SLC22A12

solute carrier family 22 member 12, the group of Solute carrier family 22

Basic information

Region (hg38): 11:64590641-64602353

Links

ENSG00000197891 ∙ NCBI:116085 ∙ OMIM:607096 ∙ HGNC:17989 ∙ Uniprot:Q96S37 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypouricemia, renal 1 (Strong), mode of inheritance: AR
• hereditary renal hypouricemia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypouricemia, renal 1	AR	Renal	The condition may be asymptomatic, but a minority of individuals can be affected by nephrolithiasis and/or exercise-induce acute renal failure, and preventive measures can be beneficial	Renal	12024214; 14655203; 18492088

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC22A12 gene.

• not provided (5 variants)
• Familial renal hypouricemia (1 variants)
• Dalmatian hypouricemia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A12 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	31	7	45
missense	2	2	78	2		84
nonsense	1	1	1			3
start loss						0
frameshift	2	1	1			4
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)		1				1
splice region			1	5		6
non coding			26	17	32	75
Total	5	5	114	51	39

Highest pathogenic variant AF is 0.0000854

Variants in SLC22A12

This is a list of pathogenic ClinVar variants found in the SLC22A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64590769-A-T			Benign (Nov 12, 2018)
11-64590793-C-T			Benign (Aug 20, 2019)
11-64590839-C-T		Dalmatian hypouricemia	Benign (Nov 12, 2018)
11-64590994-A-G		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591001-G-A		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591088-G-A		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591091-C-G		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591133-T-C		Dalmatian hypouricemia	Benign (Nov 12, 2018)
11-64591140-C-T		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591203-G-A		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591225-A-G		Dalmatian hypouricemia	Uncertain significance (Jan 13, 2018)
11-64591247-A-C		Dalmatian hypouricemia	Uncertain significance (Jan 12, 2018)
11-64591309-G-A		Dalmatian hypouricemia	Uncertain significance (Jun 14, 2016)
11-64591323-C-T		Dalmatian hypouricemia	Benign/Likely benign (Dec 08, 2019)
11-64591337-G-A		Dalmatian hypouricemia	Benign (Nov 12, 2018)
11-64591464-C-T		Dalmatian hypouricemia	Uncertain significance (Jan 13, 2018)
11-64591512-C-G		Dalmatian hypouricemia	Likely benign (Jan 13, 2018)
11-64591520-A-C		Dalmatian hypouricemia	Uncertain significance (Feb 02, 2018)
11-64591547-A-C		Dalmatian hypouricemia	Uncertain significance (Jan 13, 2018)
11-64591568-T-C		Dalmatian hypouricemia	Likely benign (Apr 20, 2022)
11-64591618-C-A		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
11-64591619-G-A			Likely benign (Dec 08, 2022)
11-64591621-T-C			Uncertain significance (Feb 08, 2022)
11-64591641-A-G			Uncertain significance (Feb 27, 2020)
11-64591656-CAG-C			Likely pathogenic (Jul 01, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A12	protein_coding	protein_coding	ENST00000377574	10	11708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-13	0.0548	125602	2	144	125748	0.000581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.372	315	334	0.943	0.0000226	3499
Missense in Polyphen		82	100.27	0.81779		1149
Synonymous	-0.901	167	153	1.09	0.0000109	1237
Loss of Function	0.437	21	23.3	0.902	0.00000120	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000676	0.000663
Ashkenazi Jewish	0.000797	0.000794
East Asian	0.00457	0.00452
Finnish	0.000165	0.000139
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.00457	0.00452
South Asian	0.000397	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient urate re-absorption in the kidney. Regulates blood urate levels. Mediates saturable urate uptake by facilitating the exchange of urate against organic anions. {ECO:0000269|PubMed:12024214}.
• Pathway: Uricosurics Pathway, Pharmacodynamics;Organic anion transport;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation/anion/zwitterion transport (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.166
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.23

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.146
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a12
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: urate transport;cellular homeostasis;response to drug;urate metabolic process;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;apical plasma membrane;brush border membrane;extracellular exosome
• Molecular function: urate transmembrane transporter activity;PDZ domain binding