Submissions for variant NM_000329.3(RPE65):c.11+5G>A

gnomAD frequency: 0.00014  dbSNP: rs61751276

Total submissions: 25

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	RCV003460766	SCV004190222	pathogenic	RPE65-related recessive retinopathy	2023-12-22	reviewed by expert panel	curation	The NM_000329.3(RPE65):c.11+5G>A variant is a putative splicing variant in intron 1 of the RPE65 gene. The computational splicing predictor SpliceAI lists a change score of 0.58 for splice donor gain, predicting a deleterious impact on splicing (PP3). VCEP-member provided data from a mini-gene assay in HEK-293 cells show that this variant reduces normal splicing and leads to >400x reduction of mature mRNA, relative to the wild-type control (PS3_Supporting, Guan et al., 2024). At least 3 patients with this variant have been reported with detailed phenotypes (PMID: 21211845, PMID: 11786058), one of whom exhibited nonrecordable ERG responses from rods (0.5 pts) and cones (1 pt), congenital night blindness (0.5 pts), absence of autofluorescence (2 pts), optic nerve pallor (0.5 pts), RPE granularity (0.5 pts), onset between birth and age 5 years (1 pt), OCT preserved at macula (1 pt), constricted Goldmann visual field (1 pt), decreased central visual acuity (1 pt), and nystagmus (1 pt), which together are highly specific for recessive RPE65 retinopathy (10 pts total, VCEP member-provided data, PP4_Moderate). This variant has been detected in at least 7 published cases with recessive retinopathy, including at least two individuals homozygous for the variant (1 pt) and three individuals compound heterozygous for this variant in trans with either the c.615_616del (p.Ile206Cysfs*27), p.Glu102Ter, or c.89dup (p.Thr31fs) variant, all which have been classified Pathogenic by this VCEP (4pts, PMID: 11095629, PMID: 17525851, PMID: 35129589), (PM3_Very-Strong). Two publications contain segregation data (PMID: 11786058 and PMID: 35001204), with one set of genotype-positive siblings exhibiting the required phenotype of absent or severely decreased rod electroretinogram response (PP1). The GrpMax Filtering AF for this variant in gnomAD v2.1.1 is 0.0001017 (PM2_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: PM3_Very-Strong, PP4_Moderate, PP1, PM2_Supporting, PP3, PS3_Supporting. (VCEP specifications version 1.0.0; date of approval 09/21/2023).
Eurofins Ntd Llc (ga)	RCV000085149	SCV000336650	pathogenic	not provided	2015-10-29	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000524808	SCV000644178	pathogenic	Leber congenital amaurosis 2; Retinitis pigmentosa 20	2025-01-23	criteria provided, single submitter	clinical testing	This sequence change falls in intron 1 of the RPE65 gene. It does not directly change the encoded amino acid sequence of the RPE65 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs61751276, gnomAD 0.02%). This variant has been observed in individual(s) with retinitis pigmentosa or Leber congenital amaurosis (PMID: 9326941, 11462243, 11786058, 19854499, 20683928, 21211845, 25257057). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 65+5G>A and IVS1+5G>A. ClinVar contains an entry for this variant (Variation ID: 98825). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics	RCV000505050	SCV001239587	pathogenic	Retinal dystrophy	2018-10-19	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000085149	SCV001245624	pathogenic	not provided	2024-06-01	criteria provided, single submitter	clinical testing	RPE65: PM3:Very Strong, PM2, PS3:Moderate
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000678614	SCV001370364	likely pathogenic	Retinitis pigmentosa 20	2019-06-12	criteria provided, single submitter	clinical testing	This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2,PM3,PP3.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV000085149	SCV001446854	pathogenic	not provided	2020-10-23	criteria provided, single submitter	clinical testing
Ocular Genomics Institute, Massachusetts Eye and Ear	RCV000678614	SCV001573683	pathogenic	Retinitis pigmentosa 20	2021-04-08	criteria provided, single submitter	research	The RPE65 c.11+5G>A variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3, PP1-S, PP3, PM1. Based on this evidence we have classified this variant as Pathogenic.
Revvity Omics, Revvity	RCV000085149	SCV002019070	likely pathogenic	not provided	2021-06-12	criteria provided, single submitter	clinical testing
GeneDx	RCV000085149	SCV002513583	pathogenic	not provided	2023-01-12	criteria provided, single submitter	clinical testing	Published functional studies suggest that the variant causes a defect in RPE65 expression (Vazquez-Dominguez et al., 2022); This variant is associated with the following publications: (PMID: 11462243, 20683928, 23891399, 17964524, 32531858, 11786058, 19854499, 9326941, 20079931, 10766140, 25257057, 17525851, 21211845, 20811047, 18441370, 30268864, 31174678, 31736247, 32581362, 32865313, 12960219, 35121194, 34492281, 35129589, 34906171, 36429068, 29332120)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001275342	SCV002572262	pathogenic	Leber congenital amaurosis	2022-08-23	criteria provided, single submitter	clinical testing	Variant summary: RPE65 c.11+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes the canonical 5' splicing donor site. Two predict the variant weakens the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 7.6e-05 in 251324 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in RPE65 causing Leber Congenital Amaurosis (7.6e-05 vs 0.0014), allowing no conclusion about variant significance. c.11+5G>A has been reported in the literature in multiple individuals affected with Leber Congenital Amaurosis/Visual impairment/Retinopathies (example, Galvin_2005, Astuti_2016, Haer-Wigman_2017, Testa_2022). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Twelve 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/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV002498448	SCV002811140	pathogenic	Leber congenital amaurosis 2; Retinitis pigmentosa 20; Retinitis pigmentosa 87 with choroidal involvement	2022-03-10	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000085149	SCV003800439	pathogenic	not provided	2022-10-21	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000022752	SCV004209224	pathogenic	Leber congenital amaurosis 2	2024-03-27	criteria provided, single submitter	clinical testing
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg	RCV000505050	SCV005070827	likely pathogenic	Retinal dystrophy	2021-01-01	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000085149	SCV005090720	pathogenic	not provided	2024-07-31	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV004955275	SCV005485957	pathogenic	Inborn genetic diseases	2024-11-20	criteria provided, single submitter	clinical testing	The c.11+5G>A intronic alteration consists of a G to A substitution 5 nucleotides after coding exon 1 of the RPE65 gene. Based on data from gnomAD, the A allele has an overall frequency of 0.008% (22/282726) total alleles studied. The highest observed frequency was 0.016% (21/129112) of European (non-Finnish) alleles. This variant has been identified in the homozygous state and in conjunction with other RPE65 variant(s) in individual(s) with features consistent with RPE65-related retinopathy (Gu, 1997; Yzer, 2003; Astuti, 2016; Deng, 2022). This nucleotide position is highly conserved in available vertebrate species. RNA studies have demonstrated that this alteration results in abnormal splicing (Vazquez-Dominguez, 2022). In silico splice site analysis predicts that this alteration will result in the creation or strengthening of a novel splice donor site. Based on the available evidence, this alteration is classified as pathogenic.
OMIM	RCV000678614	SCV000044040	pathogenic	Retinitis pigmentosa 20	2003-09-01	no assertion criteria provided	literature only
OMIM	RCV000022752	SCV000044041	pathogenic	Leber congenital amaurosis 2	2003-09-01	no assertion criteria provided	literature only
Retina International	RCV000085149	SCV000117286	not provided	not provided		no assertion provided	not provided
NIHR Bioresource Rare Diseases, University of Cambridge	RCV000505050	SCV000598728	likely pathogenic	Retinal dystrophy	2015-01-01	no assertion criteria provided	research
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000678614	SCV000804701	likely pathogenic	Retinitis pigmentosa 20	2016-09-01	no assertion criteria provided	clinical testing
Laboratory of Genetics in Ophthalmology, Institut Imagine	RCV000022752	SCV001425541	pathogenic	Leber congenital amaurosis 2		no assertion criteria provided	research
Natera, Inc.	RCV001275342	SCV001460417	pathogenic	Leber congenital amaurosis	2020-09-16	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004732661	SCV005355517	pathogenic	RPE65-related disorder	2024-08-14	no assertion criteria provided	clinical testing	The RPE65 c.11+5G>A variant is predicted to interfere with splicing. This variant has been reported as causative for severe congenital autosomal recessive retinal disorders (see for examples: Astuti et al. 2016. PubMed ID: 26626312; Coppieters et al. 2010. PubMed ID: 20683928; Ripamonti et al. 2014. PubMed ID: 25257057). This variant is one of the three most frequent causative variants in RPE65 (Astuti et al. 2016. PubMed ID: 26626312). This variant is reported in 0.016% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant has been classified as pathogenic by a ClinGen Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/98825/). Given all the evidence, we interpret this variant as pathogenic.