SLC22A2

solute carrier family 22 member 2, the group of Solute carrier family 22

Basic information

Region (hg38): 6:160171060-160277638

Links

ENSG00000112499 ∙ NCBI:6582 ∙ OMIM:602608 ∙ HGNC:10966 ∙ Uniprot:O15244 ∙ 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 SLC22A2 gene.

• Inborn genetic diseases (21 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A2 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				2	1	3
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	1

Variants in SLC22A2

This is a list of pathogenic ClinVar variants found in the SLC22A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-160224731-G-T			Benign (Jul 31, 2018)
6-160224734-C-G		not specified	Uncertain significance (Jan 24, 2023)
6-160241560-G-A		not specified	Uncertain significance (Oct 27, 2022)
6-160241585-T-C		not specified	Uncertain significance (Jul 05, 2022)
6-160243575-C-T		not specified	Uncertain significance (Sep 16, 2021)
6-160243648-G-A			Likely benign (Apr 01, 2023)
6-160243657-G-A			Likely benign (Jun 14, 2018)
6-160243707-A-C		not specified	Uncertain significance (Aug 02, 2022)
6-160243733-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-160243746-T-C		not specified	Uncertain significance (Nov 01, 2022)
6-160245544-C-T		not specified	Uncertain significance (Mar 06, 2023)
6-160245545-G-A		not specified	Uncertain significance (Oct 06, 2022)
6-160249240-T-A		not specified	Uncertain significance (Sep 29, 2022)
6-160249286-C-T		not specified	Uncertain significance (Dec 11, 2023)
6-160249318-A-G		not specified	Uncertain significance (Jan 26, 2023)
6-160249367-G-A		not specified	Uncertain significance (Feb 27, 2023)
6-160249378-T-G		not specified	Uncertain significance (Apr 07, 2022)
6-160250641-T-C		not specified	Uncertain significance (Sep 22, 2023)
6-160256660-C-T		not specified	Uncertain significance (Dec 17, 2021)
6-160256698-T-C		not specified	Uncertain significance (May 05, 2023)
6-160258385-C-T		not specified	Uncertain significance (Mar 31, 2023)
6-160258396-G-C		not specified	Uncertain significance (Dec 03, 2021)
6-160258487-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-160258513-C-T		not specified	Uncertain significance (Nov 19, 2022)
6-160258543-T-G		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A2	protein_coding	protein_coding	ENST00000366953	11	106578

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.02e-12	0.219	125543	0	205	125748	0.000815

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0667	339	336	1.01	0.0000198	3602
Missense in Polyphen		122	122.13	0.99896		1379
Synonymous	0.480	126	133	0.947	0.00000842	1124
Loss of Function	0.943	21	26.2	0.801	0.00000112	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00272	0.00272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000274	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00118	0.00116
Middle Eastern	0.000274	0.000272
South Asian	0.000362	0.000359
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates tubular uptake of organic compounds from circulation. Mediates the influx of agmatine, dopamine, noradrenaline (norepinephrine), serotonin, choline, famotidine, ranitidine, histamin, creatinine, amantadine, memantine, acriflavine, 4-[4-(dimethylamino)-styryl]-N-methylpyridinium ASP, amiloride, metformin, N-1-methylnicotinamide (NMN), tetraethylammonium (TEA), 1-methyl-4-phenylpyridinium (MPP), cimetidine, cisplatin and oxaliplatin. Cisplatin may develop a nephrotoxic action. Transport of creatinine is inhibited by fluoroquinolones such as DX-619 and LVFX. This transporter is a major determinant of the anticancer activity of oxaliplatin and may contribute to antitumor specificity. {ECO:0000269|PubMed:12089365, ECO:0000269|PubMed:12538837, ECO:0000269|PubMed:15496291, ECO:0000269|PubMed:15783073, ECO:0000269|PubMed:16006492, ECO:0000269|PubMed:16272756, ECO:0000269|PubMed:16314463, ECO:0000269|PubMed:16394027, ECO:0000269|PubMed:16914559, ECO:0000269|PubMed:16951202, ECO:0000269|PubMed:17072098, ECO:0000269|PubMed:17582384, ECO:0000269|PubMed:9260930, ECO:0000269|PubMed:9687576}.
• Pathway: Choline metabolism in cancer - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Metformin Pathway, Pharmacokinetics;Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Ethacrynic Acid Action Pathway;Quinethazone Action Pathway;Bendroflumethiazide Action Pathway;Chlorthalidone Action Pathway;Trichlormethiazide Action Pathway;Iminoglycinuria;Lysinuric Protein Intolerance;Blue diaper syndrome;Lysinuric protein intolerance (LPI);Cystinuria;Lamivudine Metabolism Pathway;Indapamide Action Pathway;Furosemide Action Pathway;Torsemide Action Pathway;Hartnup Disorder;Glucose Transporter Defect (SGLT2);Kidney Function;Glucose Transporter Defect (SGLT2);Metolazone Action Pathway;Hydrochlorothiazide Action Pathway;Cyclothiazide Action Pathway;Hydroflumethiazide Action Pathway;Chlorothiazide Action Pathway;Amine compound SLC transporters;Tyrosine metabolism;Abacavir transmembrane transport;Abacavir transport and metabolism;Metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Neuronal System;Organic cation transport;Organic cation/anion/zwitterion transport;Prostaglandin formation from arachidonate;Histidine metabolism;Tryptophan metabolism;Glycerophospholipid metabolism;Na+/Cl- dependent neurotransmitter transporters;Neurotransmitter release cycle;Neurotransmitter clearance;Transmission across Chemical Synapses;Norepinephrine Neurotransmitter Release Cycle (Consensus)

Intolerance Scores

• loftool: 0.614
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.77

Haploinsufficiency Scores

• pHI: 0.0989
• hipred: N
• hipred_score: 0.169
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.100

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a2
• Phenotype: normal phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: drug transmembrane transport;neurotransmitter secretion;body fluid secretion;organic cation transport;neurotransmitter biosynthetic process
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;extracellular exosome;presynapse
• Molecular function: neurotransmitter transporter activity;organic cation transmembrane transporter activity