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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

Gene LinkOut

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