SLC5A4

solute carrier family 5 member 4, the group of Solute carrier family 5

Basic information

Region (hg38): 22:32218463-32255347

Links

ENSG00000100191 ∙ NCBI:6527 ∙ OMIM:618633 ∙ HGNC:11039 ∙ Uniprot:Q9NY91 ∙ 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 SLC5A4 gene.

• Inborn genetic diseases (35 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A4 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
missense			34	1		35
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	3	0

Variants in SLC5A4

This is a list of pathogenic ClinVar variants found in the SLC5A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-32218527-C-T		not specified	Uncertain significance (Feb 26, 2024)
22-32218591-A-G		not specified	Uncertain significance (Apr 26, 2023)
22-32218643-C-G		not specified	Uncertain significance (Mar 01, 2023)
22-32218691-T-G		not specified	Uncertain significance (Apr 25, 2023)
22-32218719-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-32220965-C-A		not specified	Uncertain significance (Jun 10, 2022)
22-32220988-G-A		not specified	Uncertain significance (Oct 05, 2023)
22-32224301-A-G		not specified	Uncertain significance (Oct 26, 2022)
22-32224359-G-A		not specified	Uncertain significance (Jul 12, 2023)
22-32224400-C-A		not specified	Uncertain significance (Sep 06, 2022)
22-32224463-A-G		not specified	Uncertain significance (Jan 10, 2022)
22-32225723-T-C		not specified	Uncertain significance (May 05, 2023)
22-32225737-G-C		not specified	Uncertain significance (Jul 05, 2023)
22-32225743-T-C		not specified	Uncertain significance (May 01, 2022)
22-32229203-A-G		not specified	Uncertain significance (Aug 21, 2023)
22-32229221-G-A		not specified	Uncertain significance (Oct 26, 2022)
22-32229229-C-A		not specified	Uncertain significance (Oct 27, 2022)
22-32229234-G-C		not specified	Uncertain significance (Nov 18, 2022)
22-32229236-A-G		not specified	Uncertain significance (Aug 17, 2022)
22-32229289-G-A			Likely benign (Mar 01, 2023)
22-32231009-T-C		not specified	Uncertain significance (Jun 29, 2022)
22-32231025-C-G		not specified	Uncertain significance (Sep 12, 2023)
22-32231043-C-T		not specified	Uncertain significance (Nov 15, 2021)
22-32231058-C-T		not specified	Uncertain significance (Jan 04, 2024)
22-32231073-T-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC5A4	protein_coding	protein_coding	ENST00000266086	15	36864

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-16	0.0728	121728	47	3973	125748	0.0161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.839	342	389	0.880	0.0000215	4271
Missense in Polyphen		113	147.33	0.76696		1668
Synonymous	0.793	137	149	0.917	0.00000913	1330
Loss of Function	0.936	28	33.9	0.826	0.00000187	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0228	0.0209
Ashkenazi Jewish	0.00695	0.00418
East Asian	0.0324	0.0302
Finnish	0.00790	0.00449
European (Non-Finnish)	0.0235	0.0142
Middle Eastern	0.0324	0.0302
South Asian	0.0451	0.0420
Other	0.0250	0.0151

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has electrogenic activity in response to glucose, and may function as a glucose sensor (PubMed:13130073, PubMed:17110502, PubMed:20421923, PubMed:22766068). Mediates influx of sodium ions into the cell but does not transport sugars (PubMed:13130073, PubMed:22766068). Also potently activated by imino sugars such as deoxynojirimycin (DNJ) (PubMed:17110502, PubMed:20421923, PubMed:22766068). {ECO:0000269|PubMed:13130073, ECO:0000269|PubMed:17110502, ECO:0000269|PubMed:20421923, ECO:0000269|PubMed:22766068}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;SLC-mediated transmembrane transport;Transport of small molecules;Cellular hexose transport (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.187
• rvis_EVS: 0.74
• rvis_percentile_EVS: 86.33

Haploinsufficiency Scores

• pHI: 0.0844
• hipred: N
• hipred_score: 0.146
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.157

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc5a4a

Gene ontology

• Biological process: sodium ion transport;glucose transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: glucose:sodium symporter activity