ABCB10 p.Pro518=
c.1554G>A · rs140426197 · VCV2640063
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.801%, sas)
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 -8 | GERP -3.6 |
| Overall | ||
| CADD | 7.238 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.801%
South Asian · 730/91,082 alleles
Filtering AF
0.753%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.734%
Overall
0.483%
7,801/1,614,040 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.801% | 125 |
| European (non-Finnish) | 0.54% | 185 |
| Ashkenazi Jewishnot grpmax-eligible | 0.513% | 195 |
| Remaining individualsnot grpmax-eligible | 0.474% | 211 |
| Admixed American | 0.185% | 541 |
| Middle Eastern | 0.148% | 674 |
| Finnishnot grpmax-eligible | 0.0969% | 1,032 |
| African / African-American | 0.0894% | 1,119 |
| East Asian | 0.00891% | 11,218 |
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
- ABCB10
- Protein
- p.Pro518=
- Coding
- c.1554G>A
- MANE Select
- NM_012089
- dbSNP
- rs140426197
- Type
- single nucleotide variant
- Location
- chr1:229530290 (GRCh38)
- Gene constraint
- LOEUF 1.142 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.37 · 6 PDB
- Residue 518
- the abc transporter domain
Similar variants
- ABCB10 p.Asn478Lys Benign ★★ same type
- ABCB10 p.Thr179= Benign ★★ same type
- ABCB10 p.Ala110Pro Uncertain significance ★ ⚠ same type
- ABCB10 p.Ala280Val Uncertain significance ★ ⚠ same type
- ABCB10 p.Ala300Pro Uncertain significance ★ ⚠ same type
- ABCB10 p.Ala388Gly Uncertain significance ★ ⚠ same type
- ABCB10 p.Ala394Thr Uncertain significance ★ ⚠ same type
- ABCB10 p.Ala461Val 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/abcb10-p-pro518 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown