ABCG5 p.Ala508=
c.1524C>T · rs2465952686 · VCV1774494
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
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 -0.12 | GERP -3.5, phastCons 0.1 |
| Overall | ||
| CADD | 5.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,180,034 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.00041%
6/1,461,880 alleles · very 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
- ABCG5
- Protein
- p.Ala508=
- Coding
- c.1524C>T
- MANE Select
- NM_022436
- dbSNP
- rs2465952686
- Type
- single nucleotide variant
- Location
- chr2:43820040 (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 508
- the abc transmembrane type-2 domain; an α-helix
Similar variants
- ABCG5 p.Ala508Thr Uncertain significance ★★ ⚠ same residue
- ABCG5 p.Ala508Val Uncertain significance ★★ ⚠ same residue
- ABCG5 c.1325-1G>T Likely pathogenic ★★ same condition
- ABCG5 p.Gln251Ter Pathogenic ★★ same condition
- ABCG5 p.Glu146Ter Pathogenic ★★ same condition
- ABCG5 p.Ala170Asp Uncertain significance ★★ ⚠ same condition
- ABCG5 p.Ala264Val Uncertain significance ★★ ⚠ same condition
- ABCG5 p.Ala278Glu 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/abcg5-p-ala508 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown