SLC12A6

gene
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Also known as KCC3AKCC3B

Summary

SLC12A6 (solute carrier family 12 member 6, HGNC:10914) is a protein-coding gene on chromosome 15q14, encoding Solute carrier family 12 member 6 (Q9UHW9). Mediates electroneutral potassium-chloride cotransport when activated by cell swelling.

This gene is a member of the K-Cl cotransporter (KCC) family. K-Cl cotransporters are integral membrane proteins that lower intracellular chloride concentrations below the electrochemical equilibrium potential. The proteins encoded by this gene are activated by cell swelling induced by hypotonic conditions. Alternate splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are associated with agenesis of the corpus callosum with peripheral neuropathy.

Source: NCBI Gene 9990 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): agenesis of the corpus callosum with peripheral neuropathy (Definitive, GenCC) — +1 more curated relationship
  • GWAS associations: 1
  • Clinical variants (ClinVar): 1,700 total — 63 pathogenic, 134 likely-pathogenic
  • Phenotypes (HPO): 87
  • MANE Select transcript: NM_001365088

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10914
Approved symbolSLC12A6
Namesolute carrier family 12 member 6
Location15q14
Locus typegene with protein product
StatusApproved
AliasesKCC3A, KCC3B
Ensembl geneENSG00000140199
Ensembl biotypeprotein_coding
OMIM604878
Entrez9990

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 13 protein_coding, 5 retained_intron, 3 nonsense_mediated_decay

ENST00000290209, ENST00000354181, ENST00000397702, ENST00000397707, ENST00000458406, ENST00000558589, ENST00000558667, ENST00000558950, ENST00000559076, ENST00000559236, ENST00000559441, ENST00000559484, ENST00000559523, ENST00000559664, ENST00000560023, ENST00000560164, ENST00000560611, ENST00000561080, ENST00000561120, ENST00000675289, ENST00000676379

RefSeq mRNA: 7 — MANE Select: NM_001365088 NM_001042494, NM_001042495, NM_001042496, NM_001042497, NM_001365088, NM_005135, NM_133647

CCDS: CCDS10036, CCDS42010, CCDS42011, CCDS42012, CCDS58352

Canonical transcript exons

ENST00000354181 — 26 exons

ExonStartEnd
ENSE000009416913424569334245867
ENSE000009416963424066134240829
ENSE000011080723424123334241337
ENSE000011080743425029834250355
ENSE000011080763425063134250729
ENSE000011080943424528534245403
ENSE000012101123425089934251057
ENSE000012101143425217034252384
ENSE000012101183425434834254589
ENSE000012101393425764234257788
ENSE000016878973425526234255392
ENSE000017850863425622934256283
ENSE000025551363433641034336752
ENSE000025624323433733234337781
ENSE000034915653423670834236815
ENSE000035089903424210234242221
ENSE000035112513423518134235314
ENSE000035223413423823234238401
ENSE000035675073425881334258944
ENSE000035710453423896534239160
ENSE000035750263427534534275389
ENSE000036357693424397434244072
ENSE000036435793423601534236199
ENSE000036606573423741934237550
ENSE000036804663426092634261020
ENSE000038948533422978434233972

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 95.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.9371 / max 1519.8923, expressed in 1769 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1492316.26411446
1492465.34921593
1492422.0321538
1492431.7073268
1492411.5676305
1492471.4535679
1492360.8352177
1492390.421981
1492400.222353
1492370.083839

Top tissues by expression

291 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
esophagus squamous epitheliumUBERON:000692095.06gold quality
bloodUBERON:000017894.27gold quality
secondary oocyteCL:000065593.55gold quality
trabecular bone tissueUBERON:000248393.24gold quality
spermCL:000001992.90gold quality
pharyngeal mucosaUBERON:000035592.42gold quality
monocyteCL:000057692.11gold quality
oral cavityUBERON:000016792.07gold quality
gingivaUBERON:000182892.02gold quality
ponsUBERON:000098891.90gold quality
gingival epitheliumUBERON:000194991.85gold quality
mononuclear cellCL:000084291.60gold quality
leukocyteCL:000073891.56gold quality
body of tongueUBERON:001187691.54gold quality
lower esophagus mucosaUBERON:003583491.49gold quality
upper leg skinUBERON:000426291.37gold quality
superior surface of tongueUBERON:000737191.20gold quality
jejunal mucosaUBERON:000039991.14gold quality
bone elementUBERON:000147490.93gold quality
adult organismUBERON:000702390.88gold quality
amniotic fluidUBERON:000017390.87gold quality
bone marrowUBERON:000237190.82gold quality
inferior vagus X ganglionUBERON:000536390.79gold quality
epithelium of esophagusUBERON:000197690.70gold quality
tendon of biceps brachiiUBERON:000818890.66gold quality
visceral pleuraUBERON:000240190.64gold quality
superior vestibular nucleusUBERON:000722790.62gold quality
subthalamic nucleusUBERON:000190690.54gold quality
lower lobe of lungUBERON:000894990.38gold quality
esophagus mucosaUBERON:000246990.36gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

166 targeting SLC12A6, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4481100.0066.421669
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-3163100.0077.238605
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-8485100.0077.574731
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-318599.9968.121959
HSA-MIR-428299.9975.366408
HSA-MIR-186-5P99.9970.833707
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-480399.9871.993117
HSA-MIR-314899.9775.066478
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-570-3P99.9672.414910
HSA-MIR-365899.9673.874379
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-6778-3P99.9667.292693

Literature-anchored findings (GeneRIF, showing 28)

  • human osteoblasts express functional K-Cl cotransporters in their cell membrane that seem to be able to induce the indirect activation of volume-sensitive Cl- channels by KCl through an increase in the intracellular ions, water influx and cell swelling. (PMID:12637262)
  • all of the CCCs examined (NKCC1, NKCC2, KCC1, KCC3, and KCC4) can promote NH4(+) translocation, presumably through binding of the ion at the K(+) site (PMID:12657561)
  • KCC activation by IGF-1 plays an important role in IGF-1 signaling to promote growth and spread of gynecological cancers. (PMID:15262997)
  • Not only truncating but also missense mutations of the KCC3 gene are associated with Andermann syndrome. (PMID:16606917)
  • Among patients with early-stage node-negative breast cancer, disease-free survival (DFS) and overall survival (OS) curves were significantly different based on IGF-1 and KCC expression. (PMID:17133354)
  • KCC3 mutations in exon 22 constitute a recurrent mutation site for hereditary motor and sensory neuropathy with agenesis of the corpus callosum (HMSN/ACC), regardless of ethnic origin. (PMID:17893295)
  • KCC3 down-regulates E-cadherin/beta-catenin complex formation by inhibiting transcription of E-cadherin gene and accelerating proteosome-dependent degradation of beta-catenin protein (PMID:18006853)
  • study provides evidence that the upstream SLC12A6 G/A promoter SNP is functional not only by changing the DNA primary structure but also by influencing the allelic epigenotype and consequently by influencing the chromatin organization (PMID:18536702)
  • Using a yeast 2-hybrid it was discovered that the C-terminal domain of KCC3, that is lost in most hereditary motor and sensory neuropathy with agenesis of the corpus callosum-causing mutations, directly interacts with brain-specific creatine kinase. (PMID:18566107)
  • Study identified two sites in KCC3 that are rapidly dephosphorylated in hypotonic conditions in cultured cells and human red blood cells in parallel with increased transport activity. (PMID:19665974)
  • mutations of the KCC3 gene may result in non-syndromic childhood onset of demyelinating hereditary motor and sensory neuropathy (PMID:20020398)
  • The Wnk3 protein isoforms have a similar effect on SLC12 cotransporters. NKCC1/2 and NCC were inhibited, even in hypertonicity, while KCCs were activated, even in isotonic conditions. (PMID:21613606)
  • mis-trafficking of mutant protein is an important pathophysiological feature of HMSN/ACC causative KCC3 mutations. (PMID:21628467)
  • KCC3 is the dominant isoform in erythrocytes, with variable expression of KCC1 and KCC4 that could result in modulation of KCC activity (PMID:21733850)
  • Neuropathic features of hereditary motor and sensory neuropathy/agenesis of corpus callosum in transgenic mouse lines are predominantly due to a neuronal KCC3 deficit, while the auditory impairment is due to loss of non-neuronal KCC3 expression. (PMID:22423107)
  • serine residue 96 of human KCC3 is a third site that has to be dephosphorylated for full activation of the cotransporter during hypotonicity. (PMID:24043619)
  • SLC12A6 has been shown to be causative in Andermann Syndrome. (PMID:24341143)
  • SPAK may promote KCC3-mediated cervix tumor aggressiveness via the NF-kappaB/p38 MAPK/MMP2 axis. (PMID:24655550)
  • These results suggest that the expression of KCC3 in ESCC may affect cellular invasion and be related to a worse prognosis in patients with ESCC. (PMID:25110711)
  • Neurodegenerative deficits in hereditary motor and sensory neuropathy associated with agenesis of the corpus callosum are primarily caused by an axonopathy superimposed upon abnormal development, affecting peripheral but also central nervous system axons, all ultimately because of a genetic defect in the axonal cotransporter KCC3. (PMID:27230413)
  • These results suggest that the function of the peripheral nervous system depends on finely tuned, kinase-regulated KCC3 activity and implicate abnormal cell volume homeostasis as a previously unreported mechanism of axonal degeneration. (PMID:27485015)
  • we present the first Mexican patients with hereditary motor and sensory neuropathy with agenesis of the corpus callosum and a novel heterozygous frameshift variant, c.2097du p or p.(Trp700Leufs*19) of the SLC12A6 gene (PMID:30038111)
  • AS may also occur in the Roma population with a new mutation being found: frameshift mutation c.2604delT in the exon 20 of the SLC12A6 gene. Roma patients with probable AS should be primarily tested for this mutation. (PMID:30868738)
  • SLC12A ion transporter mutations in sporadic and familial human congenital hydrocephalus. (PMID:31393094)
  • De novo variants in SLC12A6 cause sporadic early-onset progressive sensorimotor neuropathy. (PMID:31439721)
  • ZnR/GPR39 controls cell migration by orchestrating recruitment of KCC3 into protrusions, re-organization of actin and activation of MMP. (PMID:33465674)
  • Novel heterozygous variants of SLC12A6 in Japanese families with Charcot-Marie-Tooth disease. (PMID:35733399)
  • Late-onset sensory-motor axonal neuropathy, a novel SLC12A6-related phenotype. (PMID:36542484)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
danio_rerioslc12a6ENSDARG00000105485
mus_musculusSlc12a6ENSMUSG00000027130
rattus_norvegicusSlc12a6ENSRNOG00000005196
drosophila_melanogasterCG10413FBGN0032689
drosophila_melanogasterNcc69FBGN0036279
drosophila_melanogasterkccFBGN0261794
caenorhabditis_elegansWBGENE00012543
caenorhabditis_elegansWBGENE00019205
caenorhabditis_elegansWBGENE00020207

Paralogs (8): SLC12A2 (ENSG00000064651), SLC12A3 (ENSG00000070915), SLC12A1 (ENSG00000074803), SLC12A7 (ENSG00000113504), SLC12A4 (ENSG00000124067), SLC12A5 (ENSG00000124140), SLC12A9 (ENSG00000146828), SLC12A8 (ENSG00000221955)

Protein

Protein identifiers

Solute carrier family 12 member 6Q9UHW9 (reviewed: Q9UHW9)

Alternative names: Electroneutral potassium-chloride cotransporter 3, K-Cl cotransporter 3

All UniProt accessions (8): Q9UHW9, A0A6Q8PH21, B3KXX3, H0YKE6, H0YKJ2, H0YKL8, H0YKQ8, H0YMQ9

UniProt curated annotations — full annotation on UniProt →

Function. Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells.

Subunit / interactions. Homodimer; adopts a domain-swap conformation at the scissor helices connecting the transmembrane domain and C-terminal domain. Heterodimer with K-Cl cotransporter SLC12A5. Interacts (via C-terminus) with CKB; the interaction may be required for potassium-chloride cotransport activity.

Subcellular location. Cell membrane. Basolateral cell membrane.

Tissue specificity. Expressed in brain (at protein level). Highly expressed in heart, brain and kidney. Detected at lower levels in skeletal muscle, placenta, lung and pancreas. Detected in umbilical vein endothelial cells. More abundant in kidney. Testis specific.

Post-translational modifications. Phosphorylated, phosphorylation regulates transporter activity. Phosphorylated at Thr-991 and Thr-1048 by OXSR1/OSR1 and STK39/SPAK downstream of WNK kinases (WNK1, WNK2, WNK3 or WNK4), inhibiting the potassium-chloride cotransport activity. N-glycosylated.

Disease relevance. Agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) [MIM:218000] A disease that is characterized by severe progressive sensorimotor neuropathy, intellectual disability, dysmorphic features and complete or partial agenesis of the corpus callosum. The disease is caused by variants affecting the gene represented in this entry. Charcot-Marie-Tooth disease, axonal, type 2II (CMT2II) [MIM:620068] A dominant axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Inhibited following phosphorylation by OXSR1/OSR1 and STK39/SPAK: phosphorylation takes place downstream of WNK kinases (WNK1, WNK2, WNK3 or WNK4) in response to hyperosmotic stress and subsequent cell shrinkage. Activated by N-ethylmaleimide (NEM). Inhibited by DIOA, bumetanide and furosemide.

Domain organisation. N-terminal loop binds to the intracellular vestibule of the transporter, arresting the transporter in an inhibited state.

Induction. Up-regulated by VEGF. Down-regulated by TNF.

Miscellaneous. Produced by alternative promoter usage. Does not differ in the osmotic set point of swelling activation but, activation is more rapid. Does not differ in the osmotic set point of swelling activation but, activation is more rapid.

Similarity. Belongs to the SLC12A transporter family. K/Cl co-transporter subfamily.

Isoforms (6)

UniProt IDNamesCanonical?
Q9UHW9-11, KCC3ayes
Q9UHW9-22, KCC3b
Q9UHW9-33, KCC3a-X2M
Q9UHW9-44, KCC3a-S3
Q9UHW9-55, KCC3a-S, KCC3a-S1, KCC3a-S2
Q9UHW9-66, KCC3b-X2M

RefSeq proteins (7): NP_001035959, NP_001035960, NP_001035961, NP_001035962, NP_001352017, NP_005126, NP_598408 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000076KCL_cotransptFamily
IPR004841AA-permease/SLC12A_domDomain
IPR004842SLC12A_famFamily
IPR018491SLC12_CDomain

Pfam: PF00324, PF03522

Catalyzed reactions (Rhea), 1 shown:

  • K(+)(in) + chloride(in) = K(+)(out) + chloride(out) (RHEA:72427)

UniProt features (181 total): helix 41, strand 35, turn 17, transmembrane region 12, modified residue 12, sequence variant 12, mutagenesis site 12, binding site 11, topological domain 10, splice variant 5, region of interest 4, glycosylation site 4, compositionally biased region 2, disulfide bond 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
6M22ELECTRON MICROSCOPY2.7
6M1YELECTRON MICROSCOPY3.2
7AINELECTRON MICROSCOPY3.2
7AIOELECTRON MICROSCOPY3.31
7D90ELECTRON MICROSCOPY3.6
7NGBELECTRON MICROSCOPY3.64
6Y5RELECTRON MICROSCOPY3.76
6Y5VELECTRON MICROSCOPY4.08

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UHW9-F179.800.54

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (11): 147; 148; 151; 443; 443; 444; 444; 446; 447; 448; 603

Post-translational modifications (12): 32, 120, 148, 736, 778, 981, 991, 1023, 1029, 1032, 1048, 1121

Disulfide bonds (2): 375–390, 410–420

Glycosylation sites (4): 379, 398, 411, 428

Mutagenesis-validated functional residues (12):

PositionPhenotype
96increases rb(+) uptake; when associated with d-991 and d-991.
96decreases rb(+) uptake; when associated with d-991 and d-1048.
505decrease in cl(-) efflux.
586decrease in cl(-) efflux.
668increases transporter activity.
715no effect on transporter activity.
746slightly reduces transporter activity.
991decreased phosphorylation by wnk kinases, leading to increased potassium-chloride cotransport activity. increases rb(+)
991decreases rb(+) uptake; when associated with d-96 and d-1048.
1032does not affect potassium-chloride cotransport activity.
1048decreased phosphorylation by wnk kinases, leading to increased potassium-chloride cotransport activity. increases rb(+)
1048decreases rb(+) uptake; when associated with d-96 and d-991.

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-426117Cation-coupled Chloride cotransporters
R-HSA-5619039Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN)
R-HSA-1643685Disease
R-HSA-382551Transport of small molecules
R-HSA-425393
R-HSA-425407SLC-mediated transmembrane transport
R-HSA-5619102SLC transporter disorders
R-HSA-5619115Disorders of transmembrane transporters

MSigDB gene sets: 434 (showing top): GOBP_POTASSIUM_ION_TRANSPORT, GOZGIT_ESR1_TARGETS_DN, GOBP_CELLULAR_RESPONSE_TO_CARBOHYDRATE_STIMULUS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_POTASSIUM_ION_HOMEOSTASIS, GOBP_INORGANIC_ANION_TRANSPORT, chr15q14, RACCACAR_AML_Q6, FOXO4_01, GGGTGGRR_PAX4_03, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_CELL_CELL_SIGNALING

GO Biological Process (14): angiogenesis (GO:0001525), monoatomic ion transport (GO:0006811), cell volume homeostasis (GO:0006884), chemical synaptic transmission (GO:0007268), chloride ion homeostasis (GO:0055064), potassium ion homeostasis (GO:0055075), cellular response to glucose stimulus (GO:0071333), cellular hypotonic response (GO:0071476), cellular hypotonic salinity response (GO:0071477), potassium ion transmembrane transport (GO:0071805), chloride transmembrane transport (GO:1902476), potassium ion import across plasma membrane (GO:1990573), potassium ion transport (GO:0006813), transmembrane transport (GO:0055085)

GO Molecular Function (8): potassium ion transmembrane transporter activity (GO:0015079), potassium:chloride symporter activity (GO:0015379), protein kinase binding (GO:0019901), metal ion binding (GO:0046872), protein binding (GO:0005515), symporter activity (GO:0015293), chloride:monoatomic cation symporter activity (GO:0015377), transmembrane transporter activity (GO:0022857)

GO Cellular Component (5): plasma membrane (GO:0005886), membrane (GO:0016020), basolateral plasma membrane (GO:0016323), axon (GO:0030424), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
SLC-mediated transport of inorganic anions1
SLC transporter disorders1
Transport of small molecules1
Disorders of transmembrane transporters1
Disease1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport2
inorganic ion homeostasis2
potassium ion transmembrane transport2
blood vessel morphogenesis1
anatomical structure formation involved in morphogenesis1
regulation of cell size1
cellular homeostasis1
anterograde trans-synaptic signaling1
monoatomic anion homeostasis1
monoatomic cation homeostasis1
intracellular glucose homeostasis1
response to glucose1
cellular response to hexose stimulus1
hypotonic response1
cellular response to osmotic stress1
hypotonic salinity response1
cellular response to salt stress1
cellular hypotonic response1
potassium ion transport1
monoatomic cation transmembrane transport1
chloride transport1
monoatomic anion transmembrane transport1
inorganic cation import across plasma membrane1
metal ion transport1
cellular process1
metal ion transmembrane transporter activity1
potassium ion transmembrane transporter activity1
chloride:monoatomic cation symporter activity1
kinase binding1
cation binding1
binding1
secondary active transmembrane transporter activity1
chloride transmembrane transporter activity1
monoatomic anion:monoatomic cation symporter activity1
transporter activity1
transmembrane transport1
membrane1
cell periphery1
cellular anatomical structure1
basal plasma membrane1

Protein interactions and networks

STRING

1174 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC12A6STK39Q9UEW8885
SLC12A6OXSR1O95747720
SLC12A6SPG11Q96JI7685
SLC12A6WNK3Q9BYP7658
SLC12A6STK24Q9Y6E0633
SLC12A6WNK1P54963625
SLC12A6ZNF618Q5T7W0564
SLC12A6SEMA6DQ8NFY4547
SLC12A6WNK4Q96J92531
SLC12A6VAV2P52735471
SLC12A6PGK1P00558470
SLC12A6WNK2Q9Y3S1460
SLC12A6SLC26A1Q9H2B4454
SLC12A6SPG7Q9UQ90441
SLC12A6SPG21Q9NZD8437

IntAct

87 interactions, top by confidence:

ABTypeScore
ENTREP1WWP2psi-mi:“MI:0914”(association)0.850
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
PDGFRBPIK3R2psi-mi:“MI:0914”(association)0.610
SLC12A6STK39psi-mi:“MI:0915”(physical association)0.560
SLC12A6CKBpsi-mi:“MI:0915”(physical association)0.530
SLC12A6CKBpsi-mi:“MI:0403”(colocalization)0.530
GPR21TMEM120Bpsi-mi:“MI:0914”(association)0.530
ZNRF4UPK3BL1psi-mi:“MI:0914”(association)0.530
LGALS1PODXLpsi-mi:“MI:0914”(association)0.530
LGALS3PODXLpsi-mi:“MI:0914”(association)0.530
SLC12A4CLGNpsi-mi:“MI:0914”(association)0.530
CLGNNPC1psi-mi:“MI:0914”(association)0.530
PTGIRTMEM63Apsi-mi:“MI:0914”(association)0.530
NRN1SLC1A1psi-mi:“MI:0914”(association)0.530
TMEM9ESYT2psi-mi:“MI:0914”(association)0.530
RAB6BRAB6Apsi-mi:“MI:0914”(association)0.530
SLC12A4JAGN1psi-mi:“MI:0914”(association)0.530
RAB6BSBF1psi-mi:“MI:0914”(association)0.530
SLC12A4LGALS3psi-mi:“MI:0914”(association)0.530
SLC12A6RPL30psi-mi:“MI:0915”(physical association)0.400
SLC12A6H1-2psi-mi:“MI:0915”(physical association)0.400
SLC12A6Ckbpsi-mi:“MI:0915”(physical association)0.400
OR2A2SLC12A6psi-mi:“MI:0915”(physical association)0.400
SLC12A6SLC25A35psi-mi:“MI:0915”(physical association)0.400

BioGRID (202): SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Proximity Label-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS), SLC12A6 (Affinity Capture-MS)

ESM2 similar proteins: A0A078H868, A0AAS4, A0JP80, A6X919, D4AD75, O70536, O77760, O77761, P23913, P35610, P53439, P56079, Q14739, Q20696, Q20735, Q28677, Q2PZI1, Q4JM44, Q4R763, Q5R7H4, Q5RK27, Q60457, Q61263, Q63632, Q63633, Q657W3, Q6AX73, Q6Z0E2, Q7T3T4, Q7TSX5, Q86VZ5, Q8IWX5, Q8NHU3, Q8VCQ6, Q91V14, Q924N4, Q965Q4, Q9D4B1, Q9FJB4, Q9H2X9

Diamond homologs: A0A0G2KTI4, A2BFP5, O60146, P38329, P55018, P59158, Q0VGW6, Q66HR0, Q924N4, Q99MR3, Q9BXP2, Q9UHW9, Q09573, Q28677, Q2UVJ5, Q5RK27, Q63632, Q63633, Q6Z0E2, Q7YRU6, Q91V14, Q9H2X9, Q9JIS8, Q9UP95, Q9WVL3, Q9Y666, Q657W3, A0AV02, Q8VI23

SIGNOR signaling

8 interactions.

AEffectBMechanism
WNK1down-regulatesSLC12A6phosphorylation
WNK3“down-regulates activity”SLC12A6phosphorylation
SLC12A6“down-regulates quantity”chloriderelocalization
STK39“down-regulates activity”SLC12A6phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 109 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
chloride transmembrane transport615.2×2e-03
transmembrane transport610.8×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1700 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic63
Likely pathogenic134
Uncertain significance559
Likely benign763
Benign95

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1029941NM_001365088.1(SLC12A6):c.1151C>G (p.Ser384Ter)Pathogenic
1073089NC_000015.9:g.(?34526072)(34631468_?)delPathogenic
1075447NM_001365088.1(SLC12A6):c.366T>G (p.Tyr122Ter)Pathogenic
1075604NM_001365088.1(SLC12A6):c.2002_2003insTGGA (p.Arg668fs)Pathogenic
1076707NM_001365088.1(SLC12A6):c.390dup (p.Lys131Ter)Pathogenic
136175NM_001365088.1(SLC12A6):c.1584_1585delinsG (p.Phe529fs)Pathogenic
136176NM_001365088.1(SLC12A6):c.2032dup (p.Tyr678fs)Pathogenic
136177NM_001365088.1(SLC12A6):c.1478_1485del (p.Phe493fs)Pathogenic
1367443NM_001365088.1(SLC12A6):c.1639del (p.Leu547fs)Pathogenic
1368157NM_001365088.1(SLC12A6):c.1620_1621del (p.Cys541fs)Pathogenic
1409721NM_001365088.1(SLC12A6):c.2142C>G (p.Tyr714Ter)Pathogenic
1423567NM_001365088.1(SLC12A6):c.1614del (p.Phe538fs)Pathogenic
1448267NM_001365088.1(SLC12A6):c.1962C>A (p.Tyr654Ter)Pathogenic
1454033NM_001365088.1(SLC12A6):c.2157C>G (p.Tyr719Ter)Pathogenic
1454158NM_001365088.1(SLC12A6):c.2036A>G (p.Tyr679Cys)Pathogenic
1455015NM_001365088.1(SLC12A6):c.550C>T (p.Gln184Ter)Pathogenic
1458003NM_001365088.1(SLC12A6):c.2015G>A (p.Trp672Ter)Pathogenic
1708538NM_001365088.1(SLC12A6):c.865G>A (p.Glu289Lys)Pathogenic
1708540NM_001365088.1(SLC12A6):c.2036A>C (p.Tyr679Ser)Pathogenic
2010893NM_001365088.1(SLC12A6):c.262_263del (p.Val88fs)Pathogenic
2041240NM_001365088.1(SLC12A6):c.2808G>A (p.Trp936Ter)Pathogenic
2085742NM_001365088.1(SLC12A6):c.1540A>T (p.Lys514Ter)Pathogenic
2091121NM_001365088.1(SLC12A6):c.563dup (p.Met189fs)Pathogenic
2094419NM_001365088.1(SLC12A6):c.629G>A (p.Trp210Ter)Pathogenic
2102681NM_001365088.1(SLC12A6):c.3146G>A (p.Trp1049Ter)Pathogenic
2103220NM_001365088.1(SLC12A6):c.3178C>T (p.Gln1060Ter)Pathogenic
2103369NM_001365088.1(SLC12A6):c.3196del (p.Glu1066fs)Pathogenic
2110920NM_001365088.1(SLC12A6):c.2180del (p.Gly727fs)Pathogenic
2427223NC_000015.9:g.(?34628591)(34628881_?)delPathogenic
2678741NM_001365088.1(SLC12A6):c.3321del (p.Asn1107fs)Pathogenic

SpliceAI

3006 predictions. Top by Δscore:

VariantEffectΔscore
15:34236008:AACTT:Adonor_loss1.0000
15:34236009:ACTTA:Adonor_loss1.0000
15:34236010:CTT:Cdonor_loss1.0000
15:34236011:TTA:Tdonor_loss1.0000
15:34236012:TAC:Tdonor_loss1.0000
15:34236013:A:ACdonor_gain1.0000
15:34236013:A:Cdonor_loss1.0000
15:34236014:C:CAdonor_gain1.0000
15:34236014:CG:Cdonor_gain1.0000
15:34236014:CGG:Cdonor_gain1.0000
15:34236014:CGGA:Cdonor_gain1.0000
15:34236033:T:TAdonor_gain1.0000
15:34236045:T:TAdonor_gain1.0000
15:34236195:TGTGC:Tacceptor_gain1.0000
15:34236196:GTGC:Gacceptor_gain1.0000
15:34236197:TGC:Tacceptor_gain1.0000
15:34236198:GC:Gacceptor_gain1.0000
15:34236199:CC:Cacceptor_gain1.0000
15:34236200:C:CAacceptor_loss1.0000
15:34236200:C:CCacceptor_gain1.0000
15:34236201:T:Gacceptor_loss1.0000
15:34236813:ATGCT:Aacceptor_loss1.0000
15:34236814:TG:Tacceptor_gain1.0000
15:34236816:C:CCacceptor_gain1.0000
15:34236820:C:CTacceptor_gain1.0000
15:34236821:A:ACacceptor_gain1.0000
15:34236821:A:Cacceptor_gain1.0000
15:34236829:C:CTacceptor_gain1.0000
15:34236831:CA:Cacceptor_gain1.0000
15:34236832:A:ACacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000021097 (15:34331273 G>T), RS1000034995 (15:34305631 A>T), RS1000047310 (15:34326595 T>C), RS1000069455 (15:34257048 G>A), RS1000070472 (15:34299612 T>A,C), RS1000075196 (15:34307767 A>T), RS1000089460 (15:34264163 C>A), RS1000168277 (15:34279309 G>A,C), RS1000236135 (15:34283067 G>A), RS1000253358 (15:34263534 A>G), RS1000268208 (15:34273730 T>C), RS1000282465 (15:34323620 C>A,T), RS1000375456 (15:34312258 G>C), RS1000380125 (15:34270114 A>T), RS1000420297 (15:34299269 A>G)

Disease associations

OMIM: gene MIM:604878 | disease phenotypes: MIM:218000, MIM:620068, MIM:118220, MIM:217990, MIM:276904

GenCC curated gene-disease

DiseaseClassificationInheritance
agenesis of the corpus callosum with peripheral neuropathyDefinitiveAutosomal recessive
Charcot-Marie-Tooth disease, axonal, IIa 2IIStrongAutosomal dominant

Mondo (6): agenesis of the corpus callosum with peripheral neuropathy (MONDO:0000902), peripheral neuropathy (MONDO:0005244), Charcot-Marie-Tooth disease, axonal, IIa 2II (MONDO:0031068), Charcot-Marie-Tooth disease (MONDO:0015626), corpus callosum, agenesis of (MONDO:0009022), Usher syndrome type 1C (MONDO:0010171)

Orphanet (6): Corpus callosum agenesis-neuronopathy syndrome (Orphanet:1496), Charcot-Marie-Tooth disease/Hereditary motor and sensory neuropathy (Orphanet:166), Isolated corpus callosum agenesis (Orphanet:200), Autosomal recessive axonal hereditary motor and sensory neuropathy (Orphanet:91024), Usher syndrome type 1 (Orphanet:231169), Usher syndrome (Orphanet:886)

HPO phenotypes

87 total (30 of 87 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000218High palate
HP:0000248Brachycephaly
HP:0000252Microcephaly
HP:0000262Turricephaly
HP:0000276Long face
HP:0000294Low anterior hairline
HP:0000316Hypertelorism
HP:0000324Facial asymmetry
HP:0000327Hypoplasia of the maxilla
HP:0000341Narrow forehead
HP:0000400Macrotia
HP:0000431Wide nasal bridge
HP:0000486Strabismus
HP:0000508Ptosis
HP:0000545Myopia
HP:0000565Esotropia
HP:0000639Nystagmus
HP:0000709Psychosis
HP:0000762Decreased nerve conduction velocity
HP:0000763Sensory neuropathy
HP:0001182Tapered finger
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001256Mild intellectual disability
HP:0001257Spasticity
HP:0001263Global developmental delay
HP:0001270Motor delay

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006528_1Barrett’s esophagus x pack-years of smoking exposure interaction3.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006526pack-years measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D061085Agenesis of Corpus CallosumC10.500.034; C16.131.666.034; C23.300.008
D002607Charcot-Marie-Tooth DiseaseC10.500.300.200; C10.574.500.495.200; C10.668.829.800.300.200; C16.131.666.300.200; C16.320.400.375.200
C536446Corpus callosum agenesis neuronopathy (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC12 family of cation-coupled chloride transporters

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
Cadmium Chloridedecreases expression, increases expression3
(+)-JQ1 compoundincreases expression2
Cyclosporinedecreases expression, increases expression2
FR900359affects phosphorylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
arseniteaffects binding, decreases reaction1
perfluorooctanoic acidincreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
potassium chromate(VI)decreases expression1
avobenzoneincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
oxamflatinincreases expression1
apicidinincreases expression1
dimethylarsinous acidincreases expression1
NSC 689534increases expression, affects binding1
Resveratrolaffects cotreatment, increases expression1
Norethindrone Acetateaffects cotreatment, increases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Copperaffects binding, increases expression1
Cytarabinedecreases expression1
Dimethylnitrosamineincreases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, increases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1

Cellosaurus cell lines

5 cell lines: 3 cancer cell line, 2 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D4DJHEK-SLC12A6-KO-c4Transformed cell lineFemale
CVCL_D4DKHEK-SLC12A6-KO-c5Transformed cell lineFemale
CVCL_D4HNHCT116-SLC12A6-KO-c17Cancer cell lineMale
CVCL_D4HPHCT116-SLC12A6-KO-c19Cancer cell lineMale
CVCL_TL54HAP1 SLC12A6 (-)Cancer cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00380965PHASE4COMPLETEDEvaluation of the Efficacy of Cesamet™ for the Treatment of Pain in Patients With Chemotherapy-Induced Neuropathy
NCT00487981PHASE4TERMINATEDSpinal Cord Stimulation for Painful Diabetic Neuropathy
NCT00904202PHASE4COMPLETEDA Study Of Lidocaine Patch 5% Alone, Gabapentin Alone, And Lidocaine Patch 5% And Gabapentin In Combination For The Relief Of Pain In Patients With Diverse Peripheral Neuropathic Pain Conditions
NCT01192113PHASE4COMPLETEDSafety and Efficacy of Mecobalamin Injection in Peripheral Neuropathies Patients (Study JGAZSY091109)
NCT01373983PHASE4COMPLETEDIntrathecal Bolus Doses of Ziconotide
NCT01458015PHASE4TERMINATEDTapentadol Versus Oxycodone - a Mechanism-based Treatment Approach in Neuropathic Pain
NCT02074267PHASE4COMPLETEDClinical Study for Assessment of the Efficacy of Gabapentin (Carbatin and Neurontin) in Patients With Neuropathy Pain
NCT02372149PHASE4UNKNOWNIVIg for Demyelination in Diabetes Mellitus
NCT02670161PHASE4ENROLLING_BY_INVITATIONQuality Improvement and Practice Based Research in Neurology Using the EMR
NCT07022938PHASE4COMPLETEDNutritional Supplement for Treating Chemotherapy Induced Neuropathy
NCT07025005PHASE4RECRUITINGFenofibrate Role in the Prophylaxis From Peripheral Neuropathy Induced by Bortezomib, Lenalidomide and Dexamethasone (VRd) Protocol in the Treatment of Patients With Multiple Myeloma (MM)
NCT00058071PHASE3COMPLETEDAmifostine in Treating Peripheral Neuropathy in Patients Who Have Received Chemotherapy for Cancer
NCT00125268PHASE3TERMINATEDNear Infrared Light for the Treatment of Painful Peripheral Neuropathy
NCT00195013PHASE3COMPLETEDRandomized Placebo-Controlled Trial of Glutamine for Breast Cancer Patients With Peripheral Neuropathy
NCT00232141PHASE3COMPLETEDStudy of Pregabalin Versus Placebo in the Treatment of Nerve Pain Associated With HIV Neuropathy
NCT00264875PHASE3COMPLETEDOpen Label Safety And Efficacy Study Of Pregabalin In Subjects With Nerve Pain Asociated With Human Immunodeficiency Virus (HIV) Neuropathy
NCT00369564PHASE3COMPLETEDGlutamic Acid in Reducing Nerve Damage Caused by Vincristine in Young Patients With Cancer
NCT00471445PHASE3COMPLETEDTopical Amitriptyline and Ketamine Cream in Treating Peripheral Neuropathy Caused by Chemotherapy in Cancer Patients
NCT00489411PHASE3COMPLETEDDuloxetine in Treating Peripheral Neuropathy Caused by Chemotherapy in Patients With Cancer
NCT00710554PHASE3COMPLETEDA Study of Sativex® for Pain Relief of Peripheral Neuropathic Pain, Associated With Allodynia
NCT00711880PHASE3COMPLETEDA Study of Sativex® for Relief of Peripheral Neuropathic Pain Associated With Allodynia.
NCT00713323PHASE3COMPLETEDA Study to Compare the Safety and Tolerability of Sativex® in Patients With Neuropathic Pain.
NCT00713817PHASE3COMPLETEDA Study to Determine the Maintenance of Effect After Long-term Treatment of Sativex® in Subjects With Neuropathic Pain
NCT00775645PHASE3COMPLETEDS0715: Acetyl-L-Carnitine in Preventing Neuropathy in Women With Stage I, II, or IIIA Breast Cancer Undergoing Chemo
NCT00872352PHASE3UNKNOWNEvaluation of Bortezomib Induced Peripheral Neuropathy of Multiple Myeloma (MM) Patients
NCT00998738PHASE3TERMINATEDCalcium and Magnesium in Preventing Peripheral Neuropathy Caused by Ixabepilone in Patients With Breast Cancer
NCT01049217PHASE3TERMINATEDPregabalin Versus Placebo In The Treatment Of Neuropathic Pain Associated With HIV Neuropathy
NCT01099449PHASE3COMPLETEDCalcium Gluconate and Magnesium Sulfate in Preventing Neurotoxicity in Patients With Colon Cancer or Rectal Cancer Receiving Oxaliplatin-Based Combination Chemotherapy
NCT01288937PHASE3TERMINATEDA Placebo Controlled, Randomized, Double Blind Trial of Milnacipran for the Treatment of Idiopathic Neuropathy Pain
NCT01492920PHASE3WITHDRAWNAcetyl-L-Carnitine Hydrochloride in Preventing Peripheral Neuropathy in Patients With Recurrent Ovarian Epithelial Cancer, Primary Peritoneal Cavity Cancer, or Fallopian Tube Cancer Undergoing Chemotherapy
NCT01775449PHASE3COMPLETEDPrevention of Oxaliplatin-induced Neuropathic Pain by a Specific Diet
NCT02024191PHASE3UNKNOWNThe Role of Glutamine for Preventing Oxaliplatin-Induced Peripheral Neuropathy
NCT02217267PHASE3COMPLETEDLong Term Outcome After Serial Lidocaine Infusion in Peripheral Neuropathic Pain
NCT02294149PHASE3UNKNOWNVit D3 and Omega 3 in Chemo Induced Neuropathy
NCT02311907PHASE3COMPLETEDGlutathione in Preventing Peripheral Neuropathy Caused by Paclitaxel and Carboplatin in Patients With Ovarian Cancer, Fallopian Tube Cancer, and/or Primary Peritoneal Cancer
NCT06071936PHASE3UNKNOWNEfficacy and Tolerability of AP707 in Patients With Chronic Pain Due to Traumatic or Post-operative Peripheral Neuropathy
NCT06071975PHASE3UNKNOWNLong Term Efficacy and Tolerability of AP707 in Patients With Chronic Pain Due to Diabetic Polyneuropathy
NCT06071988PHASE3UNKNOWNLong Term Efficacy and Tolerability of AP707 in Patients With Chronic Pain Due to Traumatic or Post-operative Peripheral Neuropathy
NCT06072573PHASE3UNKNOWNEfficacy and Tolerability of AP707 in Patients With Chronic Pain Due to Diabetic Polyneuropathy
NCT07287592PHASE3NOT_YET_RECRUITINGGlutamine for the Prophylaxis of Vincristine-induced Neuropathy in Children and Adolescents With Cancer.