SLC10A2
Chr 13ARsolute carrier family 10 member 2
Also known as: ASBT, IBAT, ISBT, NTCP2, PBAM, PBAM1
This protein is a sodium/bile acid cotransporter that mediates reabsorption of bile acids in the distal ileum and renal proximal tubules, playing a critical role in enterohepatic circulation and cholesterol homeostasis. Mutations cause primary bile acid malabsorption, an autosomal recessive disorder affecting the gastrointestinal system. The gene shows high tolerance to loss-of-function variants (LOEUF 1.944), consistent with the recessive inheritance pattern.
Primary Disease Associations & Inheritance
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
500 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 73 | 0 | 73 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 20 | 222 | 34 | 2 | 278 |
Likely Benign | 0 | 6 | 34 | 65 | 105 |
Benign | 0 | 3 | 8 | 3 | 14 |
Conflicting | — | 27 | |||
| Total | 20 | 231 | 150 | 70 | 498 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SLC10A2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools