KCTD20

Summary

KCTD20 (potassium channel tetramerization domain containing 20, HGNC:21052) is a protein-coding gene on chromosome 6p21.31, encoding BTB/POZ domain-containing protein KCTD20 (Q7Z5Y7). Promotes the phosphorylation of AKT family members.

Predicted to enable identical protein binding activity. Predicted to be involved in positive regulation of phosphorylation. Predicted to be located in membrane. Predicted to be active in cytoplasm.

Source: NCBI Gene 222658 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_173562

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21052
Approved symbol	KCTD20
Name	potassium channel tetramerization domain containing 20
Location	6p21.31
Locus type	gene with protein product
Status	Approved
Aliases	dJ108K11.3, MGC14254
Ensembl gene	ENSG00000112078
Ensembl biotype	protein_coding
OMIM	615932
Entrez	222658

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 30 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000265344, ENST00000373731, ENST00000443316, ENST00000449081, ENST00000460983, ENST00000474988, ENST00000481911, ENST00000483557, ENST00000498267, ENST00000536244, ENST00000901245, ENST00000901246, ENST00000901247, ENST00000901248, ENST00000901249, ENST00000901250, ENST00000901251, ENST00000940734, ENST00000940735, ENST00000940736, ENST00000940737, ENST00000940738, ENST00000959480, ENST00000959481, ENST00000959482, ENST00000959483, ENST00000959484, ENST00000959485, ENST00000959486, ENST00000959487, ENST00000959488, ENST00000959489, ENST00000959490, ENST00000959491

RefSeq mRNA: 3 — MANE Select: NM_173562 NM_001286579, NM_001286580, NM_173562

CCDS: CCDS4821, CCDS69096, CCDS69097

Canonical transcript exons

ENST00000373731 — 8 exons

Exon	Start	End
ENSE00001896590	36474789	36475062
ENSE00003493900	36479121	36479223
ENSE00003601860	36481562	36481759
ENSE00003644886	36479591	36479711
ENSE00003678174	36470052	36470257
ENSE00003683497	36484714	36484824
ENSE00003845461	36486883	36491141
ENSE00003848077	36443000	36443111

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 98.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.2094 / max 270.6431, expressed in 1819 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67514	25.1487	1816
67513	2.0398	1190
67512	1.9764	1007
67511	0.0445	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amniotic fluid	UBERON:0000173	98.68	gold quality
adrenal tissue	UBERON:0018303	96.08	gold quality
buccal mucosa cell	CL:0002336	96.00	gold quality
skin of hip	UBERON:0001554	95.77	gold quality
penis	UBERON:0000989	95.61	gold quality
synovial joint	UBERON:0002217	95.58	gold quality
seminal vesicle	UBERON:0000998	95.38	gold quality
tendon of biceps brachii	UBERON:0008188	95.14	gold quality
mammalian vulva	UBERON:0000997	95.13	gold quality
trabecular bone tissue	UBERON:0002483	95.06	gold quality
pericardium	UBERON:0002407	94.96	gold quality
monocyte	CL:0000576	94.95	gold quality
nipple	UBERON:0002030	94.88	gold quality
endothelial cell	CL:0000115	94.81	gold quality
stromal cell of endometrium	CL:0002255	94.73	gold quality
medial globus pallidus	UBERON:0002477	94.63	gold quality
oral cavity	UBERON:0000167	94.55	gold quality
mononuclear cell	CL:0000842	94.54	gold quality
upper leg skin	UBERON:0004262	94.53	gold quality
lower lobe of lung	UBERON:0008949	94.48	gold quality
gingiva	UBERON:0001828	94.41	gold quality
vena cava	UBERON:0004087	94.41	gold quality
trigeminal ganglion	UBERON:0001675	94.38	gold quality
leukocyte	CL:0000738	94.35	gold quality
saphenous vein	UBERON:0007318	94.32	gold quality
gingival epithelium	UBERON:0001949	94.24	gold quality
urethra	UBERON:0000057	94.20	gold quality
colonic epithelium	UBERON:0000397	93.86	gold quality
superficial temporal artery	UBERON:0001614	93.80	gold quality
globus pallidus	UBERON:0001875	93.76	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	459.72
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting KCTD20, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 4)

• KCTD20 is a positive regulator of Akt and may play an important role in regulating the death and growth of some non-nervous and nervous cells. (PMID:24156551)
• results suggest that Kctd20 impacts proliferation and invasion of non-small cell lung cancer through enhancing Fak and Akt phosphorylation (PMID:28398603)
• Cocaine’omics: Genome-wide and transcriptome-wide analyses provide biological insight into cocaine use and dependence. (PMID:30734435)
• Long noncoding RNA NEAT1 regulates glioma cell proliferation and apoptosis by competitively binding to microRNA3245p and upregulating KCTD20 expression. (PMID:33982764)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	KCTD20	ENSDARG00000114704
mus_musculus	Kctd20	ENSMUSG00000005936
rattus_norvegicus	Kctd20	ENSRNOG00000000517
drosophila_melanogaster	mri	FBGN0035107
caenorhabditis_elegans		WBGENE00019888

Paralogs (1): BTBD10 (ENSG00000148925)

Protein

Protein identifiers

BTB/POZ domain-containing protein KCTD20 — Q7Z5Y7 (reviewed: Q7Z5Y7)

Alternative names: Potassium channel tetramerization domain containing 20

All UniProt accessions (6): Q7Z5Y7, C9J5B3, C9J624, C9JY11, F8WF75, H7BXH0

UniProt curated annotations — full annotation on UniProt →

Function. Promotes the phosphorylation of AKT family members.

Subunit / interactions. Interacts with AKT1; AKT2 and AKT3. Associates with PP2CA. Part of a complex containing MARK4.

Subcellular location. Cytoplasm.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z5Y7-1	1	yes
Q7Z5Y7-2	2
Q7Z5Y7-3	3

RefSeq proteins (3): NP_001273508, NP_001273509, NP_775833* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000210	BTB/POZ_dom	Domain
IPR011333	SKP1/BTB/POZ_sf	Homologous_superfamily
IPR039885	BTBD10/KCTD20_BTB/POZ	Domain
IPR039886	BTBD10/KCTD20	Family

Pfam: PF16017

UniProt features (8 total): splice variant 3, sequence conflict 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5Y7-F1	71.19	0.45

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 146 (showing top): GOBP_REGULATION_OF_PHOSPHORYLATION, TERAMOTO_OPN_TARGETS_CLUSTER_6, GOBP_POSITIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, GOBP_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, MARSON_BOUND_BY_FOXP3_STIMULATED, BOCHKIS_FOXA2_TARGETS, NUYTTEN_NIPP1_TARGETS_DN, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, MORF_BCL2, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, JOHNSTONE_PARVB_TARGETS_2_DN, BRUINS_UVC_RESPONSE_LATE, RPS14_DN.V1_DN, HOXA9_DN.V1_DN

GO Biological Process (1): positive regulation of phosphorylation (GO:0042327)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (2): cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
phosphorylation	1
regulation of phosphorylation	1
positive regulation of phosphate metabolic process	1
protein binding	1
binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

436 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KCTD20	KCTD19	Q17RG1	643
KCTD20	KCTD10	Q9H3F6	619
KCTD20	KCTD18	Q6PI47	591
KCTD20	KCTD5	Q9NXV2	572
KCTD20	KCTD1	Q719H9	541
KCTD20	KCTD8	Q6ZWB6	539
KCTD20	KCTD12	Q96CX2	539
KCTD20	KCTD11	Q693B1	533
KCTD20	KCTD3	Q9Y597	528
KCTD20	TNFAIP1	Q13829	514
KCTD20	PNMA1	Q8ND90	512
KCTD20	KCTD16	Q68DU8	512
KCTD20	KCTD21	Q4G0X4	508
KCTD20	KCTD13	Q8WZ19	508
KCTD20	KCTD17	Q8N5Z5	502

IntAct

24 interactions, top by confidence:

A	B	Type	Score
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
BUB3	ZNF207	psi-mi:“MI:0914”(association)	0.690
CUL3	ENC1	psi-mi:“MI:0914”(association)	0.640
CUL3	RHOBTB1	psi-mi:“MI:0914”(association)	0.530
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
KCTD20	PPP1CA	psi-mi:“MI:0915”(physical association)	0.370
COPS7A	BTBD10	psi-mi:“MI:0914”(association)	0.350
Cul3	COPS6	psi-mi:“MI:0914”(association)	0.350
Cul3		psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.350
CUL3	KLHL2	psi-mi:“MI:0914”(association)	0.350
BUB3	ZNF207	psi-mi:“MI:0914”(association)	0.350
MARK4	MTCL2	psi-mi:“MI:0914”(association)	0.350
ARRDC5	PLPP1	psi-mi:“MI:0914”(association)	0.350
DUSP16	MEIOC	psi-mi:“MI:0914”(association)	0.350
SOX13	H1-5	psi-mi:“MI:0914”(association)	0.350
PPP1CC	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
TSSK1B	HERC4	psi-mi:“MI:0914”(association)	0.350
KRAS	IGKV2D-29	psi-mi:“MI:0914”(association)	0.350
FXR2	RPSA2	psi-mi:“MI:2364”(proximity)	0.270
NOLC1	ILVBL	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (32): KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-RNA), KCTD20 (Affinity Capture-RNA), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS), KCTD20 (Affinity Capture-MS)

ESM2 similar proteins: A2VE39, A4IID4, A4QP78, A9X1A0, B0BNK8, B0KWC1, B1MTG7, B2KI64, B3EX61, B4UT09, D2HRF1, D3Z5S8, F7E7M3, F8VPU6, O00763, O02019, O02810, O08561, O35099, P31266, Q06330, Q08BW6, Q29RH2, Q2M146, Q3SZ41, Q4R8X4, Q5R981, Q5RFK6, Q5RHQ8, Q5SSF7, Q5U4W6, Q5VWP2, Q5XIV0, Q5ZJT0, Q5ZL95, Q6GN16, Q6PCM2, Q7Z5Y7, Q7ZUP1, Q8BKC8

Diamond homologs: Q5R585, Q7Z5Y7, Q80X66, Q8CDD8, Q9BSF8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 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 term	Partners	Fold	FDR
cell division	6	9.2×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1911 predictions. Top by Δscore:

Variant	Effect	Δscore
6:36443110:GA:G	donor_gain	1.0000
6:36443112:G:GG	donor_gain	1.0000
6:36479585:TTACA:T	acceptor_loss	1.0000
6:36479586:TACAG:T	acceptor_loss	1.0000
6:36479588:CAGG:C	acceptor_loss	1.0000
6:36479589:AG:A	acceptor_gain	1.0000
6:36479589:AGGA:A	acceptor_loss	1.0000
6:36479590:G:T	acceptor_loss	1.0000
6:36479590:GG:G	acceptor_gain	1.0000
6:36479590:GGATT:G	acceptor_gain	1.0000
6:36479707:TCTGA:T	donor_gain	1.0000
6:36479710:GA:G	donor_gain	1.0000
6:36479712:G:GG	donor_gain	1.0000
6:36481717:G:GT	donor_gain	1.0000
6:36481717:G:T	donor_gain	1.0000
6:36481743:G:GT	donor_gain	1.0000
6:36481743:G:T	donor_gain	1.0000
6:36481744:G:GT	donor_gain	1.0000
6:36481744:G:T	donor_gain	1.0000
6:36481747:G:GT	donor_gain	1.0000
6:36481760:G:GG	donor_gain	1.0000
6:36481811:G:GT	donor_gain	1.0000
6:36484712:A:AG	acceptor_gain	1.0000
6:36484713:G:GT	acceptor_gain	1.0000
6:36484713:GTT:G	acceptor_gain	1.0000
6:36484713:GTTCT:G	acceptor_gain	1.0000
6:36484820:TGAAG:T	donor_loss	1.0000
6:36484822:AAG:A	donor_loss	1.0000
6:36484823:AGG:A	donor_loss	1.0000
6:36484825:GT:G	donor_loss	1.0000

AlphaMissense

2799 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:36474990:T:A	L121H	1.000
6:36474990:T:C	L121P	1.000
6:36475032:T:C	F135S	1.000
6:36475050:C:T	T141I	1.000
6:36475056:T:A	L143Q	1.000
6:36475056:T:C	L143P	1.000
6:36475058:G:A	G144R	1.000
6:36475058:G:C	G144R	1.000
6:36475059:G:A	G144E	1.000
6:36475059:G:T	G144V	1.000
6:36479123:T:C	M146T	1.000
6:36479124:G:A	M146I	1.000
6:36479124:G:C	M146I	1.000
6:36479124:G:T	M146I	1.000
6:36479125:T:C	F147L	1.000
6:36479126:T:C	F147S	1.000
6:36479127:T:A	F147L	1.000
6:36479127:T:G	F147L	1.000
6:36479210:T:C	F175S	1.000
6:36479597:T:G	Y182D	1.000
6:36479646:T:C	L198P	1.000
6:36479649:G:C	R199T	1.000
6:36479649:G:T	R199I	1.000
6:36479650:A:C	R199S	1.000
6:36479650:A:T	R199S	1.000
6:36479657:T:C	C202R	1.000
6:36479658:G:A	C202Y	1.000
6:36479659:T:G	C202W	1.000
6:36479663:T:C	Y204H	1.000
6:36479667:T:C	L205P	1.000

dbSNP variants (sampled 300 via entrez): RS1000003914 (6:36467933 T>A), RS1000063300 (6:36447099 A>G), RS1000094038 (6:36453410 T>G), RS1000257306 (6:36459081 G>A), RS1000393935 (6:36460455 C>A), RS1000455418 (6:36453387 T>C), RS1000460631 (6:36465919 C>T), RS1000514611 (6:36442434 G>GT), RS1000526759 (6:36451592 G>C), RS1000570956 (6:36489392 G>T), RS1000594010 (6:36448771 G>A), RS1000850777 (6:36466711 C>T), RS1000893683 (6:36472441 A>G), RS1000945643 (6:36472216 G>C), RS1000945710 (6:36483184 A>G)

Disease associations

OMIM: gene MIM:615932 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005991_87	Platelet count	7.000000e-35
GCST90002395_444	Mean platelet volume	2.000000e-35

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
lead acetate	affects cotreatment, decreases expression	1
o,p’-DDT	increases expression	1
zinc protoporphyrin	affects cotreatment, decreases expression	1
sodium arsenite	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
ICG 001	increases expression	1
Resveratrol	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Acrolein	increases abundance, affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression, affects cotreatment	1
Arsenic	affects methylation	1
Vehicle Emissions	decreases expression, increases abundance	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tunicamycin	increases expression	1
Valproic Acid	increases expression	1
Zearalenone	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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