SLC5A12

solute carrier family 5 member 12, the group of Solute carrier family 5

Basic information

Region (hg38): 11:26667020-26723427

Links

ENSG00000148942 ∙ NCBI:159963 ∙ OMIM:612455 ∙ HGNC:28750 ∙ Uniprot:Q1EHB4 ∙ 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 SLC5A12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A12 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						0
missense			50			50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	0	0

Variants in SLC5A12

This is a list of pathogenic ClinVar variants found in the SLC5A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-26671136-T-C		not specified	Uncertain significance (Jun 30, 2024)
11-26671139-C-A		not specified	Uncertain significance (Jan 18, 2022)
11-26671151-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-26671206-C-G		not specified	Uncertain significance (Oct 30, 2023)
11-26671250-T-C		not specified	Uncertain significance (Feb 23, 2025)
11-26673416-T-C		not specified	Uncertain significance (May 29, 2024)
11-26673436-C-G		not specified	Uncertain significance (Sep 12, 2023)
11-26673451-T-C		not specified	Uncertain significance (Nov 10, 2024)
11-26673490-C-T		not specified	Uncertain significance (Apr 18, 2023)
11-26673527-G-A		not specified	Uncertain significance (Mar 24, 2023)
11-26678718-T-C		not specified	Uncertain significance (Jan 26, 2023)
11-26678798-G-T		not specified	Uncertain significance (Feb 19, 2025)
11-26678801-T-C		not specified	Uncertain significance (Sep 01, 2021)
11-26681077-C-T		not specified	Uncertain significance (Feb 22, 2025)
11-26681123-C-G		not specified	Uncertain significance (Sep 03, 2024)
11-26681139-G-A		not specified	Uncertain significance (Oct 12, 2024)
11-26681142-G-C		not specified	Uncertain significance (Dec 18, 2023)
11-26681164-C-A		not specified	Uncertain significance (Jan 07, 2025)
11-26681166-C-A		not specified	Uncertain significance (Aug 04, 2023)
11-26681169-A-G		not specified	Uncertain significance (Aug 08, 2022)
11-26681174-C-T			Likely benign (Jan 01, 2025)
11-26681218-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-26683788-A-T		not specified	Uncertain significance (Mar 25, 2024)
11-26686492-C-A		not specified	Uncertain significance (Aug 29, 2024)
11-26686526-A-G		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC5A12	protein_coding	protein_coding	ENST00000396005	15	56409

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.57e-7	0.999	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	267	326	0.820	0.0000158	3963
Missense in Polyphen		95	136.72	0.69487		1640
Synonymous	-0.0941	119	118	1.01	0.00000571	1243
Loss of Function	2.95	16	34.8	0.460	0.00000189	390

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000334	0.000323
European (Non-Finnish)	0.000248	0.000246
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.000179	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an electroneutral and low-affinity sodium (Na(+))-dependent sodium-coupled solute transporter. Catalyzes the transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, nicotinate, propionate, butyrate and beta-D- hydroxybutyrate. May be responsible for the first step of reabsorption of monocarboxylates from the lumen of the proximal tubule of the kidney and the small intestine. May play also a role in monocarboxylates transport in the retina (By similarity). Mediates electroneutral uptake of lactate, with a stoichiometry of 2 Na(+) for each lactate (By similarity). {ECO:0000250, ECO:0000269|PubMed:17692818}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Fructose and mannose metabolism;Galactose metabolism;Multifunctional anion exchangers (Consensus)

Recessive Scores

• pRec: 0.0863

Intolerance Scores

• loftool: 0.278
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.0708
• hipred: N
• hipred_score: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc5a12

Gene ontology

• Biological process: ion transport;sodium ion transport;lactate transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;apical plasma membrane;extracellular exosome
• Molecular function: organic acid:sodium symporter activity;lactate transmembrane transporter activity