SLC17A1
protein-codingsolute carrier family 17 member 1, the group of Solute carrier family 17
Gene summary
Predicted to enable transmembrane transporter activity. Involved in sodium-dependent phosphate transport; urate metabolic process; and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
- NPT1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.1 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 SLC17A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005074.5. 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 | 56 | 7 | 63 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 57 | 7 | 1 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005065.2 | 11 | MANE Select | |
| Ensembl | ENSP00000244527.4 | 11 | MANE Select | |
| Ensembl | ENSP00000367118.2 | 6 | Standard | |
| Ensembl | ENSP00000420546.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Uricosurics Pathway, Pharmacodynamics
- Organic anion transporters
- Amino acid and oligopeptide SLC transporters
- Transport of inorganic cations/anions and amino acids/oligopeptides
- SLC-mediated transmembrane transport
Biological Process
- ion transport
- sodium ion transport
- phosphate ion transport
- sialic acid transport
- urate transport
Molecular Function
- sialic acid transmembrane transporter activity
- symporter activity
- sodium-dependent phosphate transmembrane transporter activity
Cellular Component
- lysosome
- plasma membrane
- integral component of plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000244527
- Coding exons
- 11
- Length
- 49163
- Individuals with no LoFs
- 125418
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 328
- Defined
- 125747
- p
- 0.00131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.418 | 235 | 254 | 0.926 | 0.0000126 | 3030 |
| Missense (PolyPhen) | 70 | 80.698 | 0.86743 | 1038 | ||
| Synonymous | 0.719 | 83 | 91.8 | 0.904 | 0.00000470 | 947 |
| Loss of Function | 0.110 | 24 | 24.6 | 0.976 | 0.00000129 | 273 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.012 | 0.012 | notable |
| Latino/Admixed American | 0.00078 | 0.00078 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00055 | 0.00055 | rare |
| South Asian | 0.00086 | 0.00085 | rare |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Important for the resorption of phosphate by the kidney. May be involved in actively transporting phosphate into cells via Na(+) cotransport in the renal brush border membrane. Plays a role in urate transport in the kidney (PubMed:27906618). {ECO:0000269|PubMed:27906618}.;
Recessive Scores
- pRec
- 0.137
Intolerance Scores
- LoFtool
- 0.928
- RVIS EVS
- 0.24
- RVIS percentile EVS
- 69.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.104
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |