SLC5A10
protein-codingsolute carrier family 5 member 10, the group of Solute carrier family 5
Gene summary
This gene is a member of the sodium/glucose transporter family. Members of this family are sodium-dependent transporters and can be divided into two subfamilies based on sequence homology, one that co-transports sugars and the second that transports molecules such as ascorbate, choline, iodide, lipoate, monocaroboxylates, and pantothenate. The protein encoded by this gene has the highest affinity for mannose and has been reported to be most highly expressed in the kidney. This protein may function as a kidney-specific, sodium-dependent mannose and fructose co-transporter. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~72.3 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 SLC5A10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001042450.4. 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 | 2 | 2 | ||||
| missense | 105 | 8 | 113 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 108 | 8 | 0 | 116 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001035915.1 | 15 | MANE Select | |
| Ensembl | ENSP00000379007.3 | 15 | MANE Select | |
| RefSeq | NP_001257577.1 | 14 | Standard | |
| RefSeq | NP_001257578.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- SLC-mediated transmembrane transport
- Transport of small molecules
- Fructose and mannose metabolism
Biological Process
- hexose transmembrane transport
- sodium ion transmembrane transport
Molecular Function
- glucose:sodium symporter activity
- solute:sodium symporter activity
Cellular Component
- plasma membrane
- integral component of membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395647
- Coding exons
- 15
- Length
- 72251
- Individuals with no LoFs
- 125222
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 526
- Defined
- 125748
- p
- 0.00209
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.821 | 362 | 409 | 0.886 | 0.0000273 | 3887 |
| Missense (PolyPhen) | 166 | 177.25 | 0.93652 | 1727 | ||
| Synonymous | 0.0119 | 183 | 183 | 0.999 | 0.0000134 | 1324 |
| Loss of Function | 1.37 | 25 | 33.6 | 0.744 | 0.00000171 | 316 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00050 | 0.00043 | rare |
| Latino/Admixed American | 0.00061 | 0.00061 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00071 | 0.00071 | rare |
| Finnish | 0.0038 | 0.0038 | notable |
| European (Non-Finnish) | 0.0018 | 0.0018 | notable |
| South Asian | 0.0060 | 0.0058 | notable |
| Other | 0.0026 | 0.0026 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: High capacity transporter for mannose and fructose and, to a lesser extent, glucose, AMG, and galactose. {ECO:0000269|PubMed:22212718}.;
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- LoFtool
- 0.119
- RVIS EVS
- -0.82
- RVIS percentile EVS
- 11.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.135
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |