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Variant: NM_000329.3(RPE65):c.1102T>C (p.Tyr368His)

CA226484

29870 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 86ff5b9c-88b5-4ac3-adc8-f384a6332bcf
Approved on: 2024-02-20
Published on: 2024-02-20

HGVS expressions

NM_000329.3:c.1102T>C
NM_000329.3(RPE65):c.1102T>C (p.Tyr368His)
NC_000001.11:g.68438213A>G
CM000663.2:g.68438213A>G
NC_000001.10:g.68903896A>G
CM000663.1:g.68903896A>G
NC_000001.9:g.68676484A>G
NG_008472.1:g.16747T>C
NG_008472.2:g.16747T>C
ENST00000262340.6:c.1102T>C
ENST00000262340.5:c.1102T>C
NM_000329.2:c.1102T>C
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Pathogenic

Met criteria codes 4
PP3_Moderate PP1 PM3_Very Strong PM2_Supporting
Not Met criteria codes 1
PP4

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.1102T>C (p.Tyr368His) is a missense variant that replaces the tyrosine at position 368 with histidine. It has been reported in the literature in at least 2 unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant (1 point, PMID: 12960219, PMID: 25257057). The variant has also been reported in at least 3 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the c.11+5G>A, c.292_311del p.Ile98Hisfs*26, or p.Arg44Ter variant confirmed in trans (3 points, PMIDs: 11786058, PMID: 34492281). All of these variants were previously classified pathogenic by the ClinGen LCA/eoRD VCEP (4 total points, PM3_VeryStrong). The variant has also been reported to segregate with childhood-onset severe retinal dystrophy through at least 1 affected meiosis from 1 family (PP1; PMID:11786058). The variant is present in gnomAD v.2.1.1 at a Grpmax allele frequency of 0.00009488, with 19/129116 in the European (Non-Finnish) population, which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). The computational predictor REVEL gives a score of 0.969, 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: PM3_VeryStrong, PP1, PM2_Supporting, PP3_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP3_Moderate
The computational predictor REVEL gives a score of 0.969, which is above the ClinGen LCA / eoRD VCEP threshold of ≥ 0.773 and predicts a damaging effect on RPE65 function (PP3_Moderate).
PP1
The variant has been reported to segregate with childhood-onset severe retinal dystrophy through at least 1 affected meiosis from 1 family, with the variant present in trans with the c.11+5G>A variant in the compound heterozygous state (PP1; PMID:11786058).
PM3_Very Strong
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, PMID: 12960219, PMID: 25257057). The variant has been reported in at least 3 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the c.11+5G>A, c.292_311del p.Ile98Hisfs*26, or p.Arg44Ter variant confirmed in trans (3 points, PMIDs: 11786058, PMID: 34492281), which were all previously classified pathogenic by the ClinGen LCA/eoRD VCEP (4 total points, PM3_VeryStrong).
PM2_Supporting
This variant is present in gnomAD v.2.1.1 at a Grpmax allele frequency of 0.00009488, with 19/129116 in the European (Non-Finnish) population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting).
Not Met criteria codes
PP4
At least one proband harboring this variant exhibits a phenotype including the requirements for absent rod ERG response (0.5 pts) and early onset night blindness (0.5 pts), as well as blindness (1 pt), nystagmus (1 pt), macular atrophy (0.5 pts), pigmentary retinopathy with attenuation of blood vessels (0.5 pts), affected cones / color vision defect (1 pt), and constriction of peripheral vision (1 pt), which together are specific for RPE65-related recessive retinopathy (6 points). PP4 has not yet been met because this patient has been counted for PM3 instead (PMID: 11786058).
Curation History
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