GeneBe

SLC22A2

protein-coding

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

Gene summary

Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003058.4

Inheritance

—

ClinVar variants

U:54B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr6:160,171,061-160,277,638

External References & Databases

Ensembl (ENSG00000112499)NCBI Gene (6582)OMIM (602608)HGNC:10966GenCCUniProt (O15244)AlphaFoldClinVar (SLC22A2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~106.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC22A2 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 55
not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003058.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
1
clinvar
 4
missense
53
clinvar
1
clinvar
 54
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total00544159
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003058.4RefSeqNP_003049.211MANE Select
ENST00000366953.8EnsemblENSP00000355920.311MANE Select
ENST00000366952.1EnsemblENSP00000355919.16Standard
ENST00001113922.1EnsemblENSP00000783727.12Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Choline metabolism in cancer - Homo sapiens (human)
  • Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics
  • Metformin Pathway, Pharmacokinetics
  • Polythiazide Action Pathway
  • Methyclothiazide Action Pathway

Biological Process

  • drug transmembrane transport
  • neurotransmitter secretion
  • body fluid secretion
  • organic cation transport
  • neurotransmitter biosynthetic process

Molecular Function

  • neurotransmitter transporter activity
  • organic cation transmembrane transporter activity

Cellular Component

  • plasma membrane
  • integral component of plasma membrane
  • membrane
  • extracellular exosome
  • presynapse

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000366953
Coding exons
11
Length
106578
Individuals with no LoFs
125543
Homozygous LoFs
0
Heterozygous LoFs
205
Defined
125748
p
0.000815
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.06673393361.010.00001983602
Missense (PolyPhen)122122.130.998961379
Synonymous0.4801261330.9470.000008421124
Loss of Function0.9432126.20.8010.00000112297

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00230.0023notable
Latino/Admixed American0.000440.00043rare
Ashkenazi Jewish00.0absent
East Asian0.000270.00027rare
Finnish0.000140.00014rare
European (Non-Finnish)0.00120.0012notable
South Asian0.000360.00036rare
Other0.000330.00033rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool
0.614
RVIS EVS
-0.51
RVIS percentile EVS
21.77

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.100

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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