with valine at position 415. This variant is present in gnomAD v.2.1.1 at an allele frequency of 0.0001638, with 1 allele / 6104 total alleles in the Remaining individuals population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was compound heterozygous with the NM_000329.3(RPE65):c.886dup (p.Arg296fs) variant suspected in trans (PMID: 27102010, PMID: 30268864, PMID: 37660736), which was previously classified pathogenic by the ClinGen LCA / eoRD VCEP (0.5 total points, PM3_Supporting). At least one proband harboring this variant has exhibited a phenotype including diagnosis of Leber congenital amaurosis (0.5 pts), onset before age 5 years (1 pt), flat ERG responses for rods (0.5 pts) and cones (1 pt), and improvement of night vision following RPE65 gene therapy (8 pts), which together are highly specific for RPE65-related recessive retinopathy (11 total pts, PMID: 37660736, PP4_Moderate). The computational predictor REVEL gives a score of 0.775, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.773 and predicts a damaging effect on RPE65 function (PP3_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, PM3_Supporting, PP3_Moderate, and PP4_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM2_Supporting
This variant is present in gnomAD v.2.1.1 at an allele frequency of 0.0001638, with 1 alleles / 6104 total alleles] in the Remaining individuals population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting).
PP4_Moderate
At least one proband harboring this variant has exhibited a phenotype including diagnosis of Leber congenital amaurosis (0.5 pts), onset before age 5 years (1 pt), flat ERG responses for rods (0.5 pts) and cones (1 pt), and improvement of night vision following RPE65 gene therapy (8 pts), which together are highly specific for RPE65-related recessive retinopathy (11 total pts, PMID: 37660736, PP4_Moderate).
PP3_Moderate
The computational predictor REVEL gives the variant a score of 0.775, which is above the ClinGen LCA / eoRD VCEP threshold of >0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
PM3_Supporting
This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was compound heterozygous with the NM_000329.3(RPE65):c.886dup (p.Arg296fs) variant suspected in trans (PMID: 27102010, PMID: 30268864, PMID: 37660736), which was previously classified pathogenic by the ClinGen LCA / eoRD VCEP (0.5 total points, PM3_Supporting). This variant is alternatively referred to as p.Lys294ins1gac.
Approved on: 2024-02-18
Published on: 2024-02-18
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.