SLC12A5 solute carrier family 12 member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC12A5provided by HGNC
Official Full Name: solute carrier family 12 member 5provided by HGNC
Primary source: HGNC:HGNC:13818
See related: Ensembl:ENSG00000124140 MIM:606726; AllianceGenome:HGNC:13818
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: KCC2; DEE34; EIG14; hKCC2; EIEE34
Summary: K-Cl cotransporters are proteins that lower intracellular chloride concentrations below the electrochemical equilibrium potential. The protein encoded by this gene is an integral membrane K-Cl cotransporter that can function in either a net efflux or influx pathway, depending on the chemical concentration gradients of potassium and chloride. The encoded protein can act as a homomultimer, or as a heteromultimer with other K-Cl cotransporters, to maintain chloride homeostasis in neurons. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Sep 2008]
Expression: Restricted expression toward brain (RPKM 26.0) See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.12

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (46021686..46060150)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (47757715..47796165)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (44650325..44688789)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Midbrain KCC2 downregulation: Implications for stress-related and substance use behaviors.
Title: Midbrain KCC2 downregulation: Implications for stress-related and substance use behaviors.
The expression system influences stability, maturation efficiency, and oligomeric properties of the potassium-chloride co-transporter KCC2.
Title: The expression system influences stability, maturation efficiency, and oligomeric properties of the potassium-chloride co-transporter KCC2.
SLC12A5 as a novel potential biomarker of glioblastoma multiforme.
Title: SLC12A5 as a novel potential biomarker of glioblastoma multiforme.
SLC12A5 promotes hepatocellular carcinoma growth and ferroptosis resistance by inducing ER stress and cystine transport changes.
Title: SLC12A5 promotes hepatocellular carcinoma growth and ferroptosis resistance by inducing ER stress and cystine transport changes.
[Expression of cation chloride cotransporter (NKCC1/KCC2) in brain tissue of children with focal cortical dysplasia type ].
Title: [Expression of cation chloride cotransporter (NKCC1/KCC2) in brain tissue of children with focal cortical dysplasia type Ⅱ].
NKCC1 to KCC2 mRNA Ratio in Schizophrenia and Its Psychopathology: a Case-Control Study.
Title: NKCC1 to KCC2 mRNA Ratio in Schizophrenia and Its Psychopathology: a Case-Control Study.
KCC2 rs2297201 Gene Polymorphism Might be a Predictive Genetic Marker of Febrile Seizures.
Title: KCC2 rs2297201 Gene Polymorphism Might be a Predictive Genetic Marker of Febrile Seizures.
Up-Regulated LncRNA FEZF1-AS1 Promotes the Progression of Cervical Carcinoma Cells via MiR-367-3p/SLC12A5 Signal Axis.
Title: Up-Regulated LncRNA FEZF1-AS1 Promotes the Progression of Cervical Carcinoma Cells via MiR-367-3p/SLC12A5 Signal Axis.
Developmental dysregulation of excitatory-to-inhibitory GABA-polarity switch may underlie schizophrenia pathology: A monozygotic-twin discordant case analysis in human iPS cell-derived neurons.
Title: Developmental dysregulation of excitatory-to-inhibitory GABA-polarity switch may underlie schizophrenia pathology: A monozygotic-twin discordant case analysis in human iPS cell-derived neurons.
Right Anterior Theta Hypersynchrony as a Quantitative Measure Associated with Autistic Traits and K-Cl Cotransporter KCC2 Polymorphism.
Title: Right Anterior Theta Hypersynchrony as a Quantitative Measure Associated with Autistic Traits and K-Cl Cotransporter KCC2 Polymorphism.

Submit: New GeneRIF Correction See all GeneRIFs (60)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Developmental and epileptic encephalopathy, 34 MedGen: C4225257 OMIM: 616645 GeneReviews: SLC12A5-Related Epilepsy of Infancy with Migrating Focal Seizures	Compare labs
Epilepsy, idiopathic generalized, susceptibility to, 14 MedGen: C4225245 OMIM: 616685 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH12005 (e-PCR)
- UniSTS:21828

RH78814 (e-PCR)
- UniSTS:61297

D20S1037 (e-PCR)
- UniSTS:77435

G65726 (e-PCR)
- UniSTS:225414

SHGC-153603 (e-PCR)
- UniSTS:177836

Z94533 (e-PCR)
- UniSTS:70865

D20S856 (e-PCR), detects polymorphism
- UniSTS:32210

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ammonium channel activity	IEA Inferred from Electronic Annotation more info
enables chloride transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables potassium:chloride symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables potassium:chloride symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables potassium:chloride symporter activity	TAS Traceable Author Statement more info
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ammonium transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in cell volume homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in chloride ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in chloride transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in dendritic spine development	IDA Inferred from Direct Assay more info	PubMed
involved_in hypotonic response	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular chloride ion homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular pH reduction	IEA Inferred from Electronic Annotation more info
involved_in learning	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in monoatomic ion transport	TAS Traceable Author Statement more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in postsynaptic neurotransmitter receptor diffusion trapping	IEA Inferred from Electronic Annotation more info
involved_in potassium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in potassium ion import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of postsynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in thermosensory behavior	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell periphery	IDA Inferred from Direct Assay more info	PubMed
located_in cell periphery	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite membrane	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic specialization membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: solute carrier family 12 member 5

Names: K-Cl cotransporter 2; electroneutral potassium-chloride cotransporter 2; erythroid K-Cl cotransporter 2; neuronal K-Cl cotransporter; solute carrier family 12 (potassium/chloride transporter), member 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_046341.2 RefSeqGene

Range

12531..43466

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001134771.2 → NP_001128243.1 solute carrier family 12 member 5 isoform 1

See identical proteins and their annotated locations for NP_001128243.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1, also known as KCC2a).

Source sequence(s)

AL162458

Consensus CDS

CCDS46610.1

UniProtKB/Swiss-Prot

A2RTX2, Q5VZ41, Q9H2X9, Q9H4Z0, Q9ULP4

UniProtKB/TrEMBL

A8K143

Related

ENSP00000387694.1, ENST00000454036.6

Conserved Domains (1) summary

TIGR00930
Location:44 → 1139

2a30; K-Cl cotransporter
NM_020708.5 → NP_065759.1 solute carrier family 12 member 5 isoform 2

See identical proteins and their annotated locations for NP_065759.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (2, also known as KCC2b) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AL162458

Consensus CDS

CCDS13391.1

UniProtKB/TrEMBL

A8K143

Related

ENSP00000243964.4, ENST00000243964.7

Conserved Domains (1) summary

TIGR00930
Location:21 → 1116

2a30; K-Cl cotransporter