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
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Variant: NM_000329.3(RPE65):c.1328T>C (p.Val443Ala)

CA340742376

870344 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: ddfaeffe-407e-4f2f-ac41-1df3ee46c3de
Approved on: 2024-05-10
Published on: 2024-05-10

HGVS expressions

NM_000329.3:c.1328T>C
NM_000329.3(RPE65):c.1328T>C (p.Val443Ala)
NC_000001.11:g.68431292A>G
CM000663.2:g.68431292A>G
NC_000001.10:g.68896975A>G
CM000663.1:g.68896975A>G
NC_000001.9:g.68669563A>G
NG_008472.1:g.23668T>C
NG_008472.2:g.23668T>C
ENST00000262340.6:c.1328T>C
ENST00000262340.5:c.1328T>C
NM_000329.2:c.1328T>C

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3_Moderate PP4_Moderate PM3_Supporting PP1

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:c.1328T>C(p.Val443Ala) is a predicted missense variant that replaces valine with alanine at position 443 in RPE65. The computational predictor REVEL gives a score of 0.877, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate). The splicing impact predictor SpliceAI gives a score of 0.27 for acceptor gain, which is above the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and predicts a damaging impact on splicing. This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was homozygous for the variant (0.5 points, VCEP member-provided data, PM3_Supporting). At least one proband harboring this variant exhibits a phenotype including onset in early childhood (1 pt), night blindness (required, 0.5 pts), undetectable rod ERG (required, 0.5 pts), decreased peripheral vision (1 pt), poor color vision (1 pt), severely reduced cone ERG responses, reduced visual acuity (1 pt), waxy optic disc (0.5 pts) with optic disc drusen (0.5 pts), and mildly attenuated retinal vessels (0.5 pts), which together are specific for RPE65-related recessive retinopathy (6.5 points, PP4, PMID: 20811047). The variant has been reported to segregate with childhood-onset severe retinal dystrophy through the proband plus 1 similarly affected relative (PMID: 20811047, PP1). The variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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, PM3_Supporting, PP1, PP3_Moderate, and PP4. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.877, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate). The splicing impact predictor SpliceAI gives a score of 0.27 for acceptor gain, which is above the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and predicts a damaging impact on splicing.
PP4_Moderate
At least one proband harboring this variant exhibits a phenotype including diagnosis of LCA or severe RP with onset in the first decade of life, previous exome, genome or 100+ retinal dystrophy gene panel testing that did not provide an alternative explanation for visual impairment (2 pts), childhood night blindness, reduced visual acuity (1 pt), globally reduced autofluorescence (2 pts), optic nerve pallor (0.5 pts), pigmentary retinopathy with attenuated vessels (0.5 pts) posterior subcapsular cataract (0.5 pts), macular atrophy (0.5 pts), and decreased peripheral vision (1 pt), which together are highly specific for RPE65-related recessive retinopathy (8 total points, VCEP member-provided data, PP4_Moderate).
PM3_Supporting
This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was homozygous for the variant (0.5 points, VCEP member-provided data, PM3_Supporting). This variant has also been reported in at least 2 other probands diagnosed with some form of inherited retinal dystrophy. The first had a diagnosis of Severe Early Childhood Onset Retinal Dystrophy and harbored the variant in the compound heterozygous state with the p.Arg118Ser variant confirmed in trans (PMID: 20811047). However, the proband was not counted for PM3 in order to avoid circularity. The second proband had been diagnosed with some form of inherited retinal dystrophy and harbored the variant in the compound heterozygous state with the p.Tyr368His variant (PMID: 30268864). While this variant has previously been classified as pathogenic by the ClinGen Leber congenital amaurosis / early onset retinal dystrophy VCEP, sufficient phenotype details were not available to meet the minimum requirement for the PM3 code.
PP1
The variant has been reported to segregate with childhood-onset severe retinal dystrophy through at least 1 affected meiosis from 1 family, with the variant present in the compound heterozygous state (PP1; PMID: 20811047).
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