KCTD13 potassium channel tetramerization domain containing 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: KCTD13provided by HGNC
Official Full Name: potassium channel tetramerization domain containing 13provided by HGNC
Primary source: HGNC:HGNC:22234
See related: Ensembl:ENSG00000174943 MIM:608947; AllianceGenome:HGNC:22234
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDIP1; FKSG86; BACURD1; POLDIP1; hBACURD1
Summary: Enables identical protein binding activity and small GTPase binding activity. Contributes to ubiquitin-protein transferase activity. Involved in several processes, including cellular protein metabolic process; negative regulation of Rho protein signal transduction; and stress fiber assembly. Located in nuclear body. Part of Cul3-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Nov 2021]
Expression: Broad expression in testis (RPKM 12.8), brain (RPKM 4.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p11.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
109.20211119	current	GRCh38.p13 (GCF_000001405.39)	16	NC_000016.10 (29906335..29926226, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (29917660..29937547, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CRISPR/Cas9-mediated Knockout of the Neuropsychiatric Risk Gene KCTD13 Causes Developmental Deficits in Human Cortical Neurons Derived from Induced Pluripotent Stem Cells.
Title: CRISPR/Cas9-mediated Knockout of the Neuropsychiatric Risk Gene KCTD13 Causes Developmental Deficits in Human Cortical Neurons Derived from Induced Pluripotent Stem Cells.
Copy number variations in KCTD13 gene is associated with proximal syndromes with intellectual disability.
Title: The effect of copy number variations in chromosome 16p on body weight in patients with intellectual disability.
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.
Title: Identification of rare variants in KCTD13 at the schizophrenia risk locus 16p11.2.
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
Title: KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant.
PDIP1 mRNA was expressed in 3T3-L1 adipocytes and THP-1 macrophages
Title: Isolation and characterization of a transcriptional cofactor and its novel isoform that bind the deoxyribonucleic acid-binding domain of peroxisome proliferator-activated receptor-gamma.

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Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
integrase	gag-pol	Analysis of HIV-1 proviral integration sites in antiretroviral treatment patients indicates that KCTD13 gene favors HIV-1 integration for expansion and persistence of infected cells, suggesting HIV-1 IN interacts with KCTD13	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102436 (e-PCR)
- UniSTS:96770

RH78940 (e-PCR)
- UniSTS:84495

D16S2638 (e-PCR)
- UniSTS:70972

D16S425E (e-PCR)
- UniSTS:147536

RH67291 (e-PCR)
- UniSTS:85337

D16S425E (e-PCR)
- UniSTS:19059

G32595 (e-PCR)
- UniSTS:117178

G32600 (e-PCR)
- UniSTS:117183

RH67286 (e-PCR)
- UniSTS:87499

Homology

Homologs of the KCTD13 gene: The KCTD13 gene is conserved in chimpanzee, dog, cow, mouse, rat, and zebrafish.
Orthologs from Annotation Pipeline: 205 organisms have orthologs with human gene KCTD13
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables small GTPase binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to ubiquitin-protein transferase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
contributes_to ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of Rho protein signal transduction	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of Rho protein signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of Rho protein signal transduction	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in neural precursor cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA replication	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein homooligomerization	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Cul3-RING ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of Cul3-RING ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1

Names: BTB/POZ domain-containing protein KCTD13; CTD-2574D22.4; TNFAIP1-like protein; polymerase delta-interacting protein 1; potassium channel tetramerisation domain containing 13

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

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

mRNA and Protein(s)

NM_178863.5 → NP_849194.1 BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1

See identical proteins and their annotated locations for NP_849194.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the supported protein.

Source sequence(s)

AF289573, BC036228, BI553707

Consensus CDS

CCDS10661.1

UniProtKB/Swiss-Prot

Q8WZ19

Related

ENSP00000455785.1, ENST00000568000.6

Conserved Domains (1) summary

cd18400
Location:40 → 142

BTB_POZ_KCTD13_BACURD1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 13 (KCTD13)

RNA

NR_110933.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses alternate splice sites in two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF289573, AK097407, BC036228, BI553707

Related

ENST00000566842.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p13 Primary Assembly

Range

29906335..29926226 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011545783.3 → XP_011544085.1 BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X1

Conserved Domains (2) summary

smart00225
Location:42 → 137

BTB; Broad-Complex, Tramtrack and Bric a brac

cl02518
Location:43 → 133

BTB; BTB/POZ domain
XM_017023104.2 → XP_016878593.1 BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X3
XM_011545784.3 → XP_011544086.1 BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X2
XM_017023105.2 → XP_016878594.1 BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X4
XM_017023106.2 → XP_016878595.1 BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X5

Related

ENSP00000497126.1, ENST00000567795.3