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 label mismatch: RPE65 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000329.3(RPE65):c.1590C>A (p.Phe530Leu)

CA340740550

1470027 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 709c7b18-a820-4522-87b5-0d68221a9f19
Approved on: 2025-03-27
Published on: 2025-03-27

HGVS expressions

NM_000329.3:c.1590C>A
NM_000329.3(RPE65):c.1590C>A (p.Phe530Leu)
NC_000001.11:g.68429788G>T
CM000663.2:g.68429788G>T
NC_000001.10:g.68895471G>T
CM000663.1:g.68895471G>T
NC_000001.9:g.68668059G>T
NG_008472.1:g.25172C>A
NG_008472.2:g.25172C>A
ENST00000262340.6:c.1590C>A
ENST00000262340.5:c.1590C>A
NM_000329.2:c.1590C>A
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Likely Pathogenic

Met criteria codes 4
PP4 PM2_Supporting PM3_Strong PP3_Moderate

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.1590C>A (p.Phe530Leu) variant is a missense variant in RPE65 causing a substitution of phenylalanine with leucine at position p.530. This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.888, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate). This variant has been reported in at least 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with the c.200T>G, p.L67R variant confirmed in trans (1 pt) or the c.118G>A p.Gly40Ser variant confirmed in trans (1 pt) (PMIDs: 36729443, 26047050), which were previously classified as pathogenic by the ClinGen LCA / eoRD VCEP (2 total points, PM3_Strong). This variant has also been reported in the compound heterozygous state with the p.Ala507Val and the c.335G>A p.Cys112Tyr, but were not counted for additional points to avoid circularity. At least one proband harboring this variant exhibits a phenotype including severely decreased rod ERG responses (0.5), symptomatic onset between birth and age five years (1), evidence of cone involvement on ERG (1), white/yellow dots on color photography in the context of severe retinal dysfunction (2), previous 100+ retinal dystrophy gene panel testing that did not provide an alternative explanation for visual impairment (2), which together are specific for RPE65-related recessive retinopathy (6.5 points, PMID: 33952291, PP4). 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, PP3_Moderate, PM3_Strong, PP4 (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP4
At least one proband harboring this variant exhibits a phenotype including severely decreased rod ERG responses (0.5), Symptomatic onset between birth and age five years (1), evidence of cone involvement on ERG (1), White/yellow dots on color photography in the context of severe retinal dysfunction (2), previous 100+ retinal dystrophy gene panel testing that did not provide an alternative explanation for visual impairment (2), which together are specific for RPE65-related recessive retinopathy (6.5 points, PMID: 33952291, PP4).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM3_Strong
This variant has been reported in at least [#] proband(s) with early-onset severe retinal dystrophy who were compound heterozygous with the c.200T>G, p.L67R variant confirmed in trans (1 pt) or the c.118G>A p.Gly40Ser variant confirmed in trans (1 pt) (PMIDs: 36729443, 26047050), which were previously classified as pathogenic by the ClinGen LCA / eoRD VCEP (2 total points, PM3_Strong). This variant has also been reported in the compound heterozygous state with the Ala507Val and the c.335G>A p.Cys112Tyr, but were not counted for additional points to avoid circularity.
PP3_Moderate
The computational predictor REVEL gives a score of 0.888, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
Curation History
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