ABCA1 p.Lys360=
c.1080G>A · rs755096584 · VCV1672186
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0406%, sas)
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 2.8 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0406%
South Asian · 37/91,082 alleles
Filtering AF
0.0303%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0267%
Overall
0.00446%
72/1,614,000 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0406% | 2,462 |
| European (non-Finnish) | 0.00288% | 34,707 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
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
- ABCA1
- Protein
- p.Lys360=
- Coding
- c.1080G>A
- MANE Select
- NM_005502
- dbSNP
- rs755096584
- Type
- single nucleotide variant
- Location
- chr9:104837542 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.50 · 7 PDB
- Residue 360
- an α-helix
Similar variants
- ABCA1 c.4175+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ABCA1 p.Thr940Met Pathogenic/Likely pathogenic ★★ same condition
- ABCA1 c.3787+5C>A Uncertain significance ★★ same condition
- ABCA1 p.Ala1855Ser Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Ala766Ser Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Arg1283Cys Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Arg1342Trp Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Arg1417Cys 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/abca1-p-lys360 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown