SEC13 p.Ser309=
c.927C>T · rs139150328 · VCV2653520
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.513%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -4.4 |
| Overall | ||
| CADD | 5.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.513%
European (non-Finnish) · 6,051/1,180,022 alleles
Filtering AF
0.502%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.498%
Overall
0.411%
6,629/1,614,120 alleles · rare
exomes 6,213/1,461,884 · genomes 416/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.513% | 195 |
| Admixed American | 0.298% | 335 |
| Remaining individualsnot grpmax-eligible | 0.269% | 372 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.104% | 959 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0878% | 1,139 |
| African / African-American | 0.08% | 1,250 |
| Finnishnot grpmax-eligible | 0.0562% | 1,779 |
| East Asian | 0.00892% | 11,216 |
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
- SEC13
- Protein
- p.Ser309=
- Coding
- c.927C>T
- MANE Select
- NM_183352
- dbSNP
- rs139150328
- Type
- single nucleotide variant
- Location
- chr3:10301303 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.44 · 14 PDB
- Residue 309
- a modified residue (phosphoserine)
Similar variants
- SEC13 p.Ser309Phe Uncertain significance ★ ⚠ same residue
- SEC13 p.Ala100Val Uncertain significance ★ ⚠ same type
- SEC13 p.Ala112Val Uncertain significance ★ ⚠ same type
- SEC13 p.Ala148Gly Uncertain significance ★ ⚠ same type
- SEC13 p.Ala148Thr Uncertain significance ★ ⚠ same type
- SEC13 p.Ala161Thr Uncertain significance ★ ⚠ same type
- SEC13 p.Ala183Thr Uncertain significance ★ same type
- SEC13 p.Ala19Thr Uncertain significance ★ ⚠ 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/sec13-p-ser309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown