KCTD13

Summary

KCTD13 (potassium channel tetramerization domain containing 13, HGNC:22234) is a protein-coding gene on chromosome 16p11.2, encoding BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 (Q8WZ19). Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for synaptic transmission.

Enables identical protein binding activity and small GTPase binding activity. Contributes to ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of Rho protein signal transduction; proteasome-mediated ubiquitin-dependent protein catabolic process; and stress fiber assembly. Located in nuclear body. Part of Cul3-RING ubiquitin ligase complex.

Source: NCBI Gene 253980 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Limited, GenCC)
• GWAS associations: 12
• Clinical variants (ClinVar): 33 total — 3 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_178863

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22234
Approved symbol	KCTD13
Name	potassium channel tetramerization domain containing 13
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Aliases	PDIP1, FKSG86, POLDIP1
Ensembl gene	ENSG00000174943
Ensembl biotype	protein_coding
OMIM	608947
Entrez	253980

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000308768, ENST00000561540, ENST00000563264, ENST00000563955, ENST00000566413, ENST00000566842, ENST00000567795, ENST00000568000, ENST00000568721, ENST00000568995, ENST00000648037, ENST00000649581, ENST00000889845, ENST00000889846, ENST00000969940, ENST00000969941, ENST00000969942

RefSeq mRNA: 2 — MANE Select: NM_178863 NM_001410898, NM_178863

CCDS: CCDS10661, CCDS92133

Canonical transcript exons

ENST00000568000 — 6 exons

Exon	Start	End
ENSE00001178633	29923190	29923359
ENSE00001305829	29906339	29907108
ENSE00002594024	29925790	29926226
ENSE00003511612	29911815	29911867
ENSE00003539684	29911960	29912049
ENSE00003653864	29910978	29911173

Expression profiles

Bgee: expression breadth ubiquitous, 244 present calls, max score 96.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.5567 / max 180.8851, expressed in 1808 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156976	14.6836	1805
156975	0.6082	231
156974	0.2625	126
156973	0.0025	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	96.40	gold quality
left testis	UBERON:0004533	96.38	gold quality
nucleus accumbens	UBERON:0001882	94.31	gold quality
testis	UBERON:0000473	94.06	gold quality
anterior cingulate cortex	UBERON:0009835	94.02	gold quality
cortical plate	UBERON:0005343	93.96	gold quality
cingulate cortex	UBERON:0003027	93.94	gold quality
right frontal lobe	UBERON:0002810	93.56	gold quality
prefrontal cortex	UBERON:0000451	93.51	gold quality
amygdala	UBERON:0001876	93.42	gold quality
CA1 field of hippocampus	UBERON:0003881	93.15	gold quality
caudate nucleus	UBERON:0001873	93.13	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.96	gold quality
cerebellar hemisphere	UBERON:0002245	92.90	gold quality
cerebellar cortex	UBERON:0002129	92.81	gold quality
putamen	UBERON:0001874	92.43	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.17	gold quality
oocyte	CL:0000023	92.15	gold quality
adenohypophysis	UBERON:0002196	92.07	gold quality
granulocyte	CL:0000094	91.40	gold quality
neocortex	UBERON:0001950	91.37	gold quality
pituitary gland	UBERON:0000007	91.33	gold quality
Ammon’s horn	UBERON:0001954	91.31	gold quality
frontal cortex	UBERON:0001870	91.24	gold quality
frontal lobe	UBERON:0016525	91.24	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.19	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.98	gold quality
cerebellum	UBERON:0002037	90.96	gold quality
male germ cell	CL:0000015	90.81	gold quality
sperm	CL:0000019	90.77	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.43

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1, TFAP2A

miRNA regulators (miRDB)

60 targeting KCTD13, 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-5692A	100.00	74.40	6850
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-325	99.58	66.55	358
HSA-MIR-3153	99.55	67.59	2337

Literature-anchored findings (GeneRIF, showing 6)

• PDIP1 mRNA was expressed in 3T3-L1 adipocytes and THP-1 macrophages (PMID:16239304)
• data suggest that KCTD13 is a major driver for the neurodevelopmental phenotypes associated with the 16p11.2 copy number variants (CNV), and reinforce the idea that one or a small number of transcripts within a CNV can underpin clinical phenotypes (PMID:22596160)
• Present study explores the role of KCTD13 in the development of SCZ and to provide a more complete picture of the allelic architecture at this risk locus. (PMID:27668412)
• Copy number variations in KCTD13 gene is associated with proximal syndromes with intellectual disability. (PMID:30518945)
• CRISPR/Cas9-mediated Knockout of the Neuropsychiatric Risk Gene KCTD13 Causes Developmental Deficits in Human Cortical Neurons Derived from Induced Pluripotent Stem Cells. (PMID:31402430)
• Gene dosage changes in KCTD13 result in penile and testicular anomalies via diminished androgen receptor function. (PMID:36196997)

Cross-species orthologs

33 orthologs

Organism	Symbol	Gene ID
danio_rerio	kctd13	ENSDARG00000044769
mus_musculus	Kctd13	ENSMUSG00000030685
rattus_norvegicus	Kctd13	ENSRNOG00000020010
drosophila_melanogaster	CG10465	FBGN0033017
caenorhabditis_elegans		WBGENE00008425
caenorhabditis_elegans		WBGENE00008932
caenorhabditis_elegans		WBGENE00011486
caenorhabditis_elegans		WBGENE00011621
caenorhabditis_elegans		WBGENE00015112
caenorhabditis_elegans		WBGENE00015113
caenorhabditis_elegans		WBGENE00015914
caenorhabditis_elegans		WBGENE00016545
caenorhabditis_elegans		WBGENE00016546
caenorhabditis_elegans		WBGENE00016547
caenorhabditis_elegans		WBGENE00016549
caenorhabditis_elegans		WBGENE00016550
caenorhabditis_elegans		WBGENE00017705
caenorhabditis_elegans		WBGENE00017707
caenorhabditis_elegans		WBGENE00017709
caenorhabditis_elegans		WBGENE00017710
caenorhabditis_elegans		WBGENE00019339
caenorhabditis_elegans		WBGENE00019342
caenorhabditis_elegans		WBGENE00022566
caenorhabditis_elegans		WBGENE00022567
caenorhabditis_elegans		WBGENE00022568
caenorhabditis_elegans		WBGENE00022569
caenorhabditis_elegans		WBGENE00022570
caenorhabditis_elegans		WBGENE00022571
caenorhabditis_elegans		WBGENE00022572
caenorhabditis_elegans		WBGENE00022573
caenorhabditis_elegans		WBGENE00022574
caenorhabditis_elegans		WBGENE00022575
caenorhabditis_elegans		WBGENE00044373

Paralogs (2): TNFAIP1 (ENSG00000109079), KCTD10 (ENSG00000110906)

Protein

Protein identifiers

BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 — Q8WZ19 (reviewed: Q8WZ19)

Alternative names: BTB/POZ domain-containing protein KCTD13, Polymerase delta-interacting protein 1, TNFAIP1-like protein

All UniProt accessions (7): Q8WZ19, A0A3B3IS35, A0A3B3IS45, H3BM90, I3L108, I3L1U2, I3L3K4

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for synaptic transmission. The BCR(KCTD13) E3 ubiquitin ligase complex mediates the ubiquitination of RHOA, leading to its degradation by the proteasome Degradation of RHOA regulates the actin cytoskeleton and promotes synaptic transmission.

Subunit / interactions. Homotetramer; forms a two-fold symmetric tetramer in solution. Interacts with CUL3; interaction is direct and forms a 5:5 heterodecamer. Component of the BCR(KCTD13) E3 ubiquitin ligase complex, at least composed of CUL3, KCTD13/BACURD1 and RBX1. Interacts with RHOA; with a preference for RhoA-GDP. Interacts with POLD2 and PCNA. Interacts with SPRTN.

Subcellular location. Nucleus.

Tissue specificity. Expressed in a wide variety of tissues.

Disease relevance. The gene represented in this entry may act as a disease modifier for autism and schizophrenia associated with recurrent deletions and duplications of chromosome 16p11.2 region.

Induction. By TNF and IL6/interleukin-6.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the BACURD family.

RefSeq proteins (2): NP_001397827, NP_849194* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000210	BTB/POZ_dom	Domain
IPR003131	T1-type_BTB	Domain
IPR011333	SKP1/BTB/POZ_sf	Homologous_superfamily
IPR045068	BACURD1-3	Family

Pfam: PF02214

UniProt features (20 total): helix 5, strand 4, turn 2, region of interest 2, sequence conflict 2, chain 1, domain 1, compositionally biased region 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4UIJ	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WZ19-F1	79.96	0.59

Functional residue map

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

Mutagenesis-validated functional residues (1):

Position	Phenotype
84–86	abolishes interaction with cul3 and induces abnormal actin stress fibers.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-9696264	RND3 GTPase cycle
R-HSA-9696270	RND2 GTPase cycle
R-HSA-162582	Signal Transduction
R-HSA-194315	Signaling by Rho GTPases
R-HSA-9012999	RHO GTPase cycle
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 134 (showing top): GOBP_POSITIVE_REGULATION_OF_DNA_REPLICATION, GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, TGCGCANK_UNKNOWN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOMF_GTPASE_BINDING, GOBP_NEGATIVE_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_CELL_CELL_SIGNALING, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEURAL_PRECURSOR_CELL_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_RHO_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_ACTIN_FILAMENT_ORGANIZATION, chr16p11, GATA1_01, GOBP_ACTOMYOSIN_STRUCTURE_ORGANIZATION

GO Biological Process (9): cell migration (GO:0016477), protein ubiquitination (GO:0016567), negative regulation of Rho protein signal transduction (GO:0035024), stress fiber assembly (GO:0043149), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), positive regulation of DNA replication (GO:0045740), positive regulation of synaptic transmission (GO:0050806), protein homooligomerization (GO:0051260), ubiquitin-dependent protein catabolic process (GO:0006511)

GO Molecular Function (5): protein domain specific binding (GO:0019904), small GTPase binding (GO:0031267), identical protein binding (GO:0042802), ubiquitin-protein transferase activity (GO:0004842), protein binding (GO:0005515)

GO Cellular Component (5): nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear body (GO:0016604), Cul3-RING ubiquitin ligase complex (GO:0031463), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
RHO GTPase cycle	2
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Signaling by Rho GTPases	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	2
cellular anatomical structure	2
cell motility	1
protein modification by small protein conjugation	1
Rho protein signal transduction	1
regulation of Rho protein signal transduction	1
negative regulation of small GTPase mediated signal transduction	1
contractile actin filament bundle assembly	1
actomyosin structure organization	1
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
DNA replication	1
regulation of DNA replication	1
positive regulation of DNA metabolic process	1
chemical synaptic transmission	1
positive regulation of cell communication	1
positive regulation of signaling	1
modulation of chemical synaptic transmission	1
protein complex oligomerization	1
protein ubiquitination	1
modification-dependent protein catabolic process	1
GTPase binding	1
ubiquitin-like protein transferase activity	1
binding	1
nuclear lumen	1
cytoplasm	1
nucleoplasm	1
intracellular membraneless organelle	1
cullin-RING ubiquitin ligase complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

776 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KCTD13	POLD2	P49005	829
KCTD13	CUL3	Q13618	819
KCTD13	ASPHD1	Q5U4P2	810
KCTD13	TAOK2	Q9UL54	779
KCTD13	SEZ6L2	Q6UXD5	724
KCTD13	RND2	P52198	720
KCTD13	PPP4C	P33172	710
KCTD13	QPRT	Q15274	704
KCTD13	KIF22	Q14807	688
KCTD13	TRIM25	Q14258	677
KCTD13	DOC2A	Q14183	671
KCTD13	TMEM219	Q86XT9	648
KCTD13	HIRIP3	Q9BW71	643
KCTD13	YPEL3	P61236	643
KCTD13	PAGR1	Q9BTK6	635

IntAct

119 interactions, top by confidence:

A	B	Type	Score
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
KCTD13	TNFAIP1	psi-mi:“MI:0915”(physical association)	0.900
TNFAIP1	KCTD13	psi-mi:“MI:0915”(physical association)	0.900
TNFAIP1	KCTD13	psi-mi:“MI:0914”(association)	0.900
CUL3	KCTD13	psi-mi:“MI:0915”(physical association)	0.870
KCTD13	CUL3	psi-mi:“MI:0915”(physical association)	0.870
KCTD13	CUL3	psi-mi:“MI:0914”(association)	0.870
KCTD13	KCTD10	psi-mi:“MI:0915”(physical association)	0.800
KCTD13	ZMYND19	psi-mi:“MI:0915”(physical association)	0.780
ZMYND19	KCTD13	psi-mi:“MI:0915”(physical association)	0.780
KCTD13	KCTD13	psi-mi:“MI:0915”(physical association)	0.770
KCTD13	KCTD13	psi-mi:“MI:0407”(direct interaction)	0.770
KCTD13	LNX1	psi-mi:“MI:0915”(physical association)	0.740
LNX1	KCTD13	psi-mi:“MI:0915”(physical association)	0.740
KCTD13	ARMC7	psi-mi:“MI:0915”(physical association)	0.670
ARMC7	KCTD13	psi-mi:“MI:0915”(physical association)	0.670
	KCTD13	psi-mi:“MI:0915”(physical association)	0.560
KCTD13		psi-mi:“MI:0915”(physical association)	0.560

BioGRID (113): KCTD13 (Affinity Capture-Western), RHOA (Affinity Capture-Western), KCTD13 (Reconstituted Complex), RHOA (Biochemical Activity), KCTD13 (Two-hybrid), KCTD13 (Two-hybrid), KCTD13 (Two-hybrid), KCTD13 (Two-hybrid), HSPA1L (Affinity Capture-MS), FLNC (Affinity Capture-MS), TNFAIP1 (Affinity Capture-MS), KCTD10 (Affinity Capture-MS), HSPB8 (Affinity Capture-MS), KCTD13 (Two-hybrid), KCTD13 (Two-hybrid)

ESM2 similar proteins: A3KMV1, A4IFA8, A8ID74, A8INQ0, A8JBB2, B4FR29, D3ZKV9, F5A894, O60292, P46062, P97287, Q07820, Q2KIL7, Q2QNS6, Q2T9W0, Q3TQF0, Q4VBF2, Q4VC12, Q53JI9, Q566Q8, Q580W5, Q5E9N0, Q5QD03, Q5XUX0, Q60764, Q69T21, Q6NWH0, Q6P7W2, Q6R2V6, Q6Z690, Q750K9, Q7YRZ9, Q8HYS5, Q8JZP9, Q8N8M0, Q8R4R9, Q8R4S0, Q8TAE6, Q8TBC3, Q8VD62

Diamond homologs: A3KMV1, A4IFB4, A5PKG7, A6H6X4, A9ULR9, B1WC97, B5DEL1, D5SHR0, O70479, P0C5J9, Q03607, Q0VD00, Q0VFV7, Q13829, Q14681, Q28DC9, Q29RJ0, Q2HJ48, Q2T9W0, Q2TUM3, Q3URF8, Q4G0X4, Q50H33, Q54KH0, Q58DF7, Q5DTY9, Q5EAX2, Q5F3E8, Q5M956, Q5RBH4, Q5XJ34, Q5ZJP7, Q68DU8, Q693B1, Q6DC02, Q6DCX3, Q6DG99, Q6DK85, Q6P3P4, Q6P7W2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
CUL3	“up-regulates activity”	KCTD13	binding
KCTD13	“down-regulates quantity”	RHOA	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	24
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
1694809	GRCh37/hg19 16p11.2(chr16:29674300-30200008)x1	Pathogenic
2672674	GRCh37/hg19 16p11.2(chr16:29495010-30212427)x1	Pathogenic
545198	Single allele	Pathogenic
223115	NC_000016.10:g.(?29390980)(30215610_?)dup	Likely pathogenic

SpliceAI

1100 predictions. Top by Δscore:

Variant	Effect	Δscore
16:29910972:TCTGA:T	donor_loss	1.0000
16:29910973:CTGAC:C	donor_loss	1.0000
16:29910974:TGAC:T	donor_loss	1.0000
16:29910975:GACCT:G	donor_loss	1.0000
16:29910976:ACCT:A	donor_loss	1.0000
16:29910977:C:T	donor_loss	1.0000
16:29911182:C:CT	acceptor_gain	1.0000
16:29911183:A:T	acceptor_gain	1.0000
16:29911864:CGGG:C	acceptor_gain	1.0000
16:29911868:C:CC	acceptor_gain	1.0000
16:29911954:CCTCA:C	donor_loss	1.0000
16:29911955:CTCA:C	donor_loss	1.0000
16:29911956:TCACC:T	donor_loss	1.0000
16:29911957:CACCT:C	donor_loss	1.0000
16:29911958:ACCT:A	donor_loss	1.0000
16:29911959:C:CA	donor_loss	1.0000
16:29912045:TTTTG:T	acceptor_gain	1.0000
16:29912046:TTTG:T	acceptor_gain	1.0000
16:29912047:TTG:T	acceptor_gain	1.0000
16:29912050:C:CA	acceptor_loss	1.0000
16:29912050:C:CC	acceptor_gain	1.0000
16:29925786:GTAC:G	donor_loss	1.0000
16:29925787:TA:T	donor_loss	1.0000
16:29925788:ACCT:A	donor_gain	1.0000
16:29925789:CCT:C	donor_gain	1.0000
16:29925789:CCTC:C	donor_gain	1.0000
16:29925791:T:TA	donor_gain	1.0000
16:29911171:GTG:G	acceptor_gain	0.9900
16:29911172:TG:T	acceptor_gain	0.9900
16:29911173:GCTGG:G	acceptor_loss	0.9900

AlphaMissense

2108 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:29907071:A:G	L264P	1.000
16:29907086:A:C	I259S	1.000
16:29907086:A:G	I259T	1.000
16:29907086:A:T	I259N	1.000
16:29907098:G:T	P255Q	1.000
16:29907100:A:C	F254L	1.000
16:29907100:A:T	F254L	1.000
16:29907102:A:G	F254L	1.000
16:29910978:C:A	K251N	1.000
16:29910978:C:G	K251N	1.000
16:29910987:C:A	K248N	1.000
16:29910987:C:G	K248N	1.000
16:29910989:T:C	K248E	1.000
16:29911004:A:C	Y243D	1.000
16:29911004:A:G	Y243H	1.000
16:29911009:A:C	I241S	1.000
16:29911009:A:G	I241T	1.000
16:29911009:A:T	I241N	1.000
16:29911013:A:G	S240P	1.000
16:29911017:G:C	C238W	1.000
16:29911018:C:T	C238Y	1.000
16:29911019:A:G	C238R	1.000
16:29911053:G:C	F226L	1.000
16:29911053:G:T	F226L	1.000
16:29911054:A:G	F226S	1.000
16:29911055:A:G	F226L	1.000
16:29911059:C:A	W224C	1.000
16:29911059:C:G	W224C	1.000
16:29911060:C:G	W224S	1.000
16:29911061:A:G	W224R	1.000

dbSNP variants (sampled 300 via entrez): RS1000097510 (16:29924311 T>A), RS1000236584 (16:29910828 G>C,T), RS1000326983 (16:29923010 G>A,C), RS1000588711 (16:29910486 T>C,G), RS1000934046 (16:29921574 C>T), RS1001060721 (16:29927507 C>G,T), RS1001082253 (16:29925608 A>G), RS1001263469 (16:29917513 G>A), RS1001388011 (16:29921741 G>A), RS1001495163 (16:29923749 G>A,C,T), RS1001512316 (16:29925998 C>A,T), RS1001612164 (16:29912334 C>T), RS1001614493 (16:29924861 G>A), RS1001839537 (16:29923586 G>A,C), RS1002015002 (16:29907221 T>C)

Disease associations

OMIM: gene MIM:608947 | disease phenotypes: MIM:209850

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder	Limited	Autosomal dominant

Mondo (3): autism spectrum disorder (MONDO:0005258), autism (MONDO:0005260), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000717	Autism

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST002539_82	Schizophrenia	5.000000e-11
GCST002541_107	Menarche (age at onset)	2.000000e-09
GCST004521_236	Autism spectrum disorder or schizophrenia	4.000000e-10
GCST004946_142	Schizophrenia	8.000000e-13
GCST005830_122	Hand grip strength	6.000000e-10
GCST006803_23	Schizophrenia	6.000000e-13
GCST007201_169	Schizophrenia	2.000000e-10
GCST007293_15	Body fat distribution (arm fat ratio)	6.000000e-06
GCST007293_81	Body fat distribution (arm fat ratio)	4.000000e-08
GCST008647_34	Urinary sodium excretion	4.000000e-10
GCST009600_79	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	4.000000e-11
GCST010703_269	Brain morphology (MOSTest)	4.000000e-13

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0006941	grip strength measurement
EFO:0004341	body fat distribution
EFO:0009282	sodium measurement
EFO:0004346	neuroimaging measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression	3
sodium arsenite	increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
Particulate Matter	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
ferrous chloride	increases expression	1
nickel sulfate	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
abrine	increases expression	1
(+)-JQ1 compound	increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Estradiol	increases expression	1
Hydrogen Peroxide	affects expression	1
Quercetin	increases expression	1
Silicon Dioxide	increases expression	1
Urethane	increases expression	1
Valproic Acid	affects expression	1
Cyclosporine	increases expression	1
Uranium Compounds	increases expression	1

Cellosaurus cell lines

4 cell lines: 2 induced pluripotent stem cell, 2 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_E4WB	KOLF2.1J KCTD13 PTC PTC/WT	Induced pluripotent stem cell	Male
CVCL_E4WC	KOLF2.1J KCTD13 PTC PTC/PTC	Induced pluripotent stem cell	Male
CVCL_UB74	AI09e-KCTD13a	Embryonic stem cell	Male
CVCL_UB75	AI10e-KCTD13b	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT01302964	PHASE3	COMPLETED	Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523	PHASE3	TERMINATED	Open Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798	PHASE3	COMPLETED	Treatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074	PHASE3	COMPLETED	Behavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749	PHASE3	COMPLETED	A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922	PHASE3	COMPLETED	Treatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917	PHASE3	TERMINATED	A Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875	PHASE3	TERMINATED	Memantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156	PHASE3	COMPLETED	Modulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502	PHASE3	WITHDRAWN	Efficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756	PHASE3	COMPLETED	Open-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder