ABCG5 p.Cys287=
c.861C>T · rs530120175 · VCV1587572
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
2
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 -0.88 | GERP -3.6 |
| Overall | ||
| CADD | 7.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,842 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.0018%
29/1,613,990 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,421 |
| Admixed American | 0.00333% | 30,015 |
| South Asian | 0.00329% | 30,357 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
| European (non-Finnish) | 0.00161% | 62,101 |
| African / African-American | 0.00133% | 75,044 |
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
- ABCG5
- Protein
- p.Cys287=
- Coding
- c.861C>T
- MANE Select
- NM_022436
- dbSNP
- rs530120175
- Type
- single nucleotide variant
- Location
- chr2:43824932 (GRCh38)
- Gene constraint
- LOEUF 1.219 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.48 · 8 PDB
- Residue 287
- the abc transporter domain
Similar variants
- ABCG5 c.1325-1G>T Likely pathogenic ★★ same condition
- ABCG5 c.1762+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCG5 c.634+1G>C Likely pathogenic ★★ same condition
- ABCG5 c.904+1G>A Pathogenic ★★ same condition
- ABCG5 p.Arg183Ter Pathogenic/Likely pathogenic ★★ same condition
- ABCG5 p.Arg243Ter Pathogenic ★★ same condition
- ABCG5 p.Arg389His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ABCG5 p.Arg408Ter Pathogenic/Likely pathogenic ★★ 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/abcg5-p-cys287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown