KCTD5

gene
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Also known as FLJ20040

Summary

KCTD5 (potassium channel tetramerization domain containing 5, HGNC:21423) is a protein-coding gene on chromosome 16p13.3, encoding BTB/POZ domain-containing protein KCTD5 (Q9NXV2). Its interaction with CUL3 suggests that it may act as a substrate adapter in some E3 ligase complex.

Enables identical protein binding activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Located in cytosol.

Source: NCBI Gene 54442 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 41 total — 1 pathogenic
  • MANE Select transcript: NM_018992

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21423
Approved symbolKCTD5
Namepotassium channel tetramerization domain containing 5
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesFLJ20040
Ensembl geneENSG00000167977
Ensembl biotypeprotein_coding
OMIM611285
Entrez54442

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000301738, ENST00000564195, ENST00000564246, ENST00000569689, ENST00000570005, ENST00000855086, ENST00000956038

RefSeq mRNA: 1 — MANE Select: NM_018992 NM_018992

CCDS: CCDS10475

Canonical transcript exons

ENST00000301738 — 6 exons

ExonStartEnd
ENSE0000111887927072982709030
ENSE0000111888326825232682800
ENSE0000348228927023532702478
ENSE0000352101626959352696043
ENSE0000358781026979062697997
ENSE0000360832226998212699916

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 99.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.4220 / max 445.3931, expressed in 1820 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15226333.42201820

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.04gold quality
oocyteCL:000002397.89gold quality
mucosa of transverse colonUBERON:000499191.90gold quality
lower esophagus mucosaUBERON:003583491.62gold quality
esophagus mucosaUBERON:000246990.02gold quality
colonic mucosaUBERON:000031789.48gold quality
mucosa of sigmoid colonUBERON:000499389.35gold quality
esophagus squamous epitheliumUBERON:000692088.56gold quality
granulocyteCL:000009488.45gold quality
epithelium of esophagusUBERON:000197688.38gold quality
ganglionic eminenceUBERON:000402388.21gold quality
ventricular zoneUBERON:000305388.00gold quality
transverse colonUBERON:000115787.84gold quality
leukocyteCL:000073887.51gold quality
monocyteCL:000057687.48gold quality
mononuclear cellCL:000084287.42gold quality
pharyngeal mucosaUBERON:000035587.27gold quality
tongue squamous epitheliumUBERON:000691987.14silver quality
stromal cell of endometriumCL:000225587.08gold quality
palpebral conjunctivaUBERON:000181286.66gold quality
gingival epitheliumUBERON:000194986.14gold quality
esophagusUBERON:000104386.11gold quality
gingivaUBERON:000182885.80gold quality
colonUBERON:000115585.73gold quality
large intestineUBERON:000005985.64gold quality
skin of legUBERON:000151185.54gold quality
C1 segment of cervical spinal cordUBERON:000646985.53gold quality
small intestine Peyer’s patchUBERON:000345485.18gold quality
intestineUBERON:000016085.16gold quality
cortical plateUBERON:000534385.16gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-112yes15.31
E-MTAB-9067yes12.21
E-ANND-3yes3.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

93 targeting KCTD5, 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-3163100.0077.238605
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
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-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-453199.9969.703181
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-314899.9775.066478
HSA-MIR-590-3P99.9674.346478
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-6753-3P99.9366.57637
HSA-MIR-7107-3P99.9366.73627
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-311999.9271.342390
HSA-MIR-568299.8972.561005
HSA-MIR-990299.8969.152250

Literature-anchored findings (GeneRIF, showing 10)

  • we have identified a novel cellular AAV-2 Rep78/Rep68 interaction partner, KCTD5, located predominantly in the cytoplasm. (PMID:17239418)
  • Analysis of the interaction with cullin3 showed that, in addition to the BTB domain, some amino acids in the N-terminus of KCTD5 are required for binding to cullin3. Findings suggest that KCTD5 is a substrate-specific adaptor for cullin3-based E3 ligases (PMID:18573101)
  • structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation (PMID:19361449)
  • Identification of MCM7, ZNF711 and FAM193 as KCTD5 interaction partners.KCTD5 is not involved in polyubiquitylation of MCM7 replication factor.The KCTD5/cullin3 complex stabilizes ZNF711 transcription factor. (PMID:26188516)
  • genetic modifier screen exposes suppressors of the KCTD5 phenotype and mechanistically demonstrates that KCTD5 acts as an off-switch for GPCR signalling by triggering proteolysis of Gbetagamma heterodimers dissociated from the Galpha subunit (PMID:28562590)
  • Cullin3/KCTD5 downregulates the DNA-binding affinity of DeltaNp63alpha, impairing either its transactivity or its transinhibitory activity. Functionally, Cullin3/KCTD5 abates the proproliferation activity of DeltaNp63alpha. These findings suggest that KCTD5-based CRL3 may mediate monoubiquitination and is a novel regulator of DeltaNp63alpha. (PMID:29782646)
  • KCTD5, a novel TRPM4-regulatory protein required for cell migration as a new predictor for breast cancer prognosis. (PMID:32301552)
  • K(+) Channel Tetramerization Domain 5 (KCTD5) Protein Regulates Cell Migration, Focal Adhesion Dynamics and Spreading through Modulation of Ca(2+) Signaling and Rac1 Activity. (PMID:33053687)
  • Members of the KCTD family are major regulators of cAMP signaling. (PMID:34934014)
  • KCTD Proteins Have Redundant Functions in Controlling Cellular Growth. (PMID:38732215)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioKCTD5ENSDARG00000098817
mus_musculusKctd5ENSMUSG00000016946
rattus_norvegicusKctd5ENSRNOG00000057186
drosophila_melanogasterincFBGN0025394
caenorhabditis_elegansWBGENE00016871

Paralogs (3): KCTD17 (ENSG00000100379), KCTD9 (ENSG00000104756), KCTD2 (ENSG00000180901)

Protein

Protein identifiers

BTB/POZ domain-containing protein KCTD5Q9NXV2 (reviewed: Q9NXV2)

All UniProt accessions (2): Q9NXV2, H3BSS5

UniProt curated annotations — full annotation on UniProt →

Function. Its interaction with CUL3 suggests that it may act as a substrate adapter in some E3 ligase complex. Does not affect the function of Kv channel Kv2.1/KCNB1, Kv1.2/KCNA2, Kv4.2/KCND2 and Kv3.4/KCNC4.

Subunit / interactions. Homopentamer. Interacts (via C-terminus) with GRASP55/GORASP2. Interacts with CUL3 and with ubiquitinated proteins. Interacts with CRY1. (Microbial infection) Interacts with adeno-associated virus 2 (AAV-2) REP proteins.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

Domain organisation. The BTB (POZ) domain is atypical and mediates the formation of a homopentamer instead of a homotetramer. Homopentamerization is due to the presence of 4 residues in the BTB (POZ) domain: Leu-56, Gly-100, Val-112 and Ala-118.

Induction. Up-regulated in peripheral blood lymphocytes stimulated through the T-cell receptor.

RefSeq proteins (1): NP_061865* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR003131T1-type_BTBDomain
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily

Pfam: PF02214

UniProt features (24 total): helix 7, strand 7, turn 2, modified residue 2, initiator methionine 1, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

9 structures.

PDBMethodResolution (Å)
3DRZX-RAY DIFFRACTION1.9
8U7ZELECTRON MICROSCOPY2.97
3DRXX-RAY DIFFRACTION3.11
3DRYX-RAY DIFFRACTION3.3
8U80ELECTRON MICROSCOPY3.6
8U81ELECTRON MICROSCOPY3.82
8U82ELECTRON MICROSCOPY3.84
8U84ELECTRON MICROSCOPY3.88
8U83ELECTRON MICROSCOPY3.98

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NXV2-F178.970.55

Functional residue map

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

Post-translational modifications (2): 2, 10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 184 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, FXR_IR1_Q6, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, CTATGCA_MIR153, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, GTGCCTT_MIR506, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, OCT1_06, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_PROTEIN_HOMOOLIGOMERIZATION, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, P53_DECAMER_Q2

GO Biological Process (2): proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein homooligomerization (GO:0051260)

GO Molecular Function (4): identical protein binding (GO:0042802), protein-containing complex binding (GO:0044877), cullin family protein binding (GO:0097602), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), Cul3-RING ubiquitin ligase complex (GO:0031463)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein binding2
binding2
cellular anatomical structure2
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
protein complex oligomerization1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

768 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KCTD5CUL3Q13618977
KCTD5KCTD11Q693B1762
KCTD5KCTD1Q719H9671
KCTD5KCTD15Q96SI1576
KCTD5KCTD20Q7Z5Y7572
KCTD5BTBD10Q9BSF8557
KCTD5KCNC4Q03721556
KCTD5KCTD19Q17RG1515
KCTD5KCNA2P16389479
KCTD5KCNB1Q14721477
KCTD5SKP1P34991473
KCTD5KCND2Q9NZV8471
KCTD5RBX1P62877431
KCTD5KCTD13Q8WZ19425
KCTD5RND2P52198422

IntAct

80 interactions, top by confidence:

ABTypeScore
NHERF2PODXLpsi-mi:“MI:0914”(association)0.770
ARRDC1NEDD4psi-mi:“MI:0914”(association)0.640
REPIN1IPO8psi-mi:“MI:0914”(association)0.640
GNG8GNB5psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
KCND2BAG3psi-mi:“MI:0914”(association)0.530
KCTD17CBX4psi-mi:“MI:0914”(association)0.530
GNG2GNB5psi-mi:“MI:0914”(association)0.530
KCTD5KCTD5psi-mi:“MI:0407”(direct interaction)0.520
PRDX2PRDX3psi-mi:“MI:0914”(association)0.510
NHERF2ACTN4psi-mi:“MI:0914”(association)0.510
Rep68KCTD5psi-mi:“MI:0915”(physical association)0.510
KCTD5Rep68psi-mi:“MI:0915”(physical association)0.510
NXF1KCTD5psi-mi:“MI:0915”(physical association)0.490
Rep78KCTD5psi-mi:“MI:0915”(physical association)0.490
KCTD5Rep78psi-mi:“MI:0915”(physical association)0.490
Kctd5CKAP5psi-mi:“MI:0915”(physical association)0.400
TMEM45AKCTD5psi-mi:“MI:0915”(physical association)0.400
KCTD5lcrDpsi-mi:“MI:0915”(physical association)0.370

BioGRID (195): KCTD5 (Affinity Capture-MS), KCTD5 (Affinity Capture-MS), KCTD5 (Affinity Capture-MS), KCTD5 (Affinity Capture-MS), KCTD5 (Affinity Capture-MS), KCTD5 (Affinity Capture-MS), KCTD5 (Reconstituted Complex), KCTD5 (Affinity Capture-MS), ZNF711 (Two-hybrid), MCM7 (Two-hybrid), FAM193B (Two-hybrid), ZNF711 (Affinity Capture-Western), MCM7 (Affinity Capture-Western), FAM193B (Affinity Capture-Western), KCTD5 (Affinity Capture-Western)

ESM2 similar proteins: A3KMV1, A4IFB4, A5PKG7, A9ULR9, B1WC97, B5DEL1, O70479, O73916, P0C5J9, Q01820, Q0VD00, Q0VFV7, Q12259, Q13829, Q28DC9, Q2HJ48, Q2T9W0, Q2TUM3, Q3URF8, Q4G0X4, Q5EAX2, Q5F3E8, Q5M956, Q5RBH4, Q5XJ34, Q5ZJP7, Q6DC02, Q6DCX3, Q6DG99, Q6P3P4, Q6P7W2, Q719H9, Q7TNY1, Q7TPL3, Q7Z3E5, Q863D4, Q8BGV7, Q8BJK1, Q8BNL5, Q8K0E1

Diamond homologs: A3KMV1, A4IFB4, A5PKG7, A6H6X4, B1WC97, B5DEL1, D5SHR0, G5EFC3, O65555, P0C5J9, P15388, P17971, P17972, P25122, P48547, P59994, P59995, Q01956, Q03607, Q03719, Q0VD00, Q0VFV7, Q14003, Q14681, Q29RJ0, Q2HJ48, Q2TUM3, Q3URF8, Q4G0X4, Q50H33, Q52PG9, Q54KH0, Q5DTY9, Q5M956, Q5XJ34, Q5ZJP7, Q62897, Q63881, Q63959, Q68DU8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance28
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4279197GRCh37/hg19 16p13.3(chr16:2747326-2817288)x1Pathogenic

SpliceAI

1731 predictions. Top by Δscore:

VariantEffectΔscore
16:2682797:CAAGG:Cdonor_loss1.0000
16:2682798:AAGG:Adonor_loss1.0000
16:2682799:AGG:Adonor_loss1.0000
16:2682800:GGTG:Gdonor_loss1.0000
16:2695930:TTTA:Tacceptor_loss1.0000
16:2695933:A:AGacceptor_gain1.0000
16:2695934:G:GGacceptor_gain1.0000
16:2696039:GGAAG:Gdonor_gain1.0000
16:2696040:GAAGG:Gdonor_gain1.0000
16:2696041:A:Tdonor_gain1.0000
16:2696041:AAGGT:Adonor_loss1.0000
16:2696044:G:GAdonor_loss1.0000
16:2696045:T:Gdonor_loss1.0000
16:2697905:GGA:Gacceptor_gain1.0000
16:2699818:CA:Cacceptor_loss1.0000
16:2699819:A:AGacceptor_gain1.0000
16:2699819:AG:Aacceptor_gain1.0000
16:2699819:AGGT:Aacceptor_gain1.0000
16:2699820:G:GCacceptor_gain1.0000
16:2699820:GG:Gacceptor_gain1.0000
16:2699820:GGT:Gacceptor_gain1.0000
16:2699820:GGTG:Gacceptor_gain1.0000
16:2699820:GGTGC:Gacceptor_gain1.0000
16:2699904:G:GTdonor_gain1.0000
16:2699913:GCAG:Gdonor_gain1.0000
16:2699914:CAGG:Cdonor_loss1.0000
16:2699915:AGGT:Adonor_loss1.0000
16:2699917:G:GAdonor_loss1.0000
16:2699918:T:Adonor_loss1.0000
16:2702348:TGCA:Tacceptor_loss1.0000

AlphaMissense

1509 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:2682681:T:AW45R1.000
16:2682681:T:CW45R1.000
16:2682683:G:CW45C1.000
16:2682683:G:TW45C1.000
16:2682691:T:AL48H1.000
16:2682691:T:CL48P1.000
16:2682695:C:AN49K1.000
16:2682695:C:GN49K1.000
16:2682697:T:AV50D1.000
16:2682699:G:CG51R1.000
16:2682699:G:TG51C1.000
16:2682700:G:AG51D1.000
16:2682700:G:TG51V1.000
16:2682702:G:CG52R1.000
16:2682703:G:AG52D1.000
16:2682703:G:TG52V1.000
16:2682711:T:CF55L1.000
16:2682712:T:CF55S1.000
16:2682713:C:AF55L1.000
16:2682713:C:GF55L1.000
16:2682718:C:TT57I1.000
16:2682721:C:TT58I1.000
16:2682733:T:AL62Q1.000
16:2682733:T:CL62P1.000
16:2682750:T:CS68P1.000
16:2682753:T:CF69L1.000
16:2682754:T:CF69S1.000
16:2682755:C:AF69L1.000
16:2682755:C:GF69L1.000
16:2682757:T:AL70Q1.000

dbSNP variants (sampled 300 via entrez): RS1000134103 (16:2704401 C>T), RS1000136576 (16:2690839 C>T), RS1000192137 (16:2696711 C>T), RS1000375491 (16:2700876 C>A,T), RS1000466453 (16:2691051 G>A), RS1000466618 (16:2705054 G>A), RS1000485787 (16:2705113 A>C), RS1000560095 (16:2704877 G>A,C), RS1000668426 (16:2688128 C>A,G,T), RS1000762790 (16:2708118 G>A), RS1000844714 (16:2687422 C>G,T), RS1000957313 (16:2687275 T>C), RS1000963644 (16:2693507 C>A,G,T), RS1000999081 (16:2708880 T>A,C), RS1001000531 (16:2709381 G>A,C)

Disease associations

OMIM: gene MIM:611285 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
cobaltous chlorideincreases expression2
Tobacco Smoke Pollutiondecreases methylation, increases expression2
Zincaffects cotreatment, increases expression, decreases expression2
Cadmium Chlorideincreases expression2
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Adecreases expression1
sodium arseniteincreases expression1
benzo(e)pyrenedecreases methylation1
4-aminophenylarsenoxideaffects binding, decreases reaction1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
abrineincreases expression1
Grape Seed Proanthocyanidinsincreases expression, affects cotreatment1
licochalcone Bincreases expression1
PCI 5002affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Zoledronic Acidincreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Acroleinincreases abundance, affects cotreatment, increases oxidation1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Benzo(a)pyreneincreases methylation1
Catechinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Methapyrilenedecreases methylation1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_D9HWUbigene HEK293 KCTD5 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.