ABCB4 p.Leu103=
c.309A>G · rs778679830 · VCV2985679
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 4.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Overall
0.000274%
4/1,459,396 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,058 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,209 |
| European (non-Finnish) | 8.49e-05% | 1,178,546 |
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
- ABCB4
- Protein
- p.Leu103=
- Coding
- c.309A>G
- MANE Select
- NM_000443
- dbSNP
- rs778679830
- Type
- single nucleotide variant
- Location
- chr7:87454570 (GRCh38)
- Gene constraint
- LOEUF 0.623 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.36 · 4 PDB
- Residue 103
- the abc transmembrane type-1 1 domain
Similar variants
- ABCB4 c.1006-2A>C Pathogenic ★★ same type
- ABCB4 c.1356+2T>C Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.1560+1G>A Likely pathogenic ★★ same type
- ABCB4 c.2064+3A>T Likely pathogenic ★★ same type
- ABCB4 c.2211+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.2682+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.2783+1G>T Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.286+1G>A 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/abcb4-p-leu103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown