ClinVar Miner

Submissions for variant NM_153717.3(EVC):c.1887-5_1904del

dbSNP: rs779275317
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665782 SCV000789954 likely pathogenic Ellis-van Creveld syndrome 2017-02-28 criteria provided, single submitter clinical testing
Invitae RCV001202364 SCV001373474 likely pathogenic Ellis-van Creveld syndrome; Curry-Hall syndrome 2024-01-04 criteria provided, single submitter clinical testing This variant results in the deletion of part of exon 14 (c.1887-5_1904del) of the EVC gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EVC are known to be pathogenic (PMID: 23220543). This variant is present in population databases (rs779275317, gnomAD 0.05%). This variant has been observed in individual(s) with Ellis-van Creveld syndrome (PMID: 19251731). This variant is also known as Del IVS13 (-9 to +14). ClinVar contains an entry for this variant (Variation ID: 550897). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
GeneDx RCV001584533 SCV001812810 pathogenic not provided 2023-04-04 criteria provided, single submitter clinical testing Deletion predicted to destroy the canonical splice acceptor site in a gene for which loss-of-function is a known mechanism of disease; Reported as likely pathogenic in ClinVar but additional evidence is not available (ClinVar Variation ID 550897; ClinVar); This variant is associated with the following publications: (PMID: 26582918, 19251731)
PreventionGenetics, part of Exact Sciences RCV003403539 SCV004104112 pathogenic EVC-related disorder 2022-12-19 criteria provided, single submitter clinical testing The EVC c.1887-5_1904del23 variant is predicted to result in a deletion affecting a canonical splice site. This variant was reported to be pathogenic for Ellis-van Creveld syndrome (see example: Figure 2A, Aubert-Mucca et al. 2022. PubMed ID: 35927022). This variant is reported in 0.046% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/4-5798739-TTCCTCAAAGGTCCACGCGGTGTG-T). This variant is interpreted as pathogenic.

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