SLC5A8
Basic information
Region (hg38): 12:101155493-101210238
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (86 variants)
- not_provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A8 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145913.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 82 | 88 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 82 | 5 | 3 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC5A8 | protein_coding | protein_coding | ENST00000536262 | 15 | 54915 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.00e-16 | 0.0472 | 125652 | 0 | 96 | 125748 | 0.000382 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.285 | 315 | 330 | 0.956 | 0.0000160 | 3924 |
Missense in Polyphen | 92 | 111.73 | 0.82341 | 1317 | ||
Synonymous | -1.55 | 150 | 128 | 1.17 | 0.00000691 | 1226 |
Loss of Function | 0.701 | 26 | 30.2 | 0.862 | 0.00000133 | 386 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00166 | 0.00164 |
Ashkenazi Jewish | 0.000214 | 0.000198 |
East Asian | 0.000546 | 0.000544 |
Finnish | 0.0000933 | 0.0000924 |
European (Non-Finnish) | 0.000266 | 0.000255 |
Middle Eastern | 0.000546 | 0.000544 |
South Asian | 0.000484 | 0.000457 |
Other | 0.000184 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as an electrogenic sodium (Na(+)) and chloride (Cl-)-dependent sodium-coupled solute transporter, including transport of monocarboxylates (short-chain fatty acids including L-lactate, D-lactate, pyruvate, acetate, propionate, valerate and butyrate), lactate, mocarboxylate drugs (nicotinate, benzoate, salicylate and 5-aminosalicylate) and ketone bodies (beta-D- hydroxybutyrate, acetoacetate and alpha-ketoisocaproate), with a Na(+):substrate stoichiometry of between 4:1 and 2:1. Catalyzes passive carrier mediated diffusion of iodide. Mediates iodide transport from the thyrocyte into the colloid lumen through the apical membrane. May be responsible for the absorption of D- lactate and monocarboxylate drugs from the intestinal tract. Acts as a tumor suppressor, suppressing colony formation in colon cancer, prostate cancer and glioma cell lines. May play a critical role in the entry of L-lactate and ketone bodies into neurons by a process driven by an electrochemical Na(+) gradient and hence contribute to the maintenance of the energy status and function of neurons. {ECO:0000269|PubMed:12107270, ECO:0000269|PubMed:12829793, ECO:0000269|PubMed:14966140, ECO:0000269|PubMed:15090606, ECO:0000269|PubMed:15361710, ECO:0000269|PubMed:15867356, ECO:0000269|PubMed:16729224, ECO:0000269|PubMed:16805814, ECO:0000269|PubMed:17178845, ECO:0000269|PubMed:17245649, ECO:0000269|PubMed:18037591}.;
- Pathway
- Nuclear Receptors Meta-Pathway;NRF2 pathway;Tyrosine metabolism;Metabolism;Organic anion transporters;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;Nicotinamide salvaging;Nicotinate metabolism;SLC-mediated transmembrane transport;Transport of small molecules;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors
(Consensus)
Recessive Scores
- pRec
- 0.196
Intolerance Scores
- loftool
- 0.221
- rvis_EVS
- 0.4
- rvis_percentile_EVS
- 76.45
Haploinsufficiency Scores
- pHI
- 0.102
- hipred
- N
- hipred_score
- 0.300
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.213
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | High | Medium | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Slc5a8
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; neoplasm;
Gene ontology
- Biological process
- ion transport;sodium ion transport;apoptotic process;propanoate transport;short-chain fatty acid import;NAD biosynthesis via nicotinamide riboside salvage pathway;lactate transmembrane transport
- Cellular component
- plasma membrane;integral component of membrane;apical plasma membrane;extracellular exosome
- Molecular function
- monocarboxylic acid transmembrane transporter activity;lactate transmembrane transporter activity;propionate transmembrane transporter activity;passive transmembrane transporter activity;monocarboxylate:sodium symporter activity