The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000329.3(RPE65):c.1355T>G (p.Val452Gly)

CA226509

13116 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 42bf6048-0344-4ea9-a9bd-d56c4645e679
Approved on: 2024-12-12
Published on: 2024-12-12

HGVS expressions

NM_000329.3:c.1355T>G
NM_000329.3(RPE65):c.1355T>G (p.Val452Gly)
NC_000001.11:g.68431160A>C
CM000663.2:g.68431160A>C
NC_000001.10:g.68896843A>C
CM000663.1:g.68896843A>C
NC_000001.9:g.68669431A>C
NG_008472.1:g.23800T>G
NG_008472.2:g.23800T>G
ENST00000262340.6:c.1355T>G
ENST00000262340.5:c.1355T>G
NM_000329.2:c.1355T>G
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Likely Pathogenic

Met criteria codes 3
PM3_Strong PP3_Moderate PM2_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
The NM_000329.3(RPE65):c.1355T>G (p.Val452Gly) variant is a missense variant in RPE65 causing a substitution of valine with glycine at position 452. This variant is present in gnomAD v.4.1.0 at a Grpmax allele frequency of 0.00001064, with 3/74896 alleles in the African/African American population, which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). The computational predictor REVEL gives a score of 0.945, 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 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the p.Arg91Trp variant or the c.11+5G>A variant confirmed in trans (2 points, PMID: 9501220; laboratory-provided internal data), which were previously classified pathogenic or likely pathogenic by the ClinGen LCA/eoRD VCEP (2 total points, PM3_Strong). 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, PM3_Strong (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM3_Strong
This variant has been reported in at least 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the p.Arg91Trp variant or the c.11+5G>A variant confirmed in trans (2 points, PMID: 9501220; laboratory-provided internal data), which were previously classified pathogenic or likely pathogenic by the ClinGen LCA / eoRD VCEP (2 total points, PM3_Strong).
PP3_Moderate
The computational predictor REVEL gives a score of 0.945, 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 present in gnomAD v.4.1.0 at a Grpmax allele frequency of 0.00001064, with 3/74896 alleles in the African/African American population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting).
Curation History
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