ST14 p.Ala490=
c.1470C>T · rs140209483 · VCV730326
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.227%, 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 1.4 | GERP -1.1, phastCons 0.99 |
| Overall | ||
| CADD | 10.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.227%
African / African-American · 170/75,034 alleles
Filtering AF
0.199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.188%
Overall
0.0149%
240/1,614,154 alleles · rare
exomes 142/1,461,838 · genomes 98/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.227% | 441 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.00999% | 10,006 |
| South Asian | 0.00549% | 18,218 |
| European (non-Finnish) | 0.00407% | 24,584 |
| East Asian | 0.00223% | 44,872 |
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.Ala490=
- Coding
- c.1470C>T
- MANE Select
- NM_021978
- dbSNP
- rs140209483
- Type
- single nucleotide variant
- Location
- chr11:130198318 (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 490
- the ldl-receptor class a 2 domain
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-ala490 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown