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KCTD1 Gene(Protein Coding)

Potassium Channel Tetramerization Domain Containing 1

GCID:
GC18M026454
GIFtS:
48
Genes Participants
UDN Logo

Aliases for KCTD1 Gene

Aliases for KCTD1 Gene

  • Potassium Channel Tetramerization Domain Containing 1 2 3 5
  • C18orf5 3 4
  • Potassium Channel Tetramerization Domain-Containing Protein 1 4
  • Potassium Channel Tetramerisation Domain Containing 1 2
  • BTB/POZ Domain-Containing Protein KCTD1 3

External Ids for KCTD1 Gene

Previous HGNC Symbols for KCTD1 Gene

  • C18orf5

Previous GeneCards Identifiers for KCTD1 Gene

  • GC18U990074
  • GC18M022286
  • GC18M022288
  • GC18M024034
  • GC18M020884

Summaries for KCTD1 Gene

Entrez Gene Summary for KCTD1 Gene

  • This gene encodes a protein containing a BTB (Broad-complex, tramtrack and bric a brac), also known as a POZ (POxvirus and zinc finger) protein-protein interaction domain. The encoded protein negatively regulates the AP-2 family of transcription factors and the Wnt signaling pathway. A mechanism for the modulation of Wnt signaling has been proposed in which the encoded protein enhances ubiquitination and degradation of the beta-catenin protein. Mutations in this gene have been identified in Scalp-ear-nipple (SEN) syndrome. [provided by RefSeq, May 2017]

GeneCards Summary for KCTD1 Gene

KCTD1 (Potassium Channel Tetramerization Domain Containing 1) is a Protein Coding gene. Diseases associated with KCTD1 include Scalp-Ear-Nipple Syndrome and Subependymal Glioma. Among its related pathways are Gene Expression and Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors. Gene Ontology (GO) annotations related to this gene include transcription factor binding and transcription corepressor activity. An important paralog of this gene is KCTD15.

UniProtKB/Swiss-Prot for KCTD1 Gene

  • May repress the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C to various extent.

Additional gene information for KCTD1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KCTD1 Gene

Genomics for KCTD1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for KCTD1 Gene

Promoters and enhancers for KCTD1 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
GH18I026655 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.5 541 2.6 ZSCAN4 MZF1 ZNF76 SIN3A ZNF48 YY1 ZNF335 SP3 ZBTB11 ZNF398 KCTD1 AQP4-AS1 PCAT18 LOC102725227
GH18I026545 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 550.1 +109.2 109168 6.1 CLOCK FOXA2 SIN3A ZNF2 IRF4 YY1 GLIS2 ZNF207 ZNF143 KLF13 KCTD1 ENSG00000277534 GC18P026566
GH18I026640 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.4 +17.1 17136 0.1 KCTD1 LOC102725227 CIAPIN1P
GH18I026599 Promoter 0.5 EPDnew 561.4 +58.1 58062 0.1 KCTD1 CIAPIN1P LOC102725227
GH18I026744 Enhancer 1 Ensembl ENCODE 14.6 -89.3 -89258 3.5 FOXA2 YY1 ZNF335 ZNF366 FOS RCOR1 RXRA USF2 CEBPB REST PCAT18 KCTD1 AQP4-AS1 GC18P026799
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KCTD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KCTD1 gene promoter:

Genomic Locations for KCTD1 Gene

Genomic Locations for KCTD1 Gene
chr18:26,454,910-26,657,401
(GRCh38/hg38)
Size:
202,492 bases
Orientation:
Minus strand
chr18:24,034,874-24,237,365
(GRCh37/hg19)

Genomic View for KCTD1 Gene

Genes around KCTD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KCTD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KCTD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for KCTD1 Gene

Proteins for KCTD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for KCTD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q719H9-KCTD1_HUMAN
    Recommended name:
    BTB/POZ domain-containing protein KCTD1
    Protein Accession:
    Q719H9
    Secondary Accessions:
    • A8K1F5

    Protein attributes for KCTD1 Gene

    Size:
    257 amino acids
    Molecular mass:
    29405 Da
    Quaternary structure:
    • Can form homodimers. Interacts with TFAP2A, TFAP2B and TFAP2C via the BTB domain.

    Three dimensional structures from OCA and Proteopedia for KCTD1 Gene

neXtProt entry for KCTD1 Gene

Protein Expression for KCTD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for KCTD1 Gene

Other Protein References for KCTD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KCTD1 Gene

Domains & Families for KCTD1 Gene

Gene Families for KCTD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for KCTD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for KCTD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with KCTD1: view

No data available for UniProtKB/Swiss-Prot for KCTD1 Gene

Function for KCTD1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for KCTD1 Gene

UniProtKB/Swiss-Prot Function:
May repress the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C to various extent.

Phenotypes From GWAS Catalog for KCTD1 Gene

Gene Ontology (GO) - Molecular Function for KCTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity IDA 19115315
GO:0005515 protein binding IPI 25416956
GO:0008134 transcription factor binding IPI 19115315
GO:0042802 identical protein binding IPI 25416956
genes like me logo Genes that share ontologies with KCTD1: view

Phenotypes for KCTD1 Gene

GenomeRNAi human phenotypes for KCTD1:
genes like me logo Genes that share phenotypes with KCTD1: view

Human Phenotype Ontology for KCTD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for KCTD1

miRNA for KCTD1 Gene

miRTarBase miRNAs that target KCTD1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for KCTD1 Gene

Localization for KCTD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for KCTD1 Gene

Nucleus.

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 KCTD1 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 1

Gene Ontology (GO) - Cellular Components for KCTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 19115315
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KCTD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for KCTD1 Gene

Pathways & Interactions for KCTD1 Gene

genes like me logo Genes that share pathways with KCTD1: view

Gene Ontology (GO) - Biological Process for KCTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0045892 negative regulation of transcription, DNA-templated IDA 19115315
GO:0051260 protein homooligomerization IEA --
genes like me logo Genes that share ontologies with KCTD1: view

No data available for SIGNOR curated interactions for KCTD1 Gene

Drugs & Compounds for KCTD1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for KCTD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for KCTD1 Gene

(7) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(122) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for KCTD1 Gene

Potassium channel tetramerisation domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for KCTD1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b
SP1: - - - - - - -
SP2: - - - - -
SP3: -
SP4: - - - -
SP5: -
SP6: - - - -
SP7: -

Relevant External Links for KCTD1 Gene

GeneLoc Exon Structure for
KCTD1
ECgene alternative splicing isoforms for
KCTD1

Expression for KCTD1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KCTD1 Gene

mRNA expression in normal human tissues for KCTD1 Gene
mRNA expression by GTEx for KCTD1 GenemRNA expression by BioGPS for KCTD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KCTD1 Gene

This gene is overexpressed in Placenta (37.9) and Fetal Brain (31.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KCTD1 Gene



Protein tissue co-expression partners for KCTD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of KCTD1 Gene:

KCTD1

SOURCE GeneReport for Unigene cluster for KCTD1 Gene:

Hs.526630

mRNA Expression by UniProt/SwissProt for KCTD1 Gene:

Q719H9-KCTD1_HUMAN
Tissue specificity: Expressed in mammary gland, kidney, brain and ovary.

Evidence on tissue expression from TISSUES for KCTD1 Gene

  • Nervous system(4.5)
  • Skin(4.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for KCTD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • skull
  • tooth
Thorax:
  • breast
  • chest wall
  • heart
Abdomen:
  • kidney
  • pancreas
Pelvis:
  • ureter
  • urethra
  • urinary bladder
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with KCTD1: view

No data available for mRNA differential expression in normal tissues for KCTD1 Gene

Orthologs for KCTD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for KCTD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia KCTD1 33 34
  • 100 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia KCTD1 34
  • 97 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia KCTD1 33 34
  • 96.24 (n)
cow
(Bos Taurus)
 Mammalia KCTD1 33 34
  • 95.07 (n)
rat
(Rattus norvegicus)
 Mammalia Kctd1 33
  • 92.71 (n)
mouse
(Mus musculus)
 Mammalia Kctd1 33 16 34
  • 92.09 (n)
oppossum
(Monodelphis domestica)
 Mammalia KCTD1 34
  • 29 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LOC101748669 33
  • 86.17 (n)
KCTD1 34
  • 68 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia KCTD1 34
  • 86 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia kctd1 33
  • 80.16 (n)
zebrafish
(Danio rerio)
 Actinopterygii kctd1 33 34
  • 70.6 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG10440 34
  • 36 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 36 (a)
 OneToMany
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.1937 33
Species where no ortholog for KCTD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for KCTD1 Gene

ENSEMBL:
Gene Tree for KCTD1 (if available)
TreeFam:
Gene Tree for KCTD1 (if available)

Paralogs for KCTD1 Gene

Paralogs for KCTD1 Gene

(6) SIMAP similar genes for KCTD1 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for KCTD1 Gene

genes like me logo Genes that share paralogs with KCTD1: view

Variants for KCTD1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for KCTD1 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs587776998 pathogenic, Scalp ear nipple syndrome, Scalp-ear-nipple syndrome (SENS) [MIM:181270] 26,501,147(-) G/A/T coding_sequence_variant, missense_variant
rs587776999 pathogenic, Scalp ear nipple syndrome, Scalp-ear-nipple syndrome (SENS) [MIM:181270], Scalp-ear-nipple syndrome (SENS) [MIM:181270] 26,501,144(-) G/A/C/T coding_sequence_variant, missense_variant
rs587777000 pathogenic, Scalp ear nipple syndrome, Scalp-ear-nipple syndrome (SENS) [MIM:181270] 26,501,137(-) G/A/T coding_sequence_variant, missense_variant, synonymous_variant
rs587777001 pathogenic, Scalp ear nipple syndrome, Scalp-ear-nipple syndrome (SENS) [MIM:181270] 26,501,138(-) T/G coding_sequence_variant, missense_variant
rs587777002 pathogenic, Scalp ear nipple syndrome, Scalp-ear-nipple syndrome (SENS) [MIM:181270] 26,476,603(-) T/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for KCTD1 Gene

Variant ID Type Subtype PubMed ID
esv1006523 CNV deletion 20482838
esv1276406 CNV deletion 17803354
esv2119422 CNV deletion 18987734
esv2669356 CNV deletion 23128226
esv2716885 CNV deletion 23290073
esv2716886 CNV deletion 23290073
esv2716887 CNV deletion 23290073
esv2761995 CNV loss 21179565
esv3380 CNV loss 18987735
esv3555151 CNV deletion 23714750
nsv1070873 CNV deletion 25765185
nsv1125316 CNV deletion 24896259
nsv1127623 CNV deletion 24896259
nsv1133423 CNV deletion 24896259
nsv1144830 CNV deletion 24896259
nsv1149862 CNV deletion 26484159
nsv1151195 CNV deletion 26484159
nsv2235 CNV deletion 18451855
nsv477544 CNV novel sequence insertion 20440878
nsv961039 CNV duplication 23825009

Variation tolerance for KCTD1 Gene

Residual Variation Intolerance Score: 30.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.47; 55.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KCTD1 Gene

Human Gene Mutation Database (HGMD)
KCTD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KCTD1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KCTD1 Gene

Disorders for KCTD1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for KCTD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
scalp-ear-nipple syndrome
  • sens
subependymal glioma
  • mixed subependymoma-ependymoma
benign ependymoma
  • epithelial ependymoma
aplasia cutis congenita
  • acc
- elite association - COSMIC cancer census association via MalaCards
Search KCTD1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

KCTD1_HUMAN
  • Scalp-ear-nipple syndrome (SENS) [MIM:181270]: A disease characterized by aplasia cutis congenita of the scalp, breast anomalies that range from hypothelia or athelia to amastia, and minor anomalies of the external ears. Less frequent clinical characteristics include nail dystrophy, dental anomalies, cutaneous syndactyly of the digits, and renal malformations. Penetrance appears to be high, although there is substantial variable expressivity within families. {ECO:0000269 PubMed:23541344}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for KCTD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with KCTD1: view

No data available for Genatlas for KCTD1 Gene

Publications for KCTD1 Gene

  1. Mutations in KCTD1 cause scalp-ear-nipple syndrome. (PMID: 23541344) Marneros AG … University of Washington Center for Mendelian Genomics (American journal of human genetics 2013) 3 4 58
  2. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. (PMID: 21658281) Aouizerat BE … Tseng ZH (BMC cardiovascular disorders 2011) 3 44 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. The interaction of KCTD1 with transcription factor AP-2alpha inhibits its transactivation. (PMID: 19115315) Ding X … Zhang J (Journal of cellular biochemistry 2009) 3 4 58
  5. Systematic identification and analysis of mammalian small ubiquitin-like modifier substrates. (PMID: 15561718) Gocke CB … Kang J (The Journal of biological chemistry 2005) 3 4 58

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Sources for KCTD1 Gene

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