SLC5A11

solute carrier family 5 member 11, the group of Solute carrier family 5

Basic information

Region (hg38): 16:24845840-24911628

Links

ENSG00000158865 ∙ NCBI:115584 ∙ OMIM:610238 ∙ HGNC:23091 ∙ Uniprot:Q8WWX8 ∙ 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 SLC5A11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A11 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			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in SLC5A11

This is a list of pathogenic ClinVar variants found in the SLC5A11 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-24858708-A-T		not specified	Uncertain significance (Oct 25, 2023)
16-24869911-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-24869931-G-A		not specified	Uncertain significance (Oct 30, 2023)
16-24875658-G-A		not specified	Uncertain significance (Nov 14, 2023)
16-24875669-A-T		not specified	Uncertain significance (Nov 29, 2023)
16-24877355-C-T		not specified	Uncertain significance (Apr 12, 2023)
16-24884090-C-T		not specified	Uncertain significance (Aug 23, 2021)
16-24890925-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-24890965-G-A		not specified	Uncertain significance (Dec 05, 2022)
16-24890995-C-T		not specified	Uncertain significance (Aug 08, 2022)
16-24891024-G-T		not specified	Uncertain significance (Jan 09, 2024)
16-24891042-A-G		not specified	Uncertain significance (May 09, 2022)
16-24891067-C-T		not specified	Uncertain significance (Apr 29, 2024)
16-24897974-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-24897979-T-G		not specified	Uncertain significance (Nov 09, 2023)
16-24898085-A-G		not specified	Uncertain significance (Sep 27, 2021)
16-24906728-G-A		not specified	Uncertain significance (Oct 25, 2022)
16-24906729-C-T		not specified	Uncertain significance (Feb 26, 2024)
16-24906751-A-C		not specified	Uncertain significance (Oct 13, 2023)
16-24907067-T-G		not specified	Uncertain significance (Jul 14, 2022)
16-24907095-T-G		not specified	Uncertain significance (Apr 26, 2023)
16-24907136-G-A		not specified	Uncertain significance (Mar 19, 2024)
16-24908019-C-A		not specified	Uncertain significance (Dec 28, 2022)
16-24908079-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-24908085-C-T		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC5A11	protein_coding	protein_coding	ENST00000347898	15	65788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-13	0.337	125391	0	356	125747	0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.514	367	396	0.927	0.0000226	4379
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00744	0.00745
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000437	0.000435
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00151	0.00151
Middle Eastern	0.000437	0.000435
South Asian	0.000710	0.000686
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Inositol transporters;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.198
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.16

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.231
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc5a11

Gene ontology

• Biological process: sodium ion transport;apoptotic process;carbohydrate transport;myo-inositol transport;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: glucose:sodium symporter activity;protein binding;polyol transmembrane transporter activity;symporter activity