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

Gene ID: 253980, updated on 5-Mar-2024

Summary

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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, Apr 2022]
Expression
Broad expression in testis (RPKM 12.8), brain (RPKM 4.9) and 23 other tissues See more
Orthologs
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Genomic context

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See KCTD13 in Genome Data Viewer
Location:
16p11.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29906339..29926226, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30188975..30208863, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29917660..29937547, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29874668-29875205 Neighboring gene CDIP transferase opposite strand, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:29889007-29889508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:29889509-29890008 Neighboring gene seizure related 6 homolog like 2 Neighboring gene Sharpr-MPRA regulatory region 6067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29912830-29913534 Neighboring gene aspartate beta-hydroxylase domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7344 Neighboring gene KCTD13 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7345 Neighboring gene transmembrane protein 219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7346 Neighboring gene uncharacterized LOC124903762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29985672-29986443 Neighboring gene TAO kinase 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. CRISPR/Cas9-mediated Knockout of the Neuropsychiatric Risk Gene KCTD13 Causes Developmental Deficits in Human Cortical Neurons Derived from Induced Pluripotent Stem Cells. Kizner V, et al. Mol Neurobiol, 2020 Feb. PMID 31402430
  2. Identification of rare variants in KCTD13 at the schizophrenia risk locus 16p11.2. Degenhardt F, et al. Psychiatr Genet, 2016 Dec. PMID 27668412, Free PMC Article
  3. The effect of copy number variations in chromosome 16p on body weight in patients with intellectual disability. Gimeno-Ferrer F, et al. J Hum Genet, 2019 Mar. PMID 30518945
  4. KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Golzio C, et al. Nature, 2012 May 16. PMID 22596160, Free PMC Article
  5. A tumor necrosis factor alpha- and interleukin 6-inducible protein that interacts with the small subunit of DNA polymerase delta and proliferating cell nuclear antigen. He H, et al. Proc Natl Acad Sci U S A, 2001 Oct 9. PMID 11593007, Free PMC Article

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Gene dosage changes in KCTD13 result in penile and testicular anomalies via diminished androgen receptor function.
    Title: Gene dosage changes in KCTD13 result in penile and testicular anomalies via diminished androgen receptor function.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
Submit: New GeneRIF Correction

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
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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
  
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
  
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 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
  
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
  
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
  
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)

  1. NM_001410898.1 → NP_001397827.1  BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC120114, KF459558
    Consensus CDS
    CCDS92133.1
    UniProtKB/TrEMBL
    A0A3B3IS45
    Related
    ENSP00000497126.1, ENST00000567795.3

  2. NM_178863.5 → NP_849194.1  BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform 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
    A8K0R5, Q8WZ19, Q96P93, Q96SA1
    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

  1. 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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    29906339..29926226 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545783.4 → 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

RNA

  1. XR_007064863.1 RNA Sequence

  2. XR_950767.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    30188975..30208863 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379993.1 → XP_054235968.1  BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X1

  2. XM_054379994.1 → XP_054235969.1  BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 isoform X2

RNA

  1. XR_008489071.1 RNA Sequence

  2. XR_008489070.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WZ19.1 GenPept UniProtKB/Swiss-Prot:Q8WZ19

Gene LinkOut

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