ABCB1 p.Pro39=
c.117G>A · rs35265821 · VCV3043940
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.536%, amr)
Conditions
1
ABCB1-related disorder
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 -5 | GERP -2.8 |
| Overall | ||
| CADD | 1.314 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.536%
Admixed American · 82/15,306 alleles
Filtering AF
0.442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.408%
Overall
0.0657%
100/152,314 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.536% | 187 |
| Remaining individualsnot grpmax-eligible | 0.378% | 264 |
| African / African-American | 0.0217% | 4,618 |
| European (non-Finnish) | 0.00147% | 68,106 |
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
- ABCB1
- Protein
- p.Pro39=
- Coding
- c.117G>A
- MANE Select
- NM_001348946 · reported on NM_001348945
- dbSNP
- rs35265821
- Type
- single nucleotide variant
- Location
- chr7:87600989 (GRCh38)
- Gene constraint
- LOEUF 0.575 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.72 · 24 PDB
- Residue 39
- an α-helix
Disease context
ABCB1-related disorder
Similar variants
- ABCB1 p.Ile849Thr Uncertain significance ⚠ same condition
- ABCB1 c.1887+4T>G Likely benign same condition
- ABCB1 c.2397+8T>A Likely benign same condition
- ABCB1 c.2786+9C>T Likely benign same condition
- ABCB1 c.338+5T>C Likely benign same condition
- ABCB1 c.702+9A>T Likely benign same condition
- ABCB1 c.-43A>G Benign same condition
- ABCB1 p.Leu662= Likely benign same condition
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/abcb1-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown