SEPSECS p.Asp381=
c.1143T>C · rs369843404 · VCV1125141
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.93 | GERP -2.6, phastCons 0.016 |
| Overall | ||
| CADD | 1.487 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/90,918 alleles
Overall
6.2e-05%
1/1,612,776 alleles · very rare
exomes 1/1,460,488 · genomes 0/152,288 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SEPSECS
- Protein
- p.Asp381=
- Coding
- c.1143T>C
- MANE Select
- NM_016955
- dbSNP
- rs369843404
- Type
- single nucleotide variant
- Location
- chr4:25125762 (GRCh38)
- Gene constraint
- LOEUF 1.096 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.63 · 7 PDB
Similar variants
- SEPSECS c.1027-2A>G Likely pathogenic ★★ same type
- SEPSECS c.389-1G>A Likely pathogenic ★★ same type
- SEPSECS c.547+1G>C Likely pathogenic ★★ same type
- SEPSECS p.Ala239Thr Pathogenic/Likely pathogenic ★★ same type
- SEPSECS p.Arg156Ter Pathogenic/Likely pathogenic ★★ same type
- SEPSECS p.Arg169Ter Pathogenic/Likely pathogenic ★★ same type
- SEPSECS p.Arg271Ter Pathogenic/Likely pathogenic ★★ same type
- SEPSECS p.Arg97Ter Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/sepsecs-p-asp381 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown