ABCG5 p.Thr388=
c.1164G>A · rs145755348 · VCV1737825
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0213%, afr)
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 3.3 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 13.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0213%
African / African-American · 16/75,044 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00142%
23/1,614,188 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0213% | 4,690 |
| Admixed American | 0.00666% | 15,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Thr388=
- Coding
- c.1164G>A
- MANE Select
- NM_022436
- dbSNP
- rs145755348
- Type
- single nucleotide variant
- Location
- chr2:43824073 (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 388
- the abc transmembrane type-2 domain; an α-helix
Similar variants
- ABCG5 p.Thr388Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-thr388 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown