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


Variant: NM_000329.3(RPE65):c.302C>T (p.Thr101Ile)

CA340748300

865946 (ClinVar)

Gene: RPE65 (HGNC:6121)
Condition: RPE65-related recessive retinopathy (MONDO:0100368)
Inheritance Mode: Autosomal recessive inheritance
UUID: e886266e-2f44-4bb3-96a0-eb3bfb13599b
Approved on: 2024-12-12
Published on: 2024-12-12

HGVS expressions

NM_000329.3:c.302C>T
NM_000329.3(RPE65):c.302C>T (p.Thr101Ile)
NC_000001.11:g.68444827G>A
CM000663.2:g.68444827G>A
NC_000001.10:g.68910510G>A
CM000663.1:g.68910510G>A
NC_000001.9:g.68683098G>A
NG_008472.1:g.10133C>T
NG_008472.2:g.10133C>T
ENST00000262340.6:c.302C>T
ENST00000262340.5:c.302C>T
NM_000329.2:c.302C>T
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PM3 PP3_Moderate PS3_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.302C>T (p.Thr101Ile) variant is a missense variant in RPE65 causing a substitution of threonine with isoleucine at position 101. This variant is present in gnomAD v.4.1.0 at a Grpmax allele frequency of 8.474e-7, with 1 / 1180026 alleles in the European (Non-Finnish) 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 0.88, 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 1.27% enzymatic activity in a retinoid isomerase assay relative to the wild-type control, which is lower than the ClinGen LCA/eoRD PS3_Supporting threshold of <10% activity, indicating that it triggers a severe defect in protein function (PS3_Supporting, PMID: 19431183). This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was compound heterozygous with the c.271C>T p.Arg91Trp variant confirmed in trans by next-generation sequencing data (1 point, VCEP member-provided data), which was previously classified pathogenic by the ClinGen LCA/eoRD VCEP (1 total point, PM3). 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, PS3_Supporting, PM3 (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM2_Supporting
This variant is present in gnomAD v.4.1.0 at a Grpmax allele frequency of 8.474e-7, with 1 / 1180026 alleles in the European (Non-Finnish) population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting).
PM3
This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was compound heterozygous with the c.271C>T p.Arg91Trp variant confirmed in trans by next-generation sequencing data (1 point, VCEP member-provided data), which was previously classified pathogenic by the ClinGen LCA / eoRD VCEP (1 total point, PM3).
PP3_Moderate
The computational predictor REVEL gives a score of 0.88, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
PS3_Supporting
The variant exhibited 1.27% enzymatic activity in a retinoid isomerase assay relative to the wild-type control, which is lower than the ClinGen LCA / eoRD PS3_Supporting threshold of <10% activity, indicating that it triggers a severe defect in protein function (PS3_Supporting, PMID: 19431183).
Curation History
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.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.