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Variant: NM_000329.3(RPE65):c.130C>T (p.Arg44Ter)

CA902588

374497 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 3634de13-1d6a-498e-ab36-1c7dc257befe
Approved on: 2024-02-20
Published on: 2024-02-20

HGVS expressions

NM_000329.3:c.130C>T
NM_000329.3(RPE65):c.130C>T (p.Arg44Ter)
NC_000001.11:g.68446825G>A
CM000663.2:g.68446825G>A
NC_000001.10:g.68912508G>A
CM000663.1:g.68912508G>A
NC_000001.9:g.68685096G>A
NG_008472.1:g.8135C>T
NG_008472.2:g.8135C>T
ENST00000262340.6:c.130C>T
ENST00000262340.5:c.130C>T
NM_000329.2:c.130C>T
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Pathogenic

Met criteria codes 3
PM2_Supporting PP4 PVS1

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.130C>T (p.Arg44Ter) is a nonsense variant that introduces a premature stop codon into exon 3 of 14, and is predicted to lead to nonsense-mediated decay in a gene in which loss-of-function is an established mechanism of disease (PVS1). At least one proband with early-onset severe retinal dystrophy and harboring this variant exhibits a phenotype including onset by age 1 (1 pt), ERG with extinguished responses from rods (0.5 pts) and cones (1 pts), nystagmus ( 1pt), and attenuated retinal blood vessels (0.5 pts), which together are specific for RPE65-related recessive retinopathy (4 points, PMID: 26626312, PP4). The variant is present in gnomAD v.2.1.1 at a Grpmax allele frequency of 0.00001685, with 7 alleles/129188 total alleles in the European non-Finnish population, which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). 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: PVS1, PP4, and PM2_Supporting. (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 a Grpmax allele frequency of 0.00001685, with 7 alleles / 129188 total alleles in the European non-Finnish population, which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting).
PP4
At least one proband harboring this variant exhibits a phenotype including onset by age 1 (1 pt), ERG with extinguished responses from rods (0.5 pts) and cones (1 pts), nystagmus ( 1pt), and attenuated retinal blood vessels (0.5 pts), which together are specific for RPE65-related recessive retinopathy (4 points, PMID: 26626312, PP4).
PVS1
This is a nonsense variant that introduces a premature stop codon into exon 3 of 14, and is predicted to lead to nonsense-mediated decay in a gene in which loss-of-function is an established mechanism of disease (PVS1).
Curation History
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