ClinVar Miner

Submissions for variant NM_033100.4(CDHR1):c.1A>G (p.Met1Val)

gnomAD frequency: 0.00003  dbSNP: rs794726954
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000173546 SCV001805397 pathogenic not provided 2021-01-19 criteria provided, single submitter clinical testing Described in an individual with adult-onset macular dystrophy and reduced visual acuity who also harbored a synonymous variant in CDHR1 in published literature (Ba-Abbad et al., 2020); Initiation codon variant in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 32681094)
DBGen Ocular Genomics RCV001589051 SCV001816063 likely pathogenic Cone-rod dystrophy 15 2021-06-01 criteria provided, single submitter clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001723745 SCV001950225 likely pathogenic Retinitis pigmentosa 2021-04-01 criteria provided, single submitter curation The p.Met1? variant in CDHR1 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 (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PP3. 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000173546 SCV002205241 pathogenic not provided 2023-09-05 criteria provided, single submitter clinical testing Disruption of the initiator codon has been observed in individuals with retinal dystrophy (PMID: 26306921, 32037395, 32681094; Invitae). This sequence change affects the initiator methionine of the CDHR1 mRNA. The next in-frame methionine is located at codon 39. This variant is present in population databases (rs794726954, gnomAD 0.005%). ClinVar contains an entry for this variant (Variation ID: 193474). For these reasons, this variant has been classified as Pathogenic.
Eurofins Ntd Llc (ga) RCV000173546 SCV000224668 uncertain significance not provided 2015-04-28 flagged submission clinical testing
PreventionGenetics, part of Exact Sciences RCV004748622 SCV005346724 pathogenic CDHR1-related disorder 2024-09-16 no assertion criteria provided clinical testing The CDHR1 c.1A>G variant is predicted to disrupt the translation initiation site (Start Loss). This variant has been reported in individuals with autosomal recessive CDHR1 related disorders (Yohe et al. 2019. PubMed ID: 31816670; Hanany et al. 2020. PubMed ID: 31964843; Zampaglione et al. 2020. PubMed ID: 32037395; Lin et al. 2024. PubMed ID: 38219857). This variant is reported in 0.0051% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.

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