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.1022T>C (p.Leu341Ser)

CA226472

13118 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: a12475a1-7bae-4034-b8bc-f41373cc8110
Approved on: 2024-02-20
Published on: 2024-02-20

HGVS expressions

NM_000329.3:c.1022T>C
NM_000329.3(RPE65):c.1022T>C (p.Leu341Ser)
NC_000001.11:g.68438293A>G
CM000663.2:g.68438293A>G
NC_000001.10:g.68903976A>G
CM000663.1:g.68903976A>G
NC_000001.9:g.68676564A>G
NG_008472.1:g.16667T>C
NG_008472.2:g.16667T>C
ENST00000262340.6:c.1022T>C
ENST00000262340.5:c.1022T>C
NM_000329.2:c.1022T>C
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Pathogenic

Met criteria codes 5
PM3_Strong PM2_Supporting PP3_Moderate PP4_Moderate PP1_Strong

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.1022T>C (p.Leu341Ser) missense variant replaces the leucine at position 341 with serine and has been reported in several patients. At least one patient (analyzed on a 100+ retinal dystrophy gene panel testing (2 pt) in PMID: 23847139) who displayed a non-detectable ERG (2 pt), visual acuity 20/400 OD and OS (1 pt), visual field of central island only (1 pt), nystagmus (1 pt), nyctalopia (1 pt), and no pigment in peripheral retina, which is highly specific for RPE65 retinopathy (PP4_Moderate). One patient was compound heterozygous for this variant and a pathogenic pathogenic variant (c.1205_1206insCCTG classified Pathogenic by the LCA/eoRD VCEP) confirmed in trans by parental testing (PMID: 9501220) and two probands were homozygous for the variant (PMID: 9501220, PMID: 15837919) (PM3_strong). The variant has been reported to segregate with RPE65 retinopathy (confirmed by absent or severely decreased rod electroretinogram response) in the proband plus 3 affected family members, all with the compound heterozygous genotype of Leu341Ser and c.1205_1206insCCTG variants. (PP1_strong; PMID: 9501220). The computational predictor REVEL gives a score of 0.988 and predicts a damaging effect on RPE65 function (PP3_Moderate). This variant is absent from gnomAD v2.1.1 and has a Grpmax Filtering AF of 0.00005290 in gnomAD v.3.1.2 (PM2_Supporting). 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: PP1_strong, PM3_strong, PP3_Moderate, PP4_Moderate, PM2_supporting. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM3_Strong
This variant has been detected in at least 3 probands with RPE65 retinopathy. One was compound heterozygous for this variant and a pathogenic variant (c.1205_1206insCCTG (p.Trp402CysfsTer6)) classified Pathogenic by the LCA/eoRD VCEP) confirmed in trans by parental testing. (PMID: 9501220; 1pt). Two probands were homozygous for the variant (PMID: 9501220, PMID: 15837919; 1pt). All three probands had the required phenotype of no detectable rod ERGs. Total points: 2pt (PM3_strong). Other cases were not considered to avoid circularity.
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and has a Popmax Filtering AF of 0.00005290 in gnomAD v.3.1.2., which is lower than the ClinGen LCA / eoRD threshold (<0.0002) for this criterion (PM2_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.88, which is above the ClinGen LCA/eoRP VCEP threshold of >0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
PP4_Moderate
At least one patient (analyzed on a 100+ retinal dystrophy gene panel testing in PMID: 23847139, 2 pt) with this variant displayed a non-detectable rod ERG (required, 1 pt), non-detectable cone ERG (1 pt), visual acuity 20/400 OD and OS (1 pt), visual field of central island only (1 pt), nystagmus (1 pt), nyctalopia (required, 1 pt), and no pigment in peripheral retina, which is highly specific for RPE65 retinopathy (PP4_Moderate).
PP1_Strong
The variant has been reported to segregate with RPE65 retinopathy (confirmed by absent or severely decreased rod electroretinogram response) in the proband plus 3 affected family members, all with the compound heterozygous genotype with Leu341Ser and c.1205_1206insCCTG variants. (PP1_strong; PMID: 9501220).
Curation History
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