ABCA2 p.Ala391=
c.1173A>T · rs536427137 · VCV2659789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.065%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.022 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.42 | acceptor loss, 2 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -2.6 |
| Overall | ||
| CADD | 0.196 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.065%
South Asian · 58/89,194 alleles
Filtering AF
0.0516%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0468%
Overall
0.00408%
65/1,591,874 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.065% | 1,538 |
| Remaining individualsnot grpmax-eligible | 0.00812% | 12,318 |
| European (non-Finnish) | 0.000171% | 585,525 |
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
- ABCA2
- Protein
- p.Ala391=
- Coding
- c.1173A>T
- MANE Select
- NM_001606
- dbSNP
- rs536427137
- Type
- single nucleotide variant
- Location
- chr9:137020786 (GRCh38)
- Gene constraint
- LOEUF 0.436 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.46
- Residue 391
- a UniProt-annotated variant site (in idpogsa)
Similar variants
- ABCA2 p.Gln1370Ter Likely pathogenic ★★ same type
- ABCA2 c.3883-3C>T Uncertain significance ★★ same type
- ABCA2 p.Ala1357Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1620Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1645Val Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1715Ser Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala2180Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala2206Val 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/abca2-p-ala391 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown