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.

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.

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			55	3		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			84	8	1	93
Total	0	0	139	11	1

Variants in SLC5A10

This is a list of pathogenic ClinVar variants found in the SLC5A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18952236-A-G		not specified	Likely benign (Jan 20, 2025)
17-18952242-G-A		not specified	Uncertain significance (Feb 08, 2023)
17-18952257-G-A		not specified	Uncertain significance (Feb 17, 2024)
17-18958682-T-C		not specified	Uncertain significance (Aug 14, 2024)
17-18958691-C-T		not specified	Uncertain significance (Apr 25, 2023)
17-18958697-A-G		not specified	Uncertain significance (Oct 06, 2023)
17-18958707-C-T		not specified	Uncertain significance (May 03, 2023)
17-18958721-T-C		not specified	Uncertain significance (Aug 05, 2024)
17-18958734-G-A		not specified	Uncertain significance (Jul 27, 2024)
17-18959147-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-18959153-G-T		not specified	Uncertain significance (Sep 20, 2023)
17-18959201-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-18959210-G-A		not specified	Uncertain significance (Nov 22, 2024)
17-18959219-G-A		not specified	Uncertain significance (Sep 06, 2024)
17-18959223-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-18959230-C-A		not specified	Uncertain significance (Oct 21, 2021)
17-18959613-G-A		not specified	Uncertain significance (Feb 06, 2023)
17-18960600-G-T		not specified	Uncertain significance (Nov 10, 2022)
17-18969052-C-A		not specified	Uncertain significance (Feb 28, 2023)
17-18969357-T-C		not specified	Uncertain significance (Dec 21, 2023)
17-18969393-T-C		not specified	Uncertain significance (Jun 16, 2023)
17-18969402-C-T		not specified	Uncertain significance (Mar 29, 2023)
17-18971109-G-A		not specified	Uncertain significance (Apr 17, 2024)
17-18971121-T-C		not specified	Uncertain significance (Feb 13, 2025)
17-18971122-G-A		not specified	Uncertain significance (Oct 05, 2022)

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