APOA4 p.Ala150=
c.450C>T · rs2234668 · VCV1253786
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 6.61%, sas) — 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 -6.7 |
| Overall | ||
| CADD | 0.024 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.61%
South Asian · 6,017/90,980 alleles
Filtering AF
6.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.42%
Overall
4.94%
79,607/1,610,160 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 6.61% | 15 |
| European (non-Finnish) | 5.55% | 18 |
| Remaining individualsnot grpmax-eligible | 4.41% | 23 |
| Middle Eastern | 3.96% | 25 |
| Finnishnot grpmax-eligible | 3.77% | 27 |
| Ashkenazi Jewishnot grpmax-eligible | 2.91% | 34 |
| Amishnot grpmax-eligible | 2.3% | 43 |
| Admixed American | 2.26% | 44 |
| African / African-American | 0.867% | 115 |
| East Asian | 0.0178% | 5,605 |
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
- APOA4
- Protein
- p.Ala150=
- Coding
- c.450C>T
- MANE Select
- NM_000482
- dbSNP
- rs2234668
- Type
- single nucleotide variant
- Location
- chr11:116821608 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.14 · 2 PDB
- Residue 150
- the '13 x 22 aa approximate tandem repeats' region; an α-helix
Similar variants
- APOA4 p.Ala172Thr Uncertain significance ★★ ⚠ same type
- APOA4 p.Ala333Val Uncertain significance ★★ ⚠ same type
- APOA4 p.Ala60Asp Uncertain significance ★★ ⚠ same type
- APOA4 p.Arg166Ser Uncertain significance ★★ ⚠ same type
- APOA4 p.Arg275Cys Uncertain significance ★★ ⚠ same type
- APOA4 p.Gln50Arg Uncertain significance ★★ ⚠ same type
- APOA4 p.Gln50Lys Uncertain significance ★★ ⚠ same type
- APOA4 p.Glu283Ala 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/apoa4-p-ala150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown