ClinVar Miner

Submissions for variant NM_001034853.2(RPGR):c.2405_2406del (p.Glu802fs)

dbSNP: rs398122960
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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000622673 SCV000743013 likely pathogenic Inborn genetic diseases 2017-10-12 criteria provided, single submitter clinical testing
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota RCV000076907 SCV000890876 pathogenic Retinitis pigmentosa 3 2017-10-11 criteria provided, single submitter clinical testing
GeneDx RCV001008073 SCV001167811 pathogenic not provided 2022-04-13 criteria provided, single submitter clinical testing Also known as g.ORF15+652_653delAG using alternate nomenclature; Frameshift variant predicted to result in protein truncation, as the last 351 amino acids are replaced with 31 different amino acids, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (HGMD); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25494902, 24938718, 24043777, 29190250, 30567410, 20021257, 27032803, 10932196, 22264887, 28322733, 18552978, 29785639, 31953110, 33355362, 31054281, 32000842, 32702353, 31047384, 30543658, 33090715, 33576794, 33946315, 24077912)
Blueprint Genetics RCV001074955 SCV001240562 pathogenic Retinal dystrophy 2017-08-25 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001008073 SCV001247427 pathogenic not provided 2024-02-01 criteria provided, single submitter clinical testing RPGR: PP1:Strong, PVS1:Strong, PM2, PS4:Moderate
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001003195 SCV001950369 likely pathogenic Retinitis pigmentosa 2021-04-01 criteria provided, single submitter curation The p.Glu802GlyfsTer32 variant in RPGR was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab ( Through a review of available evidence we were able to apply the following criteria: PVS1, PM2. Based on this evidence we have classified this variant as Likely Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.
3billion RCV001807778 SCV002058832 likely pathogenic Macular degeneration, X-linked atrophic 2022-01-03 criteria provided, single submitter clinical testing The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000091389). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
Invitae RCV001854345 SCV002193247 pathogenic Primary ciliary dyskinesia 2024-01-01 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu802Glyfs*32) in the RPGR (ORF15) gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 351 amino acid(s) of the RPGR (ORF15) protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with retinitis pigmentosa (PMID: 10932196, 18552978, 20021257, 22264887, 25544989). It has also been observed to segregate with disease in related individuals. This variant is also known as g.ORF15+652_653delAG. ClinVar contains an entry for this variant (Variation ID: 91389). This variant disrupts a region of the RPGR (ORF15) protein in which other variant(s) (p.Leu1130Lysfs*13) have been determined to be pathogenic (PMID: 22264887; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV002286702 SCV002577559 pathogenic X-linked cone-rod dystrophy 1 2022-02-09 criteria provided, single submitter clinical testing PVS1, PM2, PP5
MGZ Medical Genetics Center RCV002286702 SCV002581667 pathogenic X-linked cone-rod dystrophy 1 2022-08-02 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV001008073 SCV002759652 pathogenic not provided 2016-08-29 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002498372 SCV002811517 pathogenic X-linked cone-rod dystrophy 1; Retinitis pigmentosa 3; Retinitis pigmentosa, X-linked, and sinorespiratory infections, with or without deafness; Macular degeneration, X-linked atrophic 2021-09-22 criteria provided, single submitter clinical testing
Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel RCV001003195 SCV004030310 pathogenic Retinitis pigmentosa 2023-07-24 criteria provided, single submitter research Clinical significance based on ACMG v2.0
Dept Of Ophthalmology, Nagoya University RCV001074955 SCV004707081 likely pathogenic Retinal dystrophy 2023-10-01 criteria provided, single submitter research
OMIM RCV000076907 SCV000030807 pathogenic Retinitis pigmentosa 3 2000-08-01 no assertion criteria provided literature only
Sharon lab, Hadassah-Hebrew University Medical Center RCV001003195 SCV001161272 pathogenic Retinitis pigmentosa 2019-06-23 no assertion criteria provided research

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