ABCB6 p.Pro104=
c.312A>G · rs2106431010 · VCV1571224
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. | ||
| REVEL | 0.017 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.75 | GERP -4.4, phastCons 0.036 |
| Overall | ||
| CADD | 7.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,922 alleles
Overall
6.2e-05%
1/1,612,888 alleles · very rare
exomes 1/1,460,580 · genomes 0/152,308 · joint denominator
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.Pro104=
- Coding
- c.312A>G
- MANE Select
- NM_005689
- dbSNP
- rs2106431010
- Type
- single nucleotide variant
- Location
- chr2:219218362 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.17 · 16 PDB
- Residue 104
- the 'required for atpase activity' region; the 'required for the lysosomal targeting' region
Similar variants
- ABCB6 p.Ala164Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Ala57Thr 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-pro104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown