SLC5A11
protein-codingsolute carrier family 5 member 11, the group of Solute carrier family 5
Gene summary
Cotransporters, such as SLC5A11, represent a major class of proteins that make use of ion gradients to drive active transport for the cellular accumulation of nutrients, neurotransmitters, osmolytes, and ions Roll et al. (2002) [PubMed 12039040].[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~65.8 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 SLC5A11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001352248.3. 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 | 62 | 2 | 64 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 64 | 2 | 0 | 66 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001339177.1 | 15 | MANE Select | |
| Ensembl | ENSP00000416782.3 | 15 | MANE Select | |
| RefSeq | NP_001245340.1 | 14 | Standard | |
| RefSeq | NP_001245341.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- Inositol transporters
- Transport of bile salts and organic acids, metal ions and amine compounds
- SLC-mediated transmembrane transport
Biological Process
- sodium ion transport
- apoptotic process
- carbohydrate transport
- myo-inositol transport
- transmembrane transport
Molecular Function
- glucose:sodium symporter activity
- protein binding
- polyol transmembrane transporter activity
- symporter activity
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000347898
- Coding exons
- 15
- Length
- 65788
- Individuals with no LoFs
- 125391
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 356
- Defined
- 125747
- p
- 0.00142
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.514 | 367 | 396 | 0.927 | 0.0000226 | 4379 |
| Missense (PolyPhen) | 147 | 170.97 | 0.85982 | 1853 | ||
| Synonymous | -0.103 | 165 | 163 | 1.01 | 0.0000102 | 1391 |
| Loss of Function | 1.26 | 24 | 31.6 | 0.759 | 0.00000142 | 354 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0063 | 0.0063 | notable |
| Latino/Admixed American | 0.0012 | 0.0011 | notable |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.0015 | 0.0015 | notable |
| South Asian | 0.00071 | 0.00069 | rare |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the sodium-dependent cotransport of myo- inositol (MI) with a Na(+):MI stoichiometry of 2:1. Exclusively responsible for apical MI transport and absorption in intestine. Also can transport D-chiro-inositol (DCI) but not L-fructose. Exhibits stereospecific cotransport of both D-glucose and D- xylose. May induce apoptosis through the TNF-alpha, PDCD1 pathway. May play a role in the regulation of MI concentration in serum, involving reabsorption in at least the proximal tubule of the kidney. {ECO:0000269|PubMed:15172003}.;
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- LoFtool
- 0.198
- RVIS EVS
- 0.07
- RVIS percentile EVS
- 59.16
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.207
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |