ST14 p.Pro40=
c.120A>G · rs62642510 · VCV1599867
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 28.8%, afr) — too common for a highly-penetrant pathogenic allele
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 -20 | GERP -3.1 |
| Overall | ||
| CADD | 0.002 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
28.8%
African / African-American · 21,607/74,986 alleles
Filtering AF
28.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 28.4%
Overall
5.16%
83,343/1,614,114 alleles · common
exomes 66,857/1,461,870 · genomes 16,486/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 28.8% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 8.51% | 12 |
| Remaining individualsnot grpmax-eligible | 5.72% | 17 |
| Middle Eastern | 5.63% | 18 |
| Admixed American | 4.96% | 20 |
| European (non-Finnish) | 4.22% | 24 |
| Finnishnot grpmax-eligible | 2.53% | 39 |
| South Asian | 0.929% | 108 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| East Asian | 0.0223% | 4,488 |
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
- ST14
- Protein
- p.Pro40=
- Coding
- c.120A>G
- MANE Select
- NM_021978
- dbSNP
- rs62642510
- Type
- single nucleotide variant
- Location
- chr11:130188152 (GRCh38)
- Gene constraint
- LOEUF 0.589 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.23 · 25 PDB
Similar variants
- ST14 p.Ala557Thr Uncertain significance ★★ ⚠ same type
- ST14 p.Arg227Gly Uncertain significance ★★ ⚠ same type
- ST14 p.Gly272Ser Uncertain significance ★★ ⚠ same type
- ST14 p.Gly642Ser Uncertain significance ★★ ⚠ same type
- ST14 p.Lys743Asn Uncertain significance ★★ ⚠ same type
- ST14 p.Pro526Leu Uncertain significance ★★ ⚠ same type
- ST14 p.Ser449Phe Uncertain significance ★★ ⚠ same type
- ST14 p.Thr419Ala 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/st14-p-pro40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown