ClinVar Miner

Submissions for variant NM_153717.3(EVC):c.1886+5G>T

gnomAD frequency: 0.00036  dbSNP: rs794726665
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000438781 SCV000520945 pathogenic not provided 2024-04-30 criteria provided, single submitter clinical testing Intronic variant directly or indirectly altering the +5 splice site in a gene for which loss of function is a known mechanism of disease, and splice predictors support a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 10700184, 23348723, 10700162, 17024374, 29068549, 31028937, 29173298, 23220543)
Labcorp Genetics (formerly Invitae), Labcorp RCV001851677 SCV002116127 likely pathogenic Ellis-van Creveld syndrome; Curry-Hall syndrome 2024-10-08 criteria provided, single submitter clinical testing This sequence change falls in intron 13 of the EVC gene. It does not directly change the encoded amino acid sequence of the EVC protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs794726665, gnomAD 0.002%). This variant has been observed in individual(s) with Ellis-van Creveld syndrome (PMID: 10700184, 23220543, 31028937). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS13+5G>T. ClinVar contains an entry for this variant (Variation ID: 5338). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 13, but is expected to preserve the integrity of the reading-frame (PMID: 17024374). 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.
Fulgent Genetics, Fulgent Genetics RCV001851677 SCV005662710 pathogenic Ellis-van Creveld syndrome; Curry-Hall syndrome 2024-06-22 criteria provided, single submitter clinical testing
OMIM RCV000005666 SCV000025848 pathogenic Ellis-van Creveld syndrome 2000-03-01 no assertion criteria provided literature only
Dan Cohn Lab, University Of California Los Angeles RCV000516013 SCV000612081 pathogenic Short-rib thoracic dysplasia 6 with or without polydactyly 2017-06-01 no assertion criteria provided research
Counsyl RCV000005666 SCV000798161 pathogenic Ellis-van Creveld syndrome 2018-02-27 no assertion criteria provided clinical testing
Natera, Inc. RCV000005666 SCV001456834 pathogenic Ellis-van Creveld syndrome 2020-09-16 no assertion criteria provided clinical testing
University of Washington Center for Mendelian Genomics, University of Washington RCV000516013 SCV001479596 likely pathogenic Short-rib thoracic dysplasia 6 with or without polydactyly no assertion criteria provided research

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