SLCO1A2
protein-codingsolute carrier organic anion transporter family member 1A2, the group of Solute carrier organic anion transporter family
Gene summary
This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]
- SLC21A3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~155.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLCO1A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001386879.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 77 | 1 | 78 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 80 | 0 | 2 | 82 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001373808.1 | 14 | MANE Select | |
| Ensembl | ENSP00000508235.1 | 14 | MANE Select | |
| RefSeq | NP_001373807.1 | 14 | Standard | |
| RefSeq | NP_001373809.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Methotrexate Pathway (Brain Cell), Pharmacokinetics
- Methotrexate Pathway, Pharmacokinetics
- Bile secretion - Homo sapiens (human)
- Statin Pathway - Generalized, Pharmacokinetics
- Metabolism of lipids
Biological Process
- organic anion transport
- bile acid and bile salt transport
- sodium-independent organic anion transport
- transmembrane transport
Molecular Function
- organic anion transmembrane transporter activity
- bile acid transmembrane transporter activity
- sodium-independent organic anion transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000307378
- Coding exons
- 14
- Length
- 154995
- Individuals with no LoFs
- 125593
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 154
- Defined
- 125747
- p
- 0.000613
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0668 | 334 | 337 | 0.990 | 0.0000158 | 4343 |
| Missense (PolyPhen) | 112 | 118.7 | 0.94354 | 1532 | ||
| Synonymous | -0.298 | 121 | 117 | 1.04 | 0.00000573 | 1263 |
| Loss of Function | 0.420 | 26 | 28.4 | 0.915 | 0.00000120 | 423 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00031 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0043 | 0.0043 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00039 | 0.00038 | rare |
| South Asian | 0.00045 | 0.00042 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mediates the Na(+)-independent transport of organic anions such as sulfobromophthalein (BSP) and conjugated (taurocholate) and unconjugated (cholate) bile acids (By similarity). Selectively inhibited by the grapefruit juice component naringin. {ECO:0000250, ECO:0000269|PubMed:17301733}.;
Recessive Scores
- pRec
- 0.0835
Intolerance Scores
- LoFtool
- 0.994
- RVIS EVS
- -0.33
- RVIS percentile EVS
- 30.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.338
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |