Submissions for variant NM_000329.3(RPE65):c.65T>C (p.Leu22Pro)

gnomAD frequency: 0.00004  dbSNP: rs61751277

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGen	RCV003764796	SCV004697380	likely pathogenic	RPE65-related recessive retinopathy	2024-02-18	reviewed by expert panel	curation	NM_000329.3(RPE65):c.65T>C is a missense variant causing substitution of leucine with proline at position 22. This variant is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.00002137, with 2 alleles / 16214 total alleles in the African/African-American population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). At least one proband harboring this variant exhibits a phenotype including onset in infancy (1 pt), nyctalopia since childhood (0.5 pts), diagnosis based on a 300-gene testing panel that did not provide an alternative explanation for visual impairment (2 pts), non-detectable rod ERG response (0.5 pts), reduced cone ERG response (1 pt), reduced visual acuity (1 pt), light-seeking behavior (1 pt), retinal vessel attenuation (0.5 pts), optic nerve pallor (0.5 pts), and pigment clumping (0.5 pts), which together are highly specific for RPE65-related recessive retinopathy (8 total points, VCEP member-provided data, PP4_Moderate). This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who was homozygous for the variant (0.5 pts, PMID: 35129589, PMID: 28127548, VCEP member-provided data). 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.1067dup (p.Asn356fs) or NM_000329.3(RPE65):c.10C>T (p.Gln4Ter) variants suspected in trans (1 pt, PMID: 35129589), which were previously classified pathogenic by the ClinGen LCA / eoRD VCEP (1.5 total pts, PM3). The computational predictor REVEL gives a score of 0.711, which is above the ClinGen LCA / eoRD VCEP PP3 threshold of >=0.644 and predicts a damaging effect on RPE65 function (PP3). The variant exhibited 2.8-13.5% enzymatic activity in retinoid isomerase assays relative to the wild-type control, which is lower than the ClinGen LCA / eoRD PS3_Supporting threshold of <10% activity, indicating that it triggers a severe defect in protein function (PS3_Supporting, PMID: 18599565, PMID: 24849605, PMID: 26427455). 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 / eoRD VCEP: PS3_Supporting, PM2_Supporting, PM3, PP3, and PP4_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
CeGaT Center for Human Genetics Tuebingen	RCV000085218	SCV001245622	pathogenic	not provided	2017-08-01	criteria provided, single submitter	clinical testing
Invitae	RCV001218527	SCV001390413	pathogenic	Leber congenital amaurosis 2; Retinitis pigmentosa 20	2023-12-20	criteria provided, single submitter	clinical testing	This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 22 of the RPE65 protein (p.Leu22Pro). This variant is present in population databases (rs61751277, gnomAD 0.01%). This missense change has been observed in individuals with autosomal recessive retinal dystrophy (PMID: 9801879, 17724218; Invitae). ClinVar contains an entry for this variant (Variation ID: 98888). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt RPE65 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects RPE65 function (PMID: 18599565, 24849605, 26427455). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002222384	SCV002500680	pathogenic	Leber congenital amaurosis	2022-03-28	criteria provided, single submitter	clinical testing	Variant summary: RPE65 c.65T>C (p.Leu22Pro) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 251322 control chromosomes. c.65T>C has been reported in the literature as a homozygous and compound heterozygous genotypes in individuals with inherited retinal degeneration/retinal dystrophy/Leber Congenital Amaurosis (example, Marlhens_1998, Hamel_2001, Sallum_2020, Tests_2022). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (Jin_2016). The most pronounced variant effect results in <10% of normal Retinoid isomerase activity in vitro. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
GeneDx	RCV000085218	SCV003918424	pathogenic	not provided	2023-04-16	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect with reduced protein expression and reduced RPE65 isomerase activity (Li et al., 2014; Lorenz et al., 2008); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25525159, 26427455, 18599565, 19373675, 9801879, 11264131, 32865313, 35835501, 24849605, 10800710)
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine	RCV001250672	SCV004101561	pathogenic	Leber congenital amaurosis 2		criteria provided, single submitter	clinical testing	The c.65T>C(p.Leu22Pro) missense variant in RPE65 gene has been reported in the literature as a homozygous and compound heterozygous genotypes in individuals with inherited retinal degeneration/retinal dystrophy/Leber Congenital Amaurosis (Sallum et al., 2020; Testa et al., 2022). Experimental studies have shown that this variant has an impact on protein function (Jin et al., 2016). This variant is reported with the allele frequency (0.002%) in the gnomAD and novel in 1000 genome database. It has been submitted to ClinVar as a Pathogenic variant. The amino acid Leu at position 22 is changed to a Pro changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Leu22Pro in RPE65 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. This variant is unrelat ed to the fetal hydrops and IUDs in the previous children, however since this is a previously report ed pathogenic variant , the same has been report ed here in the couple.
Baylor Genetics	RCV001250672	SCV004209220	pathogenic	Leber congenital amaurosis 2	2023-10-11	criteria provided, single submitter	clinical testing
Retina International	RCV000085218	SCV000117355	not provided	not provided		no assertion provided	not provided
Laboratory of Genetics in Ophthalmology, Institut Imagine	RCV001250672	SCV001425542	likely pathogenic	Leber congenital amaurosis 2		no assertion criteria provided	research