ABCB11 p.Arg830=
c.2490G>A · rs775663263 · VCV594303
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.21 | GERP -1.6, phastCons 0.25 |
| Overall | ||
| CADD | 10.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,832 alleles
Filtering AF
0.00545%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00062%
10/1,612,664 alleles · ultra-rare
exomes 9/1,460,692 · genomes 1/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,547 |
| South Asian | 0.0022% | 45,516 |
| European (non-Finnish) | 8.48e-05% | 1,179,181 |
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.Arg830=
- Coding
- c.2490G>A
- MANE Select
- NM_003742
- dbSNP
- rs775663263
- Type
- single nucleotide variant
- Location
- chr2:168944725 (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 830
- an α-helix; the abc transmembrane type-1 2 domain
Similar variants
- ABCB11 p.Arg830fs 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
- ABCB11 c.150+2T>C 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-arg830 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown