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.

not_specified (39 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000006933.7. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	1	0

Loading clinvar variants...

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
essential_gene_gene_trap
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