ABCG5 p.Ser88=
c.264A>C · rs2466139898 · VCV2571075
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.23 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 16.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,746 alleles
Overall
6.84e-05%
1/1,461,444 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.Ser88=
- Coding
- c.264A>C
- MANE Select
- NM_022436
- dbSNP
- rs2466139898
- Type
- single nucleotide variant
- Location
- chr2:43837835 (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 88
- the abc transporter domain; a binding site; an α-helix
Similar variants
- ABCG5 c.1325-1G>T Likely pathogenic ★★ same type
- ABCG5 c.1464-1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCG5 c.1762+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCG5 c.634+1G>C Likely pathogenic ★★ same type
- ABCG5 c.904+1G>A Pathogenic ★★ same type
- ABCG5 p.Arg183Ter Pathogenic/Likely pathogenic ★★ same type
- ABCG5 p.Arg243Ter Pathogenic ★★ same type
- ABCG5 p.Arg389His Pathogenic/Likely pathogenic ★★ ⚠ 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/abcg5-p-ser88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown