SLC2A9

solute carrier family 2 member 9, the group of Solute carrier family 2

Basic information

Region (hg38): 4:9771152-10054936

Links

ENSG00000109667 ∙ NCBI:56606 ∙ OMIM:606142 ∙ HGNC:13446 ∙ Uniprot:Q9NRM0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary renal hypouricemia (Supportive), mode of inheritance: AR
• hypouricemia, renal, 2 (Strong), mode of inheritance: AR
• hypouricemia, renal, 2 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypouricemia, renal, 2	AD/AR	Renal	The condition may be associated with complications including exercise-induced acute renal failure and nephrolithiasis, and preventive measures (eg, related to exercise) may be beneficial	Renal	9026395; 19926891; 22132964; 21536615
The youngest reported individual was an adult, but morbidity could theoretically appear earlier

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC2A9 gene.

• not provided (164 variants)
• Hypouricemia, renal, 2 (88 variants)
• Inborn genetic diseases (12 variants)
• SLC2A9-related condition (4 variants)
• Dalmatian hypouricemia (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC2A9 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			7	28	12	47
missense		2	60	5	10	77
nonsense						0
start loss						0
frameshift	1	1				2
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1	1			2
splice region			2	3	2	7
non coding			4	22	48	74
Total	1	4	73	55	70

Highest pathogenic variant AF is 0.000151

Variants in SLC2A9

This is a list of pathogenic ClinVar variants found in the SLC2A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-9781804-G-C			Benign (Jun 18, 2021)
4-9782025-C-G		DRD5-related disorder	Likely benign (Feb 26, 2020)
4-9782088-A-C		not specified	Uncertain significance (Jun 18, 2021)
4-9782098-G-C		not specified	Uncertain significance (Feb 07, 2023)
4-9782112-G-A		not specified	Uncertain significance (Jul 14, 2021)
4-9782151-T-C		not specified	Uncertain significance (Sep 06, 2022)
4-9782215-C-A		DRD5-related disorder	Likely benign (Dec 06, 2019)
4-9782245-C-G		DRD5-related disorder	Likely benign (Feb 19, 2019)
4-9782262-T-G		not specified	Uncertain significance (Aug 31, 2022)
4-9782280-C-T		not specified	Uncertain significance (Nov 22, 2021)
4-9782291-C-T		not specified • DRD5-related disorder	Benign (Oct 31, 2019)
4-9782361-C-A		not specified	Uncertain significance (Dec 01, 2023)
4-9782369-G-A		not specified	Uncertain significance (Jan 20, 2023)
4-9782492-C-T		not specified	Uncertain significance (Feb 05, 2024)
4-9782502-T-G		not specified	Uncertain significance (Jun 02, 2023)
4-9782520-C-A		not specified	Uncertain significance (Jan 03, 2024)
4-9782565-A-G		not specified	Uncertain significance (Mar 07, 2024)
4-9782583-C-T		not specified	Uncertain significance (Apr 25, 2022)
4-9782660-G-A		DRD5-related disorder	Likely benign (Feb 18, 2019)
4-9782752-G-T		not specified	Uncertain significance (Aug 03, 2022)
4-9782753-A-G		not specified	Uncertain significance (Jun 11, 2021)
4-9782789-G-A		not specified	Uncertain significance (Nov 14, 2023)
4-9782799-G-A		not specified	Uncertain significance (Jan 23, 2023)
4-9782801-A-T		not specified	Uncertain significance (Feb 01, 2023)
4-9782817-A-G		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC2A9	protein_coding	protein_coding	ENST00000264784	12	283784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.95e-10	0.435	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.124	305	299	1.02	0.0000170	3457
Missense in Polyphen		114	124.54	0.91538		1538
Synonymous	-1.90	157	129	1.21	0.00000806	1148
Loss of Function	1.05	17	22.4	0.761	9.67e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000626	0.000626
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000599	0.000598
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transport urate and fructose. May have a role in the urate reabsorption by proximal tubules. Also transports glucose at low rate. {ECO:0000269|PubMed:14739288, ECO:0000269|PubMed:18327257}.
• Disease: DISEASE: Hypouricemia renal 2 (RHUC2) [MIM:612076]: A disorder characterized by impaired uric acid reabsorption at the apical membrane of proximal renal tubule cells, and high urinary urate excretion. Patients often appear asymptomatic, but may be subject to exercise-induced acute renal failure, chronic renal dysfunction and nephrolithiasis. {ECO:0000269|PubMed:19026395, ECO:0000269|PubMed:19926891, ECO:0000269|PubMed:21810765}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Uricosurics Pathway, Pharmacodynamics;Nuclear Receptors Meta-Pathway;NRF2 pathway;SLC-mediated transmembrane transport;Transport of small molecules;Fructose and mannose metabolism;Galactose metabolism;Cellular hexose transport (Consensus)

Intolerance Scores

• loftool: 0.433
• rvis_EVS: 1.23
• rvis_percentile_EVS: 93.25

Haploinsufficiency Scores

• pHI: 0.0278
• hipred: N
• hipred_score: 0.197
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.340

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Slc2a9
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype; digestive/alimentary 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: hexose transmembrane transport;urate transport;urate metabolic process;proton transmembrane transport;glucose transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;basolateral plasma membrane;apical plasma membrane
• Molecular function: carbohydrate:proton symporter activity;glucose transmembrane transporter activity;urate transmembrane transporter activity;transmembrane transporter activity