SLC22A2
solute carrier family 22 member 2, the group of Solute carrier family 22
Basic information
Region (hg38): 6:160171061-160277638
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (45 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. These statistics are base on transcript: NM_000003058.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 43 | 44 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 43 | 4 | 1 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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