SLC5A8

solute carrier family 5 member 8, the group of Solute carrier family 5

Basic information

Region (hg38): 12:101155492-101210238

Links

ENSG00000256870 ∙ NCBI:160728 ∙ OMIM:608044 ∙ HGNC:19119 ∙ Uniprot:Q8N695 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC5A8 gene.

• Inborn genetic diseases (18 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			18		3	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	18	1	4

Variants in SLC5A8

This is a list of pathogenic ClinVar variants found in the SLC5A8 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-101157286-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-101157287-G-A			Benign (Nov 20, 2018)
12-101157298-C-T		not specified	Uncertain significance (Jun 06, 2023)
12-101157319-T-A		not specified	Uncertain significance (Dec 16, 2023)
12-101157325-T-A		not specified	Uncertain significance (Jun 10, 2022)
12-101157328-A-C		not specified	Uncertain significance (Dec 27, 2023)
12-101157341-C-G		not specified	Uncertain significance (Jan 10, 2023)
12-101157395-G-T		not specified	Uncertain significance (Sep 06, 2022)
12-101166587-T-G		not specified	Uncertain significance (Apr 07, 2022)
12-101168140-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-101180039-G-A		not specified	Uncertain significance (Jan 19, 2024)
12-101180087-T-C		not specified	Uncertain significance (Jul 12, 2023)
12-101182857-G-A		not specified	Uncertain significance (Jan 24, 2024)
12-101184180-C-T		not specified	Uncertain significance (Jun 30, 2023)
12-101187504-A-G		not specified	Uncertain significance (Apr 07, 2022)
12-101190480-A-C		not specified	Uncertain significance (Jun 29, 2023)
12-101190530-G-A			Likely benign (Jan 01, 2023)
12-101190538-T-C		not specified	Uncertain significance (Mar 02, 2023)
12-101190550-A-C			Benign (Feb 26, 2018)
12-101190552-G-T		not specified	Uncertain significance (Jul 06, 2021)
12-101190555-C-T		not specified	Uncertain significance (May 23, 2023)
12-101190591-A-G		not specified	Uncertain significance (Oct 25, 2022)
12-101193652-T-C		not specified	Uncertain significance (Jan 27, 2022)
12-101193685-T-A		not specified	Uncertain significance (Jan 31, 2024)
12-101195099-G-A		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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