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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
    mouse all
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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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