The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000329.3(RPE65):c.907A>T (p.Lys303Ter)

CA226589

29872 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 2efb1bf5-edae-42c7-99c1-e59c170d9550
Approved on: 2024-02-20
Published on: 2024-02-20

HGVS expressions

NM_000329.3:c.907A>T
NM_000329.3(RPE65):c.907A>T (p.Lys303Ter)
NC_000001.11:g.68439033T>A
CM000663.2:g.68439033T>A
NC_000001.10:g.68904716T>A
CM000663.1:g.68904716T>A
NC_000001.9:g.68677304T>A
NG_008472.1:g.15927A>T
NG_008472.2:g.15927A>T
ENST00000262340.6:c.907A>T
ENST00000262340.5:c.907A>T
NM_000329.2:c.907A>T
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Pathogenic

Met criteria codes 3
PP4_Moderate PM2_Supporting 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.907A>T (p.Lys303Ter) is a nonsense variant that introduces a premature stop codon into exon 9 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). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). At least one proband harboring this variant exhibits a phenotype including diagnosis of Leber congenital amaurosis (0.5 pts) with infantile onset (1 pt), night blindness (0.5 pts), reduced visual acuity (0.5 pts), absence of electroretinogram responses from rods (0.5 pts) and cones, nystagmus (1 pt), loss of color vision (1 pt), severely constricted visual fields (1 pt), optic nerve head pallor (0.5 pts), attenuation of retinal arterioles (0.5 pts) with pigmentary changes, macular atrophy (0.5 pts), and significant improvement of dark-adapted vision following RPE65 gene therapy (8 pts), which together are highly specific for RPE65-related recessive retinopathy (15.5 total pts, PMID: 14962443, PMID: 22323828, PP4_Moderate). 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, PM2_supporting, and PP4_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP4_Moderate
At least one proband harboring this variant exhibits a diagnosis of Leber congenital amaurosis (0.5 pts) with a phenotype including infantile onset (1 pt), night blindness (0.5 pts), reduced visual acuity (0.5 pts), absence of electroretinogram responses from rods (0.5 pts) and cones, nystagmus (1 pt), loss of color vision (1 pt), severely constricted visual fields (1 pt), optic nerve head pallor (0.5 pts), attenuation of retinal arterioles (0.5 pts) with pigmentary changes, macular atrophy (0.5 pts), and significant improvement following gene therapy (8 pts), which together are specific for RPE65-related recessive retinopathy (15.5 points, PMID: 14962443, PMID: 22323828, PP4_Moderate).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PVS1
This nonsense variant in exon 9 of RPE65 is predicted to cause a premature stop codon in biologically-relevant-exon 9/14 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Curation History
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