ClinVar Miner

Submissions for variant NM_000329.3(RPE65):c.859G>T (p.Val287Phe)

dbSNP: rs281865289
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGen RCV004527320 SCV005038783 likely pathogenic RPE65-related recessive retinopathy 2024-04-22 reviewed by expert panel curation NM_000329.3(RPE65):c.859G>T (p.Val287Phe) is both a missense variant, changing the valine at position 287 to phenylalanine, and a possible splicing variant, located at the first nucleotide of exon 9. SpliceAI's highest score is for Acceptor Loss, at 0.07, predicting a non-deleterious effect on splicing. The computational predictor REVEL has a score of 0.887, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.774 and predicts a damaging effect on RPE65 function (PP3_moderate). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). At least one proband harboring this variant exhibits a phenotype including diagnosis of LCA (0.5 pts) and significant improvement after gene therapy treatment (8 pts), which together are highly specific for RPE65-related recessive retinopathy (8.5 points, PMID: 21911650 , PP4_Moderate). This variant has been reported in at least 2 unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant (1 point, PMIDs: 18722466, 21911650). (1.0 total points, PM3). 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: PP3_moderate, PM2_supporting, PP4_moderate, PM3. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Institute of Human Genetics, University of Leipzig Medical Center RCV002226457 SCV002505528 pathogenic Leber congenital amaurosis 2 2022-04-21 criteria provided, single submitter clinical testing _x000D_ Criteria applied: PVS1, PM3, PM2_SUP
Baylor Genetics RCV002226457 SCV004209286 likely pathogenic Leber congenital amaurosis 2 2023-01-27 criteria provided, single submitter clinical testing
Retina International RCV000085226 SCV000117363 not provided not provided no assertion provided not provided

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