SLC26A9
protein-codingsolute carrier family 26 member 9, the group of Solute carrier family 26
Gene summary
This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures yet have markedly different tissue expression patterns. The product of this gene is a highly selective chloride ion channel regulated by WNK kinases. Alternative splicing results in multiple transcript variants encoding differing isoforms.[provided by RefSeq, Dec 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009061
Submitter: Orphanet
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC26A9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_052934.4. 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 | ||||
| missense | 113 | 2 | 1 | 116 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 113 | 3 | 1 | 117 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_443166.1 | 20 | MANE Select | |
| Ensembl | ENSP00000356103.3 | 20 | MANE Select | |
| RefSeq | NP_599152.2 | 21 | Standard | |
| Ensembl | ENSP00000341682.4 | 21 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mineral absorption - Homo sapiens (human)
- Transport of inorganic cations/anions and amino acids/oligopeptides
- SLC-mediated transmembrane transport
- Transport of small molecules
- Methionine and cysteine metabolism
Biological Process
- ion transport
- anion transport
- chloride transport
- positive regulation of gene expression
- bicarbonate transport
Molecular Function
- chloride channel activity
- secondary active sulfate transmembrane transporter activity
- bicarbonate transmembrane transporter activity
- chloride transmembrane transporter activity
- sulfate transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- cell surface
- apical plasma membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367134
- Coding exons
- 21
- Length
- 30413
- Individuals with no LoFs
- 125726
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 125748
- p
- 0.0000875
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.397 | 499 | 525 | 0.951 | 0.0000300 | 5780 |
| Missense (PolyPhen) | 138 | 182.95 | 0.75431 | 2038 | ||
| Synonymous | -0.559 | 236 | 225 | 1.05 | 0.0000152 | 1769 |
| Loss of Function | 4.10 | 11 | 38.4 | 0.286 | 0.00000170 | 454 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: DIDS- and thiosulfate- sensitive anion exchanger mediating chloride, sulfate and oxalate transport. Mediates chloride/bicarbonate exchange or chloride-independent bicarbonate extrusion thus assuring bicarbonate secretion. Inhibited by ammonium and thiosulfate. {ECO:0000269|PubMed:11834742, ECO:0000269|PubMed:15800055}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.0289
- RVIS EVS
- -0.14
- RVIS percentile EVS
- 42.35
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.404
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |