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Variant: NM_000329.3(RPE65):c.1087C>A (p.Pro363Thr)

CA256730

13117 (ClinVar)

Gene: RPE65
Condition: RPE65-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 2a06ba5b-9a33-453f-9155-c4652c7b97b3
Approved on: 2023-12-22
Published on: 2023-12-22

HGVS expressions

NM_000329.3:c.1087C>A
NM_000329.3(RPE65):c.1087C>A (p.Pro363Thr)
NC_000001.11:g.68438228G>T
CM000663.2:g.68438228G>T
NC_000001.10:g.68903911G>T
CM000663.1:g.68903911G>T
NC_000001.9:g.68676499G>T
NG_008472.1:g.16732C>A
NG_008472.2:g.16732C>A
ENST00000262340.6:c.1087C>A
ENST00000262340.5:c.1087C>A
NM_000329.2:c.1087C>A
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Pathogenic

Met criteria codes 6
PP4_Moderate PM2_Supporting PP1_Strong PM3 PP3 PS3_Supporting

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.1087C>A (p.Pro363Thr) variant is reported in the literature in a homozygous state in at least two probands affected with Leber congenital amaurosis or early onset severe retinal dystrophy (1 point, PM3, PMID: 9326941, PMID: 26352687). At least one patient harboring the variant exhibited reduced or nondetectable rod ERG (required, 0.5 pts), decreased central visual acuity (1 pt), symptomatic onset between birth and age 5 years (1 pt), evidence of cone involvement on ERG (1 pt), light staring (1 pt), nyctalopia (0.5 pts), and positive response to RPE65 gene therapy (8 pts), which together are specific for RPE65-related recessive retinopathy (13 pts total, VCEP member-provided data, PP4_Moderate). The variant has been reported to segregate with childhood-onset severe retinal dystrophy in multiple families with at least 3 members (PP1_strong, PMID:9326941, PMID: 26352687). This variant is reported in ClinVar (Variation ID: 13117), and its Popmax Filtering AF in gnomAD v.2.1.1 is 0.00004443 (4/30608 alleles) in the South Asian population, which is lower than the ClinGen LCA / eoRD VCEP threshold (<0.0002) (PM2_Supporting). The meta-predictor REVEL gives a score of 0.702, which is above the ClinGen LCA/eoRD VCEP PP3 threshold of >0.644 and predicts a damaging effect on RPE65 function (PP3). An in vitro isomerohydrolase activity assay performed in adenovirus-infected 293A-LRAT cells showed that the p.Pro363Thr mutant exhibits complete loss of 11-cis-retinol production relative to the wild-type RPE65 control, confirming that this variant has a damaging effect on protein function (PMID: 16828753, PS3_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, PP4_Moderate, PS3_Supporting, PM2_Supporting, PP3. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Met criteria codes
PP4_Moderate
At least one patient harboring the variant exhibited reduced or nondetectable rod ERG (required, 2 pts), decreased central visual acuity (1 pt), symptomatic onset between birth and age 5 years (1 pt), evidence of cone involvement on ERG (1 pt), light staring (1 pt), nyctalopia (1 pt), and positive response to RPE65 gene therapy (8 pts), exceeding the 8 phenotype points required for this criterion (VCEP member-provided data, PP4_Moderate). A second affected patient harboring the variant met PP4 only (PMID: 9326941).
PM2_Supporting
The PopMax filtering allele frequency in gnomAD v2.1.1 is 0.00004443 (4/30608 alleles) in the South Asian population, which is lower than the ClinGen LCA / eoRD VCEP threshold (<0.0002) for this criterion (PM2_Supporting).
PP1_Strong
The variant has been reported to segregate with childhood-onset severe retinal dystrophy in the proband plus 3 affected family members (PP1_strong, PMID:9326941).
PM3
This variant has been detected in at least 2 individuals with early-onset severe retinal dystrophy who were homozygous for the variant (1 point, PM3, PMID: 9326941, PMID: 26352687). This variant has been detected in another individual with early-onset LCA who was compound heterozygous with the p.Val473Asp variant confirmed in trans (classified likely pathogenic by this VCEP, VCEP member-provided data) but was not counted for this criterion in order to avoid circularity.
PP3
The computational predictor REVEL gives a score of 0.702, which is above the ClinGen LCA / eoRD VCEP threshold of >0.644 and predicts a damaging effect on RPE65 function (PP3).
PS3_Supporting
In vitro isomerohydrolase activity assay performed with the p.Pro363Thr mutant expressed by adenovirus-infected 293A-LRAT cells showed complete loss of 11-cis-retinol production relative to the wild-type RPE65 control, indicating that this variant has a damaging effect on protein function (PMID: 16828753, PS3_supporting).
Curation History
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