APOA4 p.Leu109=
c.325C>T · rs6413456 · VCV1601361
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.37%, eas) — 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 3.6 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 3.115 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.37%
East Asian · 2,389/44,498 alleles
Filtering AF
5.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.12%
Overall
0.238%
3,665/1,536,736 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 5.37% | 19 |
| Finnishnot grpmax-eligible | 0.609% | 164 |
| Remaining individualsnot grpmax-eligible | 0.293% | 342 |
| South Asian | 0.16% | 625 |
| European (non-Finnish) | 0.049% | 2,041 |
| Middle Eastern | 0.0338% | 2,962 |
| African / African-American | 0.0232% | 4,315 |
| Admixed American | 0.00842% | 11,876 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00344% | 29,076 |
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.Leu109=
- Coding
- c.325C>T
- MANE Select
- NM_000482
- dbSNP
- rs6413456
- Type
- single nucleotide variant
- Location
- chr11:116821733 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.14 · 2 PDB
- Residue 109
- 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-leu109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown