ClinVar Miner

Submissions for variant NM_016955.4(SEPSECS):c.811C>T (p.Arg271Ter)

gnomAD frequency: 0.00005  dbSNP: rs745870736
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001389025 SCV001590229 pathogenic not provided 2023-09-28 criteria provided, single submitter clinical testing This variant is present in population databases (rs745870736, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with SEPSECS-related conditions. ClinVar contains an entry for this variant (Variation ID: 1075426). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Arg271*) in the SEPSECS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SEPSECS are known to be pathogenic (PMID: 25558065, 25590979, 26115735).
Fulgent Genetics, Fulgent Genetics RCV002499811 SCV002810613 likely pathogenic Pontocerebellar hypoplasia type 2D 2022-02-12 criteria provided, single submitter clinical testing
Ambry Genetics RCV002551567 SCV003528338 pathogenic Inborn genetic diseases 2022-09-19 criteria provided, single submitter clinical testing The c.811C>T (p.R271*) alteration, located in exon 7 (coding exon 7) of the SEPSECS gene, consists of a C to T substitution at nucleotide position 811. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 271. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the T allele has an overall frequency of <0.01% (3/281860) total alleles studied. The highest observed frequency was 0.01% (1/19950) of East Asian alleles. Based on the available evidence, this alteration is classified as pathogenic.

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