ABCB6 p.Ala57=
c.171T>C · rs771029888 · VCV1619088
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00297%, nfe)
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 · A>T here scores Δ0.60 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -4.4 |
| Overall | ||
| CADD | 0.461 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00297%
European (non-Finnish) · 35/1,178,452 alleles
Filtering AF
0.00216%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.00224%
36/1,609,258 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00297% | 33,670 |
| African / African-American | 0.00134% | 74,898 |
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
- ABCB6
- Protein
- p.Ala57=
- Coding
- c.171T>C
- MANE Select
- NM_005689
- dbSNP
- rs771029888
- Type
- single nucleotide variant
- Location
- chr2:219218503 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.17 · 16 PDB
- Residue 57
- the 'required for atpase activity' region; the 'required for the lysosomal targeting' region; a UniProt-annotated variant site (in mcopcb7; uncertain significance; hypomorphic mutation)
Similar variants
- ABCB6 p.Ala57Thr Uncertain significance ★★ ⚠ same residue
- ABCB6 p.Ala164Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Ala66Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Ala681Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg135Ser Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg439Cys Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg450Gln Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg685His Uncertain significance ★★ ⚠ 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/abcb6-p-ala57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown