GeneBe

SLC22A6

protein-coding

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

Gene summary

The protein encoded by this gene is involved in the sodium-dependent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and may be localized to the basolateral membrane. Four transcript variants encoding four different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_153276.3

Inheritance

—

ClinVar variants

U:79B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr11:62,936,385-62,984,967

External References & Databases

Ensembl (ENSG00000197901)NCBI Gene (9356)OMIM (607582)HGNC:10970GenCCUniProt (Q4U2R8)AlphaFoldClinVar (SLC22A6)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~48.6 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 SLC22A6 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 85
not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153276.3. 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
79
clinvar
4
clinvar
 83
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00797187
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_153276.3RefSeqNP_695008.110MANE Select
ENST00000360421.9EnsemblENSP00000353597.410MANE Select
NM_004790.5RefSeqNP_004781.210Standard
NM_153277.3RefSeqNP_695009.110Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Methotrexate Pathway (Brain Cell), Pharmacokinetics
  • Methotrexate Pathway, Pharmacokinetics
  • Statin Pathway - Generalized, Pharmacokinetics
  • Pravastatin Pathway, Pharmacokinetics
  • Tenofovir/Adefovir Pathway, Pharmacodynamics

Biological Process

  • inorganic anion transport
  • organic anion transport
  • alpha-ketoglutarate transport
  • response to methotrexate
  • sodium-independent organic anion transport

Molecular Function

  • inorganic anion exchanger activity
  • protein binding
  • organic anion transmembrane transporter activity
  • anion:anion antiporter activity
  • sodium-independent organic anion transmembrane transporter activity

Cellular Component

  • plasma membrane
  • integral component of plasma membrane
  • caveola
  • basolateral plasma membrane
  • protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000377871
Coding exons
10
Length
48599
Individuals with no LoFs
125703
Homozygous LoFs
0
Heterozygous LoFs
44
Defined
125747
p
0.000175
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5833053350.9100.00001983602
Missense (PolyPhen)108129.930.831231424
Synonymous0.2401371410.9740.000008241223
Loss of Function1.601523.30.6430.00000117232

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.000390.00038rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000110.00011rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000920.000088rare
South Asian0.000390.00036rare
Other0.000510.00049rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.190

Intolerance Scores

LoFtool
0.705
RVIS EVS
-0.49
RVIS percentile EVS
22.51

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.812

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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