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    KCTD3 potassium channel tetramerization domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 51133, updated on 27-Nov-2024

    Summary

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    Official Symbol
    KCTD3provided by HGNC
    Official Full Name
    potassium channel tetramerization domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:21305
    See related
    Ensembl:ENSG00000136636 MIM:613272; AllianceGenome:HGNC:21305
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NY-REN-45
    Summary
    This gene encodes a member of the potassium channel tetramerization-domain containing (KCTD) protein family. Members of this protein family regulate the biophysical characteristics of ion channels. In mouse, this protein interacts with hyperpolarization-activated cyclic nucleotide-gated channel complex 3 and enhances its cell surface expression and current density. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in adrenal (RPKM 47.4), small intestine (RPKM 24.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KCTD3 in Genome Data Viewer
    Location:
    1q41
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (215567304..215621807)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (214807705..214862209)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (215740647..215795149)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:215588487-215589150 Neighboring gene uncharacterized LOC124904598 Neighboring gene voltage dependent anion channel 1 pseudogene 10 Neighboring gene MPRA-validated peak693 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:215677085-215677330 Neighboring gene uncharacterized LOC124904599 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:215740861-215741721 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:215756646-215757845 Neighboring gene MPRA-validated peak696 silencer Neighboring gene small nucleolar RNA SNORD116 Neighboring gene usherin Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4139 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:216230868-216232067 Neighboring gene USH2A antisense RNA 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. Phenotypic characterization of KCTD3-related developmental epileptic encephalopathy. Faqeih EA, et al. Clin Genet, 2018 May. PMID 29406573
    2. Disruption of CNTNAP2 and additional structural genome changes in a boy with speech delay and autism spectrum disorder. Poot M, et al. Neurogenetics, 2010 Feb. PMID 19582487
    3. Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Alazami AM, et al. Cell Rep, 2015 Jan 13. PMID 25558065
    4. Up-regulation of hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) by specific interaction with K+ channel tetramerization domain-containing protein 3 (KCTD3). Cao-Ehlker X, et al. J Biol Chem, 2013 Mar 15. PMID 23382386, Free PMC Article
    5. Proximity Labeling Reveals Spatial Regulation of the Anaphase-Promoting Complex/Cyclosome by a Microtubule Adaptor. Cao X, et al. ACS Chem Biol, 2022 Sep 16. PMID 35952650, Free PMC Article

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. this largest series to date on KCTD3-mutated patients, we show that biallelic loss of function mutations in KCTD3 lead to a consistent phenotype of developmental epileptic encephalopathy and abnormal cerebellum on brain imaging.
      Title: Phenotypic characterization of KCTD3-related developmental epileptic encephalopathy.
    2. KCTD3 is an accessory subunit of native HCN3 complexes
      Title: Up-regulation of hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) by specific interaction with K+ channel tetramerization domain-containing protein 3 (KCTD3).
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC43935

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in protein homooligomerization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    BTB/POZ domain-containing protein KCTD3
    Names
    NY-REN-45 antigen
    potassium channel tetramerisation domain containing 3
    renal carcinoma antigen NY-REN-45

    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.

    Genomic

    1. NG_047148.1 RefSeqGene

      Range
      5120..59623
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001319294.2 → NP_001306223.1  BTB/POZ domain-containing protein KCTD3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AL365315, BC094879, BC143963, CK902987, HY029594
      UniProtKB/Swiss-Prot
      Q9Y597
      Conserved Domains (1) summary
      cd18393
      Location:17 → 119
      BTB_POZ_SHKBP1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in SH3KBP1-binding protein 1 (SHKBP1)

    2. NM_001319295.2 → NP_001306224.1  BTB/POZ domain-containing protein KCTD3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform 3, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL365315, BC094879, BC143963, CK902987, HY029594
      UniProtKB/Swiss-Prot
      Q9Y597

    3. NM_016121.5 → NP_057205.2  BTB/POZ domain-containing protein KCTD3 isoform 1

      See identical proteins and their annotated locations for NP_057205.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL365315, BC094879, BC117188, CK902987, HY029594
      Consensus CDS
      CCDS1515.1
      UniProtKB/Swiss-Prot
      A0AV15, D3DTA6, Q49AG7, Q504Q9, Q6PJN6, Q8ND58, Q8NDJ0, Q8WX16, Q9Y597
      Related
      ENSP00000259154.2, ENST00000259154.9
      Conserved Domains (1) summary
      cd18393
      Location:17 → 119
      BTB_POZ_SHKBP1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in SH3KBP1-binding protein 1 (SHKBP1)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      215567304..215621807
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422104.1 → XP_047278060.1  BTB/POZ domain-containing protein KCTD3 isoform X2

      UniProtKB/TrEMBL
      B4DJX2

    2. XM_005273158.3 → XP_005273215.1  BTB/POZ domain-containing protein KCTD3 isoform X1

      See identical proteins and their annotated locations for XP_005273215.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      214807705..214862209
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336903.1 → XP_054192878.1  BTB/POZ domain-containing protein KCTD3 isoform X2

      UniProtKB/TrEMBL
      B4DJX2

    2. XM_054336902.1 → XP_054192877.1  BTB/POZ domain-containing protein KCTD3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y597.2 GenPept UniProtKB/Swiss-Prot:Q9Y597

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