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
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000329.3(RPE65):c.1501_1505del (p.Tyr501fs)

CA2573132570

1384701 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: cba8ee55-d302-4f0e-944f-ca137444be3e

HGVS expressions

NM_000329.3:c.1501_1505del
NM_000329.3(RPE65):c.1501_1505del (p.Tyr501fs)
NC_000001.11:g.68429875_68429879del
CM000663.2:g.68429875_68429879del
NC_000001.10:g.68895558_68895562del
CM000663.1:g.68895558_68895562del
NC_000001.9:g.68668146_68668150del
NG_008472.1:g.25083_25087del
NG_008472.2:g.25083_25087del
ENST00000262340.6:c.1501_1505del
ENST00000262340.5:c.1501_1505del
NM_000329.2:c.1501_1505del

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4

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.1501_1505del (p.Tyr501ProfsTer10) is a frameshift variant in RPE65 that creates a premature translational stop codon in exon 14 of 14 and is predicted not to trigger nonsense-mediated decay but rather to C-terminally truncate the protein product before position 528, disrupting functionally critical residues required for the active site (PVS1). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). At least one proband harboring this variant exhibits a phenotype including diagnosis of retinal dystrophy with onset before age 2 years (1 pt), genotyping by targeted exome sequencing of 126 retinal genes without identifying an alternative cause of disease (2 pts), visual impairment (1 pt), night blindness (0.5 pts), tapetoretinal degeneration of the fundus with attenuated retinal vessels (0.5 pts), and extinguished ERG responses from rods (0.5 pts) and cones (1 pt), which together are specific for RPE65-related recessive retinopathy (6.5 points, PMID: 31273949, PP4). In summary, this variant meets the criteria to be classified as pathogenic for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA / eoRD VCEP: PSV1, PM2_Supporting, and PP4. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM2_Supporting
Absent from gnomAd in a region with a per-base mean depth of coverage ~ 30.
PVS1
This is a frameshift variant that introduces a premature stop codon into exon 14 of 14 that is predicted not to trigger nonsense-mediated decay but rather to C-terminally truncate the protein product. Truncating variants between codons 2 and 528 meet PVS1.
PP4
At least one proband harboring this variant exhibits a phenotype including diagnosis of retinal dystrophy with onset before age 2 years (1 pt), genotyping by targeted exome sequencing of 126 retinal genes without identifying an alternative cause of disease (2 pts), visual impairment (1 pt), night blindness (0.5 pts), tapetoretinal degeneration of the fundus with attenuated retinal vessels (0.5 pts), and extinguished ERG responses from rods (0.5 pts) and cones (1 pt), which together are specific for RPE65-related recessive retinopathy (6.5 points, PMID: 31273949, PP4).
Approved on: 2024-04-22
Published on: 2024-04-22
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.