ClinVar Miner

Submissions for variant NM_001039958.2(MESP2):c.11C>A (p.Ser4Ter)

dbSNP: rs1555439013
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000670586 SCV000795456 likely pathogenic Spondylocostal dysostosis 2, autosomal recessive 2017-11-08 criteria provided, single submitter clinical testing
Invitae RCV001385866 SCV001585870 pathogenic not provided 2023-04-12 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 554878). This variant has not been reported in the literature in individuals affected with MESP2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser4*) in the MESP2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MESP2 are known to be pathogenic (PMID: 9242490, 18485326). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000670586 SCV003800850 likely pathogenic Spondylocostal dysostosis 2, autosomal recessive 2023-01-11 criteria provided, single submitter clinical testing Variant summary: MESP2 c.11C>A (p.Ser4X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic within ClinVar (e.g. c.116C>A [p.Ser39Ter], c.258_261del [p.Glu88fs]). The variant was absent in 126698 control chromosomes (gnomAD). To our knowledge, no occurrence of c.11C>A in individuals affected with Spondylocostal Dysostosis 2 and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submitters have assessed the variant since 2014: one classified the variant as likely pathogenic and one as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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