The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000329.3(RPE65):c.544C>T (p.His182Tyr)

CA226559

98875 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 08f5d49e-8b51-4825-a7cf-652155a5682d
Approved on: 2024-04-22
Published on: 2024-04-22

HGVS expressions

NM_000329.3:c.544C>T
NM_000329.3(RPE65):c.544C>T (p.His182Tyr)
NC_000001.11:g.68440952G>A
CM000663.2:g.68440952G>A
NC_000001.10:g.68906635G>A
CM000663.1:g.68906635G>A
NC_000001.9:g.68679223G>A
NG_008472.1:g.14008C>T
NG_008472.2:g.14008C>T
ENST00000262340.6:c.544C>T
ENST00000262340.5:c.544C>T
NM_000329.2:c.544C>T

Pathogenic

Met criteria codes 6
PM3_Strong PS3_Supporting PM1 PP1_Moderate PP3_Moderate PM2_Supporting
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
The NM_000329.3(RPE65):c.544C>T (p.His182Tyr) variant in RPE65 is a missense variant resulting in a substitution of histidine by tyrosine at codon 182. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant has been reported in at least 1 unrelated proband with early-onset severe retinal dystrophy who was homozygous for the variant (0.5 point, PMID: 27874104). This variant has also been reported in 2 unrelated probands with early-onset severe retinal dystrophy who were compound heterozygous with the NM_000329.3(RPE65):c.118G>A (p.Gly40Ser) confirmed in trans (2 points, PMID: 9501220, PMID: 27102010), which was previously classified as pathogenic by the ClinGen LCA / eoRD VCEP (2.5 total points, PM3_Strong). The variant has been reported to segregate with childhood-onset severe retinal dystrophy through the proband plus 2 similarly affected relatives, with the variant present in the homozygous state (PP1_Moderate; PMID: 27874104). This variant is a missense substitution at p.His182, which is located within the active site, a well-characterized functional domain required for enzymatic activity (PM1, PMID: 34492281). The variant exhibited approximately 10% enzymatic activity in a retinoid isomerase assay relative to the wildtype control, which meets the ClinGen LCA / eoRD PS3_Supporting threshold of ≤10% activity, indicating that it triggers a severe defect in protein function (PS3_Supporting, PMID: 16150724). The computational predictor REVEL gives a score of 0.912, 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 pathogenic for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: PM2_Supporting, PM3_Strong, PP1_Moderate, PM1, PS3_Supporting, PP3_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PM3_Strong
This variant has been reported in at least 1 unrelated probands with early-onset severe retinal dystrophy who was homozygous for the variant (0.5 point, PMID: 27874104). This variant has also been reported in at least 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with the NM_000329.3(RPE65):c.118G>A (p.Gly40Ser) confirmed in trans (2 points, PMID: 9501220, PMID: 27102010), which was previously classified pathogenic by the ClinGen LCA / eoRD VCEP (2.5 total points, PM3_Strong).
PS3_Supporting
The variant exhibited approximately 10% enzymatic activity in a retinoid isomerase assay relative to the wildtype control, which meets the ClinGen LCA / eoRD PS3_Supporting threshold of ≤10% activity, indicating that it triggers a severe defect in protein function (PS3_Supporting, PMID: 16150724)
PM1
This variant is a missense substitution at His 182, which is located within the active site, a well-characterized functional domain required for enzymatic activity (PM1, PMID: 34492281).
PP1_Moderate
The variant has been reported to segregate with childhood-onset severe retinal dystrophy through the proband plus 2 similarly affected relatives, with the variant present in the homozygous state (PP1_Moderate; PMID: 27874104)
PP3_Moderate
The computational predictor REVEL gives a score of 0.912, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PM5
To avoid circularity of evidence.
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