ST14 p.Arg7=
c.21C>T · rs372702262 · VCV2038778
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.712%, afr)
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 0.17 | GERP -2.8, phastCons 0.38 |
| Overall | ||
| CADD | 9.899 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.712%
African / African-American · 477/67,000 alleles
Filtering AF
0.659%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.638%
Overall
0.0497%
703/1,414,390 alleles · rare
exomes 412/1,262,560 · genomes 291/151,830 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.712% | 140 |
| Middle Eastern | 0.225% | 444 |
| Remaining individualsnot grpmax-eligible | 0.149% | 670 |
| Admixed American | 0.058% | 1,724 |
| European (non-Finnish) | 0.0105% | 9,511 |
| South Asian | 0.00452% | 22,132 |
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.Arg7=
- Coding
- c.21C>T
- MANE Select
- NM_021978
- dbSNP
- rs372702262
- Type
- single nucleotide variant
- Location
- chr11:130160000 (GRCh38)
- Gene constraint
- LOEUF 0.589 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.23 · 25 PDB
- Residue 7
- the 'disordered' region
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-arg7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown