SLC22A9
protein-codingsolute carrier family 22 member 9, the group of Solute carrier family 22
Gene summary
Enables secondary active transmembrane transporter activity and short-chain fatty acid transmembrane transporter activity. Involved in hormone transport; short-chain fatty acid transmembrane transport; and sodium-independent organic anion transport. Located in basolateral plasma membrane. Implicated in Lynch syndrome and mismatch repair cancer syndrome. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.5 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 SLC22A9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_080866.3. 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 | 0 | |||||
| missense | 66 | 7 | 73 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 67 | 7 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_543142.2 | 10 | MANE Select | |
| Ensembl | ENSP00000279178.3 | 10 | MANE Select | |
| Ensembl | ENSP00000440206.1 | 4 | Standard | |
| Ensembl | ENSP00000533079.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- hormone transport
- short-chain fatty acid import
- sodium-independent organic anion transport
- anion transmembrane transport
Molecular Function
- anion:anion antiporter activity
- sodium-independent organic anion transmembrane transporter activity
- short-chain fatty acid transmembrane transporter activity
Cellular Component
- integral component of membrane
- basolateral plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000279178
- Coding exons
- 10
- Length
- 40506
- Individuals with no LoFs
- 125608
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 133
- Defined
- 125742
- p
- 0.000533
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.24 | 364 | 303 | 1.20 | 0.0000149 | 3632 |
| Missense (PolyPhen) | 78 | 74.701 | 1.0442 | 912 | ||
| Synonymous | 0.427 | 105 | 111 | 0.948 | 0.00000551 | 1113 |
| Loss of Function | -0.716 | 26 | 22.3 | 1.16 | 0.00000108 | 255 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.00029 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0023 | 0.0022 | notable |
| Finnish | 0.00033 | 0.00032 | rare |
| European (Non-Finnish) | 0.00044 | 0.00044 | rare |
| South Asian | 0.00061 | 0.00059 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sodium-independent organic anion transporter which exhibits high specificity for sulfated conjugates of xenobiotics and steroid hormones. It is also specifically activated by 3 to 5 carbons-containing short-chain fatty acids/SCFAs, including propionate, butyrate and valerate. May operate the exchange of sulfated organic components against short-chain fatty acids/SCFAs at the sinusoidal membrane of hepatocytes. {ECO:0000269|PubMed:17393504}.;
Intolerance Scores
- LoFtool
- 0.955
- RVIS EVS
- 0.18
- RVIS percentile EVS
- 66.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.353
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |