SOAT2 p.Leu402=
c.1206G>C · rs36020119 · VCV787400
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.06%, 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 0.73 | GERP -4.1, phastCons 1 |
| Overall | ||
| CADD | 6.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.06%
African / African-American · 796/75,050 alleles
Filtering AF
0.999%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.975%
Overall
0.0585%
945/1,614,152 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.06% | 94 |
| Remaining individualsnot grpmax-eligible | 0.101% | 992 |
| Middle Eastern | 0.099% | 1,010 |
| Admixed American | 0.0916% | 1,091 |
| South Asian | 0.00549% | 18,216 |
| European (non-Finnish) | 0.00169% | 59,000 |
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
- SOAT2
- Protein
- p.Leu402=
- Coding
- c.1206G>C
- MANE Select
- NM_003578
- dbSNP
- rs36020119
- Type
- single nucleotide variant
- Location
- chr12:53121371 (GRCh38)
- Gene constraint
- LOEUF 1.403 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.59 · 2 PDB
Similar variants
- SOAT2 p.Ala67= Benign ★★ same type
- ACAT2 p.Ala230Pro Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala323Gly Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala330Val Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala348Ser Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala357Gly Uncertain significance ★ ⚠ same type
- ACAT2 p.Arg223His Uncertain significance ★ ⚠ same type
- ACAT2 p.Arg272Cys 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/soat2-p-leu402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown