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 ... See more...

Aliases for KCTD3 Gene

Aliases for KCTD3 Gene

  • Potassium Channel Tetramerization Domain Containing 3 2 3 5
  • Potassium Channel Tetramerisation Domain Containing 3 2 3
  • BTB/POZ Domain-Containing Protein KCTD3 3 4
  • Renal Carcinoma Antigen NY-REN-45 3 4
  • NY-REN-45 2 3
  • NY-REN-45 Antigen 3
  • KCTD3 5

External Ids for KCTD3 Gene

Previous GeneCards Identifiers for KCTD3 Gene

  • GC01P212357
  • GC01P212797
  • GC01P212129
  • GC01P213807
  • GC01P215740
  • GC01P186414

Summaries for KCTD3 Gene

Entrez Gene Summary for KCTD3 Gene

  • 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]

GeneCards Summary for KCTD3 Gene

KCTD3 (Potassium Channel Tetramerization Domain Containing 3) is a Protein Coding gene. Diseases associated with KCTD3 include Variegate Porphyria and Niemann-Pick Disease, Type C2. Among its related pathways are Sweet Taste Signaling and Hepatic ABC Transporters. An important paralog of this gene is SHKBP1.

UniProtKB/Swiss-Prot Summary for KCTD3 Gene

  • Accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) upregulating its cell-surface expression and current density without affecting its voltage dependence and kinetics.

Additional gene information for KCTD3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for KCTD3 Gene

Genomics for KCTD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for KCTD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J215565 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 602.3 +1.9 1892 7 HNRNPL CREB1 GATAD2A TEAD4 PRDM10 ZNF629 ZNF512 LEF1 IKZF1 NFKBIZ KCTD3 LOC105372919 lnc-USH2A-1 NONHSAG004278.2 USH2A
GH01J214566 Enhancer 1.1 Ensembl ENCODE dbSUPER 9.9 -996.8 -996768 10.5 ATF7 PRDM10 FOXA1 PRDM1 ZSCAN4 IKZF2 ZNF600 ZNF341 ZNF37A SCRT2 CENPF KCTD3 PTPN14 lnc-PTPN14-4
GH01J215599 Enhancer 0.6 Ensembl 17 +32.6 32597 1.4 TCF7L2 ZXDB OSR2 NFIC ZNF335 ZNF513 ZNF18 ZNF843 FEZF1 PRDM6 KCTD3 NONHSAG004278.2 lnc-USH2A-1 USH2A
GH01J215542 Enhancer 0.8 Ensembl ENCODE 11.5 -24.1 -24107 1.4 CEBPG IKZF2 SP1 CEBPA CEBPB YY1 JUND NR2F2 SPI1 HNF4A KCTD3 piR-37170-009 KCNK2
GH01J215523 Enhancer 0.7 Ensembl ENCODE 11.1 -43.6 -43593 1.4 CTCF RAD21 CUX1 CSDE1 HNF4A TOE1 GATAD2B KCTD3 piR-37170-009 KCNK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KCTD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KCTD3

Top Transcription factor binding sites by QIAGEN in the KCTD3 gene promoter:
  • AREB6
  • c-Myc
  • CUTL1
  • E47
  • FOXI1
  • Hand1
  • HFH-3
  • Max
  • MZF-1
  • YY1

Genomic Locations for KCTD3 Gene

Genomic Locations for KCTD3 Gene
chr1:215,567,304-215,621,807
(GRCh38/hg38)
Size:
54,504 bases
Orientation:
Plus strand
chr1:215,740,735-215,795,149
(GRCh37/hg19)
Size:
54,415 bases
Orientation:
Plus strand

Genomic View for KCTD3 Gene

Genes around KCTD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KCTD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KCTD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KCTD3 Gene

Proteins for KCTD3 Gene

  • Protein details for KCTD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y597-KCTD3_HUMAN
    Recommended name:
    BTB/POZ domain-containing protein KCTD3
    Protein Accession:
    Q9Y597
    Secondary Accessions:
    • A0AV15
    • D3DTA6
    • Q49AG7
    • Q504Q9
    • Q6PJN6
    • Q8ND58
    • Q8NDJ0
    • Q8WX16

    Protein attributes for KCTD3 Gene

    Size:
    815 amino acids
    Molecular mass:
    88984 Da
    Quaternary structure:
    • Interacts with HCN3.
    SequenceCaution:
    • Sequence=AAH13868.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
    Miscellaneous:
    • Reacts with sera from 5-25 per cent of cancer patients but not with sera from normal donors. Seventy per cent of renal cancer patients have antibodies against one or a panel of these antigens.

    Alternative splice isoforms for KCTD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KCTD3 Gene

Post-translational modifications for KCTD3 Gene

  • Ubiquitination at Lys503 and Lys510
  • Modification sites at PhosphoSitePlus

Other Protein References for KCTD3 Gene

No data available for DME Specific Peptides for KCTD3 Gene

Domains & Families for KCTD3 Gene

Gene Families for KCTD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for KCTD3 Gene

Suggested Antigen Peptide Sequences for KCTD3 Gene

GenScript: Design optimal peptide antigens:
  • Renal carcinoma antigen NY-REN-45 (KCTD3_HUMAN)
  • Potassium channel tetramerisation domain containing 3 (Q5VWQ3_HUMAN)
  • Potassium channel tetramerisation domain containing 3 (Q5VWQ4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y597

UniProtKB/Swiss-Prot:

KCTD3_HUMAN :
  • Belongs to the KCTD3 family.
Family:
  • Belongs to the KCTD3 family.
genes like me logo Genes that share domains with KCTD3: view

Function for KCTD3 Gene

Molecular function for KCTD3 Gene

UniProtKB/Swiss-Prot Function:
Accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) upregulating its cell-surface expression and current density without affecting its voltage dependence and kinetics.

Phenotypes From GWAS Catalog for KCTD3 Gene

Gene Ontology (GO) - Molecular Function for KCTD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with KCTD3: view
genes like me logo Genes that share phenotypes with KCTD3: view

Animal Model Products

CRISPR Products

miRNA for KCTD3 Gene

miRTarBase miRNAs that target KCTD3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KCTD3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for KCTD3 Gene

Localization for KCTD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for KCTD3 Gene

Cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KCTD3 gene
Compartment Confidence
plasma membrane 4
cytosol 3
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for KCTD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with KCTD3: view

Pathways & Interactions for KCTD3 Gene

PathCards logo

SuperPathways for KCTD3 Gene

SuperPathway Contained pathways
1 Sweet Taste Signaling
.72
.72
.46
.44
.37
2 Activation of cAMP-Dependent PKA
.77
.77
.56
3 Neuropathic Pain-Signaling in Dorsal Horn Neurons
.47
.47
.40
4 Hepatic ABC Transporters
.41
.41
genes like me logo Genes that share pathways with KCTD3: view

Pathways by source for KCTD3 Gene

13 Qiagen pathways for KCTD3 Gene
  • Activation of cAMP-Dependent PKA
  • Aldosterone Signaling in Epithelial Cells
  • Bitter Taste Signaling
  • cAMP Pathway
  • Cellular Effects of Sildenafil

Gene Ontology (GO) - Biological Process for KCTD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051260 protein homooligomerization IEA --
genes like me logo Genes that share ontologies with KCTD3: view

No data available for SIGNOR curated interactions for KCTD3 Gene

Drugs & Compounds for KCTD3 Gene

No Compound Related Data Available

Transcripts for KCTD3 Gene

mRNA/cDNA for KCTD3 Gene

3 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KCTD3

Alternative Splicing Database (ASD) splice patterns (SP) for KCTD3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b · 14c ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ·
SP1: - -
SP2: - -
SP3: - - - -
SP4: - -
SP5:
SP6:

ExUns: 18c · 18d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for KCTD3 Gene

GeneLoc Exon Structure for
KCTD3

Expression for KCTD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for KCTD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KCTD3 Gene

This gene is overexpressed in Lung (62.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for KCTD3 Gene



Protein tissue co-expression partners for KCTD3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KCTD3

SOURCE GeneReport for Unigene cluster for KCTD3 Gene:

Hs.335139

mRNA Expression by UniProt/SwissProt for KCTD3 Gene:

Q9Y597-KCTD3_HUMAN
Tissue specificity: Broadly expressed in normal tissues.

Evidence on tissue expression from TISSUES for KCTD3 Gene

  • Nervous system(4.7)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with KCTD3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for KCTD3 Gene

Orthologs for KCTD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for KCTD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia KCTD3 30 31
  • 99.71 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia KCTD3 31
  • 92 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia KCTD3 30 31
  • 91.66 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia KCTD3 30 31
  • 91.38 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia KCTD3 31
  • 88 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Kctd3 30 17 31
  • 83.91 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Kctd3 30
  • 83.13 (n)
Chicken
(Gallus gallus)
Aves KCTD3 30 31
  • 78.18 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia KCTD3 31
  • 86 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia kctd3 30
  • 74.12 (n)
Zebrafish
(Danio rerio)
Actinopterygii kctd3 30 31
  • 68.58 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004087 30
  • 60.2 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG9467 30 31
  • 55.54 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea T23B12.6 30 31
  • 55.33 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 65 (a)
OneToMany
Species where no ortholog for KCTD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for KCTD3 Gene

ENSEMBL:
Gene Tree for KCTD3 (if available)
TreeFam:
Gene Tree for KCTD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KCTD3: view image

Paralogs for KCTD3 Gene

Paralogs for KCTD3 Gene

(3) SIMAP similar genes for KCTD3 Gene using alignment to 4 proteins:

  • KCTD3_HUMAN
  • H0Y566_HUMAN
  • H0Y5P8_HUMAN
  • L0R4Z3_HUMAN
genes like me logo Genes that share paralogs with KCTD3: view

Variants for KCTD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KCTD3 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
712896 Benign: not provided 215,620,510(+) C/T SYNONYMOUS_VARIANT
780092 Likely Benign: not provided 215,573,778(+) A/G INTRON_VARIANT
782801 Benign: not provided 215,620,593(+) C/A MISSENSE_VARIANT
rs1558228402 Uncertain Significance: not specified 215,575,952(+) CG/C FRAMESHIFT_VARIANT,FIVE_PRIME_UTR_VARIANT
rs730882243 Likely Pathogenic: Seizures; Congenital cerebellar hypoplasia; Severe global developmental delay 215,602,098(+) CCCCTTGCGAATGAAA FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for KCTD3 Gene

Variation tolerance for KCTD3 Gene

Residual Variation Intolerance Score: 8.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.02; 84.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KCTD3 Gene

Human Gene Mutation Database (HGMD)
KCTD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KCTD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for KCTD3 Gene

Disorders for KCTD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for KCTD3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
variegate porphyria
  • vp
niemann-pick disease, type c2
  • npc2
- elite association - COSMIC cancer census association via MalaCards
Search KCTD3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with KCTD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KCTD3 Gene

Publications for KCTD3 Gene

  1. Antigens recognized by autologous antibody in patients with renal-cell carcinoma. (PMID: 10508479) Scanlan MJ … Old LJ (International journal of cancer 1999) 2 3 4
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3
  5. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. (PMID: 29509190) Giurato G … Tarallo R (Scientific data 2018) 3

Products for KCTD3 Gene

Sources for KCTD3 Gene