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.394G>A (p.Ala132Thr)

CA226547

13119 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: c96cbaae-09fb-4a90-9c7a-dcd5435fd7ff
Approved on: 2023-12-22
Published on: 2023-12-22

HGVS expressions

NM_000329.3:c.394G>A
NM_000329.3(RPE65):c.394G>A (p.Ala132Thr)
NC_000001.11:g.68444632C>T
CM000663.2:g.68444632C>T
NC_000001.10:g.68910315C>T
CM000663.1:g.68910315C>T
NC_000001.9:g.68682903C>T
NG_008472.1:g.10328G>A
NG_008472.2:g.10328G>A
ENST00000262340.6:c.394G>A
ENST00000262340.5:c.394G>A
NM_000329.2:c.394G>A

Benign

Met criteria codes 2
BS3_Supporting BA1
Not Met criteria codes 1
BP4

Evidence Links 1

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.394G>A is a missense variant that replaces alanine with threonine at codon 132. This variant is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.01113, with 372 alleles / 30614 total alleles in the South Asian population (with 6 homozygotes), which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.008 (BA1). The computational predictor REVEL gives a score of 0.548, which is above the ClinGen LCA / eoRD VCEP threshold of <0.3 and does not strongly predict a non-damaging effect on RPE65 function. The splicing impact predictor SpliceAI gives a score of 0.03 for splice acceptor loss, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and does not strongly predict an impact on splicing. The variant exhibited 50% enzymatic activity in an isomerohydrolase assay relative to the wild-type control, which is higher than the ClinGen LCA / eoRD BS3_Supporting threshold of >50% activity, indicating that it largely preserves] normal protein function (PMID: 16150724, BS3_Supporting). In summary, this variant meets the criteria to be classified as benign for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1, BS3_Supporting. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
BS3_Supporting
Exogenous expression of wild-type or variant RPE65 (in 293-F cells co-transfected to express the LRAT enzyme) shows that the variant exhibits 50% isomerohydrolase activity relative to the wild-type control (PMID: 16150724, BS3_Supporting). Please note the 55% isomerohydrolase activity of the p.Ala434Val variant (classified benign by the ClinGen LCA / eoRD VCEP) and <2% isomerohydrolase activity of the p.Glu417Gln variant (classified pathogenic by the ClinGen LCA / eoRD VCEP).

BA1
This variant is present in gnomAD v.2.1.1 at a PopMax allele frequency of 0.01113, with 372 alleles / 30614 total alleles in the South Asian population (with 6 homozygotes), which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.008 (BA1).
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.548, which is above the ClinGen LCA / eoRD VCEP threshold of <0.3 and does not predict a non-damaging effect on RPE65 function. The splicing impact predictor SpliceAI gives a score of 0.03 for splice acceptor loss, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥ 0.2 and does not strongly predict an impact on splicing.
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