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    KCTD1 potassium channel tetramerization domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 284252, updated on 27-Nov-2024

    Summary

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    Official Symbol
    KCTD1provided by HGNC
    Official Full Name
    potassium channel tetramerization domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:18249
    See related
    Ensembl:ENSG00000134504 MIM:613420; AllianceGenome:HGNC:18249
    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
    C18orf5
    Summary
    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]
    Expression
    Broad expression in skin (RPKM 10.7), esophagus (RPKM 8.1) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KCTD1 in Genome Data Viewer
    Location:
    18q11.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26454910..26657473, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (26649034..26851482, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (24034874..24237437, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13183 Neighboring gene long intergenic non-protein coding RNA 1543 Neighboring gene MPRA-validated peak3087 silencer Neighboring gene uncharacterized LOC124904274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13188 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:24060471-24061670 Neighboring gene uncharacterized LOC124904273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24126836-24127820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9374 Neighboring gene Sharpr-MPRA regulatory region 2175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24129451-24130092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:24128809-24129450 Neighboring gene Sharpr-MPRA regulatory region 221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24130735-24131376 Neighboring gene microRNA 8057 Neighboring gene cytokine induced apoptosis inhibitor 1 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr18:24230978-24231479 Neighboring gene uncharacterized LOC102725227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13192 Neighboring gene prostate cancer associated transcript 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:24301517-24302018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:24302019-24302518 Neighboring gene uncharacterized LOC124904272 Neighboring gene Sharpr-MPRA regulatory region 3190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13193

    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. Characterization and expression of a human KCTD1 gene containing the BTB domain, which mediates transcriptional repression and homomeric interactions. Ding XF, et al. DNA Cell Biol, 2008 May. PMID 18358072
    2. Expression, purification, and secondary structure characterization of recombinant KCTD1. Mei F, et al. Biochemistry (Mosc), 2012 Aug. PMID 22860917
    3. Mutations in KCTD1 cause scalp-ear-nipple syndrome. Marneros AG, et al. Am J Hum Genet, 2013 Apr 4. PMID 23541344, Free PMC Article
    4. Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction. Balasco N, et al. Int J Biol Macromol, 2024 Oct. PMID 39111466
    5. Bivalent Copper Ions Promote Fibrillar Aggregation of KCTD1 and Induce Cytotoxicity. Liu Z, et al. Sci Rep, 2016 Sep 6. PMID 27596723, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction.
      Title: Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction.
    2. Genetic Variants in KCTD1 Are Associated with Isolated Dental Anomalies.
      Title: Genetic Variants in KCTD1 Are Associated with Isolated Dental Anomalies.
    3. KCTD1/KCTD15 complexes control ectodermal and neural crest cell functions, and their impairment causes aplasia cutis.
      Title: KCTD1/KCTD15 complexes control ectodermal and neural crest cell functions, and their impairment causes aplasia cutis.
    4. Magnesium and Calcium Homeostasis Depend on KCTD1 Function in the Distal Nephron.
      Title: Magnesium and Calcium Homeostasis Depend on KCTD1 Function in the Distal Nephron.
    5. KCTD1 mutants in scalpearnipple syndrome and AP2alpha P59A in Char syndrome reciprocally abrogate their interactions, but can regulate Wnt/betacatenin signaling.
      Title: KCTD1 mutants in scalp‑ear‑nipple syndrome and AP‑2α P59A in Char syndrome reciprocally abrogate their interactions, but can regulate Wnt/β‑catenin signaling.
    6. AP-2beta/KCTD1 Control Distal Nephron Differentiation and Protect against Renal Fibrosis.
      Title: AP-2β/KCTD1 Control Distal Nephron Differentiation and Protect against Renal Fibrosis.
    7. Molecular basis of the scalp-ear-nipple syndrome unraveled by the characterization of disease-causing KCTD1 mutants.
      Title: Molecular basis of the scalp-ear-nipple syndrome unraveled by the characterization of disease-causing KCTD1 mutants.
    8. results reveal a novel role for Cu(2+) in determining the structure and function of KCTD1
      Title: Bivalent Copper Ions Promote Fibrillar Aggregation of KCTD1 and Induce Cytotoxicity.
    9. The authors find that the KCTD proteins 5, 6, 9 and 17 bind to Cul3 with high affinity, while the KCTD proteins 1 and 16 do not have detectable binding.
      Title: Structural Insights into KCTD Protein Assembly and Cullin3 Recognition.
    10. Mutations in KCTD1 cause scalp-ear-nipple syndrome.
      Title: Mutations in KCTD1 cause scalp-ear-nipple syndrome.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    Associated conditions

    Description Tests
    Scalp-ear-nipple syndrome
    MedGen: C1867020 OMIM: 181270 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.
    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)

    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

    Clone Names

    • DKFZp451C132

    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 transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein homooligomerization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    BTB/POZ domain-containing protein KCTD1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_054919.2 RefSeqGene

      Range
      113920..207563
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136205.2 → NP_001129677.1  BTB/POZ domain-containing protein KCTD1 isoform a

      See identical proteins and their annotated locations for NP_001129677.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 3. Variants 1, 2, 4 and 6 all encode the same isoform (a), which has a shorter N-terminus compared to isoform b.
      Source sequence(s)
      AK289870, BC063652, BX366041, CN290475
      Consensus CDS
      CCDS11888.1
      UniProtKB/Swiss-Prot
      A8K1F5, Q719H9
      UniProtKB/TrEMBL
      J3QRK1
      Related
      ENSP00000384367.3, ENST00000408011.7
      Conserved Domains (2) summary
      cd18387
      Location:28 → 132
      BTB_POZ_KCTD1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 1 (KCTD1)
      cl41727
      Location:154 → 237
      H1_KCTD12-like; H1 domain found in potassium channel tetramerization domain-containing proteins

    2. NM_001142730.3 → NP_001136202.1  BTB/POZ domain-containing protein KCTD1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (b).
      Source sequence(s)
      AC007996
      UniProtKB/TrEMBL
      A0A2U3U043
      Related
      ENSP00000463041.2, ENST00000580059.7
      Conserved Domains (3) summary
      smart00225
      Location:640 → 735
      BTB; Broad-Complex, Tramtrack and Bric a brac
      pfam12012
      Location:284 → 439
      DUF3504; Domain of unknown function (DUF3504)
      cl02518
      Location:640 → 732
      BTB; BTB/POZ domain

    3. NM_001258221.2 → NP_001245150.1  BTB/POZ domain-containing protein KCTD1 isoform a

      See identical proteins and their annotated locations for NP_001245150.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 3. Variants 1, 2, 4 and 6 all encode the same isoform (a), which has a shorter N-terminus compared to isoform b.
      Source sequence(s)
      AC007996
      Consensus CDS
      CCDS11888.1
      UniProtKB/Swiss-Prot
      A8K1F5, Q719H9
      UniProtKB/TrEMBL
      J3QRK1
      Related
      ENSP00000408405.2, ENST00000417602.5
      Conserved Domains (2) summary
      cd18387
      Location:28 → 132
      BTB_POZ_KCTD1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 1 (KCTD1)
      cl41727
      Location:154 → 237
      H1_KCTD12-like; H1 domain found in potassium channel tetramerization domain-containing proteins

    4. NM_001258222.3 → NP_001245151.1  BTB/POZ domain-containing protein KCTD1 isoform c

      See identical proteins and their annotated locations for NP_001245151.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 3. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform b.
      Source sequence(s)
      AC007996, AC012588
      UniProtKB/TrEMBL
      J3QRK1
      Related
      ENSP00000464261.1, ENST00000580191.5
      Conserved Domains (2) summary
      cd18387
      Location:36 → 140
      BTB_POZ_KCTD1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 1 (KCTD1)
      cl41727
      Location:162 → 245
      H1_KCTD12-like; H1 domain found in potassium channel tetramerization domain-containing proteins

    5. NM_001351443.1 → NP_001338372.1  BTB/POZ domain-containing protein KCTD1 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 3. Variants 1, 2, 4 and 6 all encode the same isoform (a), which has a shorter N-terminus compared to isoform b.
      Source sequence(s)
      AC007996, BC063652, CN290475
      Consensus CDS
      CCDS11888.1
      UniProtKB/Swiss-Prot
      A8K1F5, Q719H9
      UniProtKB/TrEMBL
      J3QRK1
      Conserved Domains (2) summary
      cd18387
      Location:28 → 132
      BTB_POZ_KCTD1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 1 (KCTD1)
      cl41727
      Location:154 → 237
      H1_KCTD12-like; H1 domain found in potassium channel tetramerization domain-containing proteins

    6. NM_198991.4 → NP_945342.1  BTB/POZ domain-containing protein KCTD1 isoform a

      See identical proteins and their annotated locations for NP_945342.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 3. Variants 1, 2, 4 and 6 all encode the same isoform (a), which has a shorter N-terminus compared to isoform b.
      Source sequence(s)
      AC007996, AC090206
      Consensus CDS
      CCDS11888.1
      UniProtKB/Swiss-Prot
      A8K1F5, Q719H9
      UniProtKB/TrEMBL
      J3QRK1
      Related
      ENSP00000464170.1, ENST00000579973.5
      Conserved Domains (2) summary
      cd18387
      Location:28 → 132
      BTB_POZ_KCTD1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 1 (KCTD1)
      cl41727
      Location:154 → 237
      H1_KCTD12-like; H1 domain found in potassium channel tetramerization domain-containing proteins

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      26454910..26657473 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      26649034..26851482 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q719H9.1 GenPept UniProtKB/Swiss-Prot:Q719H9

    Gene LinkOut

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

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