ClinVar Miner

Submissions for variant NM_016955.4(SEPSECS):c.1A>G (p.Met1Val)

gnomAD frequency: 0.00006  dbSNP: rs1025711998
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001596551 SCV001831799 pathogenic not provided 2024-06-21 criteria provided, single submitter clinical testing Initiation codon variant in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26888482, 29709707, 25590979)
Duke University Health System Sequencing Clinic, Duke University Health System RCV003223424 SCV003919038 likely pathogenic Pontocerebellar hypoplasia type 2D 2023-04-20 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV001596551 SCV004526239 pathogenic not provided 2023-11-05 criteria provided, single submitter clinical testing This sequence change affects the initiator methionine of the SEPSECS mRNA. The next in-frame methionine is located at codon 61. This variant is present in population databases (no rsID available, gnomAD 0.01%). Disruption of the initiator codon has been observed in individual(s) with clinical features of pontocerebellar hypoplasia (PMID: 25590979, 35091508). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1223757). For these reasons, this variant has been classified as Pathogenic.

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