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Variant: NM_000329.3(RPE65):c.1292A>G (p.Tyr431Cys)

CA226500

29873 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 73c10d63-6456-4cf2-bf6b-506b7e13cfde
Approved on: 2024-01-31
Published on: 2024-01-31

HGVS expressions

NM_000329.3:c.1292A>G
NM_000329.3(RPE65):c.1292A>G (p.Tyr431Cys)
NC_000001.11:g.68431328T>C
CM000663.2:g.68431328T>C
NC_000001.10:g.68897011T>C
CM000663.1:g.68897011T>C
NC_000001.9:g.68669599T>C
NG_008472.1:g.23632A>G
NG_008472.2:g.23632A>G
ENST00000262340.6:c.1292A>G
ENST00000262340.5:c.1292A>G
NM_000329.2:c.1292A>G
More

Likely Pathogenic

Met criteria codes 4
PP4_Moderate PM2_Supporting PP3_Moderate PM3_Strong
Not Met criteria codes 1
PM5

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(RPE65):c.1292A>G is a missense variant predicted to cause substitution of tyrosine by cysteine at amino acid 431. This variant is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.00002, with 1/113326 total alleles in the European (Non-Finnish) population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). This variant has been reported in at least 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the c.907A>T (p.Lys303Ter) or c.1102T>C (p.Tyr368His) variants confirmed in trans (2 point, PMIDs: 14962443, 30268864), which were previously classified pathogenic by the ClinGen LCA / eoRD VCEP (2 total points, PM3_Strong). At least one proband harboring this variant exhibits a phenotype including clinical diagnosis of Leber congenital amaurosis (0.5 pts), absent or severely decreased rod electroretinogram responses (0.5 pts), congenital night blindness (0.5 pts), optic nerve pallor (0.5 pts), Pigmentary retinopathy with attenuated vessels (0.5 pts), macular atrophy (0.5 pts), symptomatic onset between birth and age five years (1 pt), decreased central visual acuity (1 pt), abnormal color vision or evidence of cone involvement on ERG (1 pt), nystagmus (1 pt), and significant improvement following gene therapy (8 pt) which together are highly specific for RPE65-related recessive retinopathy (PMIDs: 14962443, 19117922, 22323828, 15 points, PP4_Moderate). The computational predictor REVEL gives a score of 0.94, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate). 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/eoRP VCEP: PM3_Strong, PP4_Moderate, PM2_Supporting, and PP3_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP4_Moderate
At least one proband harboring this variant exhibits a phenotype including Absent or severely decreased rod electroretinogram (ERG) responses (0.5 pt), Congenital night blindness/nyctalopia (0.5 pt), Clinical diagnosis of Leber congenital amaurosis (0.5 pt), Optic nerve pallor (0.5 pt), Pigmentary retinopathy with attenuated vessels (0.5 pt), Macular atrophy (0.5 pt), Symptomatic onset between birth and age five years (1 pt), Decreased central visual acuity (1 pt), Abnormal color vision or evidence of cone involvement on ERG (1 pt), Nystagmus (1 pt), and significant improvement following gene therapy (8 pt) which together are highly specific for RPE65-related recessive retinopathy (PMIDs: 14962443, 19117922, 22323828) (15 points, PP4_Moderate).
PM2_Supporting
This variant is present in gnomAD v.2.1.1 at a PopMax allele frequency of 0.00002, with 1/113326 total alleles in the European (Non-Finnish) population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.002 (PM2_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.94, 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 0.02 for splice acceptor gain, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥ 0.2 and does not predict a damaging impact on splicing.
PM3_Strong
This variant has been reported in at least 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the c.907A>T (p.Lys303Ter) or c.1102T>C (p.Tyr368His) variants confirmed in trans (2 point, PMIDs: 14962443, 30268864), which were previously classified pathogenic by the ClinGen LCA / eoRD VCEP (2 total points, PM3_Strong).
Not Met criteria codes
PM5
c.1291T>C (p.Tyr431His) variant has been reported in ClinVar as VUS. Has not been evaluated by the LCA/eoRD VCEP
Curation History
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