SEPSECS p.Ser5=
c.15C>T · VCV4733636
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,548,692)
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 1.5 | GERP -0.6, phastCons 0.84 |
| Overall | ||
| CADD | 13.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,548,692). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SEPSECS
- Protein
- p.Ser5=
- Coding
- c.15C>T
- MANE Select
- NM_016955
- Type
- single nucleotide variant
- Location
- chr4:25160355 (GRCh38)
- Gene constraint
- LOEUF 1.096 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.63 · 7 PDB
- Residue 5
- the 'tetramerization' region
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-ser5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown