APOA1 p.Gln93=
c.279G>A · rs763439449 · VCV2724538
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
Conditions
1
Cardiovascular phenotype
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 0.2 | GERP 2.3, phastCons 0.003 |
| Overall | ||
| CADD | 8.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/60,016 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00681%
Overall
0.00062%
10/1,614,084 alleles · ultra-rare
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
- APOA1
- Protein
- p.Gln93=
- Coding
- c.279G>A
- MANE Select
- NM_000039
- dbSNP
- rs763439449
- Type
- single nucleotide variant
- Location
- chr11:116836333 (GRCh38)
- Gene constraint
- LOEUF 1.168 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 31 PDB
- Residue 93
- the '10 x approximate tandem repeats' region; a UniProt-annotated variant site (in fha2; no protein expression); a UniProt-annotated variant site (in hdl deficiency; with periorbital xanthelasmas; decreased protein abundance); an α-helix
Similar variants
- APOA1 p.Gln93His Uncertain significance ★ ⚠ same residue
- APOA1 p.Ala176Thr Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala176Val Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala204Val Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala218Thr Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala256Thr Uncertain significance ★★ ⚠ same condition
- APOA1 p.Arg140Leu Uncertain significance ★★ ⚠ same condition
- APOA1 p.Arg175Gly Uncertain significance ★★ ⚠ same condition
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/apoa1-p-gln93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown