SLC5A3

solute carrier family 5 member 3, the group of Solute carrier family 5

Basic information

Region (hg38): 21:34073578-34106260

Links

ENSG00000198743 ∙ NCBI:6526 ∙ OMIM:600444 ∙ HGNC:11038 ∙ Uniprot:P53794 ∙ 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 SLC5A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A3 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SLC5A3

This is a list of pathogenic ClinVar variants found in the SLC5A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-34073744-G-A		not specified	Uncertain significance (Dec 30, 2024)
21-34095266-T-C		not specified	Uncertain significance (Feb 08, 2025)
21-34095304-G-A		not specified	Uncertain significance (Jan 26, 2022)
21-34095308-G-T		not specified	Uncertain significance (Feb 19, 2025)
21-34095421-A-G		not specified	Uncertain significance (Oct 05, 2023)
21-34095472-C-T		not specified	Uncertain significance (Dec 28, 2022)
21-34095752-A-G		not specified	Uncertain significance (Aug 30, 2022)
21-34095787-C-G		not specified	Uncertain significance (Dec 04, 2024)
21-34095881-T-C		not specified	Uncertain significance (Jan 27, 2025)
21-34095901-A-G		not specified	Uncertain significance (Jul 05, 2024)
21-34096280-T-C		not specified	Uncertain significance (Jan 07, 2025)
21-34096331-A-G		not specified	Uncertain significance (Jan 23, 2025)
21-34096385-A-C		not specified	Uncertain significance (Dec 17, 2023)
21-34096393-C-T		not specified	Uncertain significance (Jun 05, 2023)
21-34096401-C-T			Likely benign (Aug 06, 2018)
21-34096402-G-A		not specified	Uncertain significance (Feb 08, 2025)
21-34096447-T-G		not specified	Uncertain significance (Sep 08, 2024)
21-34096459-A-G		not specified	Uncertain significance (Aug 20, 2024)
21-34096480-A-G		not specified	Uncertain significance (Oct 27, 2022)
21-34096714-A-G		not specified	Uncertain significance (Feb 07, 2025)
21-34096718-A-G		not specified	Uncertain significance (Sep 10, 2024)
21-34096834-T-C		not specified	Uncertain significance (Dec 12, 2023)
21-34096921-T-C		not specified	Uncertain significance (Oct 03, 2024)
21-34096990-C-T		not specified	Uncertain significance (Jul 14, 2024)
21-34097002-G-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC5A3	protein_coding	protein_coding	ENST00000381151	1	32690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0326	125723	0	12	125735	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	247	403	0.613	0.0000211	4708
Missense in Polyphen		31	144.62	0.21435		1637
Synonymous	-1.55	172	148	1.16	0.00000792	1472
Loss of Function	3.66	2	19.4	0.103	9.78e-7	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000528
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Prevents intracellular accumulation of high concentrations of myo-inositol (an osmolyte) that result in impairment of cellular function.
• 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;Fructose and mannose metabolism (Consensus)

Recessive Scores

• pRec: 0.381

Intolerance Scores

• loftool: 0.0843
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.477
• hipred: Y
• hipred_score: 0.507
• ghis: 0.401

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc5a3
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: inositol metabolic process;sodium ion transport;peripheral nervous system development;myo-inositol transport;regulation of respiratory gaseous exchange;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: myo-inositol:sodium symporter activity;glucose:sodium symporter activity