SLC5A10

solute carrier family 5 member 10, the group of Solute carrier family 5

Basic information

Region (hg38): 17:18950345-19022595

Links

ENSG00000154025

∙ NCBI:125206 ∙ OMIM:618636 ∙ HGNC:23155 ∙ Uniprot:A0PJK1 ∙ 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 SLC5A10 gene.

not_specified (230 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001042450.4. 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						0
missense			93 clinvar	7 clinvar		100
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	7	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC5A10	protein_coding	protein_coding	ENST00000395647	15	72251

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.07e-14	0.404	125222	0	526	125748	0.00209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.821	362	409	0.886	0.0000273	3887
Missense in Polyphen		166	177.25	0.93652		1727
Synonymous	0.0119	183	183	0.999	0.0000134	1324
Loss of Function	1.37	25	33.6	0.744	0.00000171	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00104
Ashkenazi Jewish	0.000597	0.000595
East Asian	0.000707	0.000707
Finnish	0.00380	0.00380
European (Non-Finnish)	0.00180	0.00179
Middle Eastern	0.000707	0.000707
South Asian	0.00600	0.00583
Other	0.00264	0.00261

dbNSFP

Source: dbNSFP

Function: FUNCTION: High capacity transporter for mannose and fructose and, to a lesser extent, glucose, AMG, and galactose. {ECO:0000269|PubMed:22212718}.;
Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;SLC-mediated transmembrane transport;Transport of small molecules;Fructose and mannose metabolism;Galactose metabolism;Cellular hexose transport (Consensus)

Recessive Scores

pRec: 0.129

Intolerance Scores

loftool: 0.119
rvis_EVS: -0.82
rvis_percentile_EVS: 11.98

Haploinsufficiency Scores

pHI: 0.134
hipred: N
hipred_score: 0.284
ghis: 0.412

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc5a10
Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); renal/urinary system phenotype; liver/biliary system phenotype;

Gene ontology

Biological process: hexose transmembrane transport;sodium ion transmembrane transport
Cellular component: plasma membrane;integral component of membrane;extracellular exosome
Molecular function: glucose:sodium symporter activity;solute:sodium symporter activity