ST14 p.Asp489=
c.1467C>T · VCV3711858
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, 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 -11 | GERP -4.6 |
| Overall | ||
| CADD | 1.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,922 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00335%
54/1,614,012 alleles · ultra-rare
exomes 43/1,461,820 · genomes 11/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,763 |
| South Asian | 0.0121% | 8,281 |
| Admixed American | 0.00667% | 15,002 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| European (non-Finnish) | 0.00186% | 53,638 |
| Finnishnot grpmax-eligible | 0.00156% | 63,986 |
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.Asp489=
- Coding
- c.1467C>T
- MANE Select
- NM_021978
- Type
- single nucleotide variant
- Location
- chr11:130198315 (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 489
- 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-asp489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown