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Variant: NM_000329.3(RPE65):c.95-2A>T

CA226591

98899 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: fc9cecf0-9f39-4908-bb45-1376706fa870
Approved on: 2023-12-22
Published on: 2023-12-22

HGVS expressions

NM_000329.3:c.95-2A>T
NM_000329.3(RPE65):c.95-2A>T
NC_000001.11:g.68446862T>A
CM000663.2:g.68446862T>A
NC_000001.10:g.68912545T>A
CM000663.1:g.68912545T>A
NC_000001.9:g.68685133T>A
NG_008472.1:g.8098A>T
NG_008472.2:g.8098A>T
ENST00000262340.6:c.95-2A>T
ENST00000262340.5:c.95-2A>T
NM_000329.2:c.95-2A>T
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Pathogenic

Met criteria codes 5
PM2_Supporting PP1 PM3 PP4_Moderate PVS1
Not Met criteria codes 1
BS1

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.95-2A>T variant disrupts a canonical splice site in intron 2 and is predicted to lead to skipping of a critical exon in which missense variants have previously been established as a mechanism of disease (PVS1). At least 6 probands have been reported with this variant, one of whom displayed markedly impaired night vision (0.5 pts), reduced visual acuity 20/60 from an early age (1 pt), nystagmus (1 pt), RPE demelanization (0.5 pts), poor pupillary light response (0.5 pts), significant outer nuclear layer preservation for the severity of visual loss (1 pt), nondetectable ERG responses from rods (0.5 pts) and cones (1 pt), and minimal autofluorescence (2 pts), which together are highly specific for RPE65 retinopathy (8 pts total, PP4_Moderate, PMID: 20604683). The proband's affected sibling II:2 is also homozygous for this variant (PP1). At least 3 probands with the required phenotype of extinguished ERG harbor the variant in the homozygous state (1 point, PMID: 20604683, PMID: 17724218, PMID: 15024725, PM3). This variant is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.00002298, with 3 alleles / 34592 total alleles in the Admixed American 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_Moderate, PM2_Supporting, PM3, and PP1. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM2_Supporting
The Popmax Filtering AF for this variant in gnomAD v2.1.1 is 0.00002298. This allele frequency is lower than the ClinGen LCA/eoRD VCEP threshold (<0.0002) for this criterion (PM2_Supporting).
PP1
The variant has been reported to segregate with RPE65 retinopathy (confirmed by nondetectable rod electroretinogram response) in the proband plus 1 affected sibling, both with a homozygous genotype (PP1; PMID: 20604683).
PM3
Patients MOL0701 II:3 (PMID: 20604683), A38 (PMID: 17724218), and 122 (PMID: 15024725) all have the required phenotype of extinguished ERG and are homozygous for c.95-2A>T (1 point, PM3). Other patients harboring the variant did not meet the required phenotype.
PP4_Moderate
At least one patient (MOL0701 II:3 in PMID: 20604683) with this variant displayed markedly impaired night vision (required, 1 pt), reduced visual acuity (1 pt), nystagmus (1 pt), RPE demelanization, poor pupillary light response (0.5 pt), significantly greater amount of ONL preservation for the severity of visual loss (1 pt), nondetectable rod ERG (required, 1 pt), nondetectable cone ERG (1 pt). and minimal autofluorescence (2 pt) which together are highly specific for RPE65 retinopathy (PP4_Moderate).
PVS1
This canonical splice variant at an acceptor site in intron 2 is predicted to cause a skipping of exon 2 generating a frameshift and premature stop codon in biologically-relevant-exon 3/14. Thus it is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Not Met criteria codes
BS1
The Popmax Filtering AF for this variant in gnomAD v2.1.1 is 0.00002298. This allele frequency is lower than the ClinGen LCA/eoRD VCEP threshold (>0.000816) for this criterion.
Curation History
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