ABCB11 p.Ile569=
c.1707C>T · rs773712534 · VCV1099374
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0268%, eas)
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 -0.31 | GERP -4.2, phastCons 0.001 |
| Overall | ||
| CADD | 7.483 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0268%
East Asian · 12/44,790 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.000992%
16/1,612,780 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0268% | 3,732 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,572 |
| African / African-American | 0.00134% | 74,840 |
| European (non-Finnish) | 0.00017% | 589,650 |
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
- ABCB11
- Protein
- p.Ile569=
- Coding
- c.1707C>T
- MANE Select
- NM_003742
- dbSNP
- rs773712534
- Type
- single nucleotide variant
- Location
- chr2:168970147 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.23 · 9 PDB
- Residue 569
- an α-helix; the abc transporter 1 domain
Similar variants
- ABCB11 p.Ile569Thr Uncertain significance ★ ⚠ same residue
- ABCB11 p.Ile569fs Pathogenic ★ same residue
- ABCB11 c.1084-2A>G Pathogenic ★★ same type
- ABCB11 c.1197+1G>T Pathogenic/Likely pathogenic ★★ same type
- ABCB11 c.1198-1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCB11 c.1198-2A>C Likely pathogenic ★★ same type
- ABCB11 c.1435-2A>T Pathogenic/Likely pathogenic ★★ same type
- ABCB11 c.150+1G>A 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/abcb11-p-ile569 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown