SLC22A6

solute carrier family 22 member 6, the group of Solute carrier family 22

Basic information

Region (hg38): 11:62936384-62984967

Links

ENSG00000197901 ∙ NCBI:9356 ∙ OMIM:607582 ∙ HGNC:10970 ∙ Uniprot:Q4U2R8 ∙ 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 SLC22A6 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A6 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					1	1
missense			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	1

Variants in SLC22A6

This is a list of pathogenic ClinVar variants found in the SLC22A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62977279-G-A			Benign (Jul 10, 2017)
11-62977293-G-T		not specified	Uncertain significance (Oct 05, 2023)
11-62977295-A-G		not specified	Uncertain significance (May 31, 2023)
11-62977311-C-T		not specified	Uncertain significance (Apr 06, 2022)
11-62977318-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-62977321-G-T		not specified	Uncertain significance (Mar 22, 2023)
11-62977357-C-A		not specified	Uncertain significance (Sep 22, 2023)
11-62979489-G-A		not specified	Uncertain significance (Jul 20, 2021)
11-62979839-G-A		not specified	Uncertain significance (Jan 10, 2022)
11-62979887-T-G		not specified	Uncertain significance (Jul 05, 2023)
11-62981093-C-T		not specified	Likely benign (Nov 10, 2022)
11-62981288-C-T		not specified	Likely benign (Dec 14, 2021)
11-62981323-C-A		not specified	Uncertain significance (Feb 06, 2023)
11-62981854-A-G		not specified	Uncertain significance (Jun 26, 2023)
11-62981939-G-C		not specified	Uncertain significance (Aug 16, 2021)
11-62981975-C-T		not specified	Uncertain significance (Feb 17, 2023)
11-62981999-T-A		not specified	Uncertain significance (Dec 27, 2023)
11-62983545-A-T		not specified	Uncertain significance (May 03, 2023)
11-62983596-G-A		not specified	Uncertain significance (Nov 16, 2021)
11-62983968-A-G		not specified	Uncertain significance (Dec 02, 2022)
11-62984372-C-T		not specified	Uncertain significance (Jul 08, 2022)
11-62984452-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-62984506-C-G		not specified	Uncertain significance (Jan 23, 2023)
11-62984527-G-A		not specified	Uncertain significance (Jan 03, 2022)
11-62984647-C-T		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A6	protein_coding	protein_coding	ENST00000377871	10	48599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.32e-8	0.858	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	305	335	0.910	0.0000198	3602
Missense in Polyphen		108	129.93	0.83123		1424
Synonymous	0.240	137	141	0.974	0.00000824	1223
Loss of Function	1.60	15	23.3	0.643	0.00000117	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000516	0.000511
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000111	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000916	0.0000879
Middle Eastern	0.000111	0.000109
South Asian	0.000392	0.000359
Other	0.000506	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS) (By similarity). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid (By similarity). PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate. {ECO:0000250, ECO:0000269|PubMed:12538807, ECO:0000269|PubMed:15644426, ECO:0000269|PubMed:17038320, ECO:0000269|PubMed:17502342, ECO:0000269|PubMed:9762842, ECO:0000269|PubMed:9887087}.
• Pathway: Methotrexate Pathway (Brain Cell), Pharmacokinetics;Methotrexate Pathway, Pharmacokinetics;Statin Pathway - Generalized, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Tenofovir/Adefovir Pathway, Pharmacodynamics;Tenofovir/Adefovir Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Ibuprofen Pathway, Pharmacokinetics;Uricosurics Pathway, Pharmacodynamics;Ibuprofen Action Pathway;Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Ibuprofen Metabolism 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;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;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: 0.190

Intolerance Scores

• loftool: 0.705
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.367
• hipred: N
• hipred_score: 0.234
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.812

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a6
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: inorganic anion transport;organic anion transport;alpha-ketoglutarate transport;response to methotrexate;sodium-independent organic anion transport;protein homooligomerization;renal tubular secretion;anion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;caveola;basolateral plasma membrane;protein-containing complex;extracellular exosome
• Molecular function: inorganic anion exchanger activity;protein binding;organic anion transmembrane transporter activity;anion:anion antiporter activity;sodium-independent organic anion transmembrane transporter activity;chloride ion binding;protein homodimerization activity