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KCMF1 (potassium channel modulatory factor 1)

Written2009-07Roshan Mandrawalia, Ranjan Tamuli
Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati-781 039, Assam, India

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)DEBT91
PCMF
DKFZP434L1021
ZZZ1
HGNC (Hugo) KCMF1
LocusID (NCBI) 56888
Atlas_Id 46364
Location 2p11.2  [Link to chromosome band 2p11]
Location_base_pair Starts at 85198231 and ends at 85286595 bp from pter ( according to hg19-Feb_2009)  [Mapping KCMF1.png]
Fusion genes
(updated 2016)
AAK1 (2p13.3) / KCMF1 (2p11.2)KCMF1 (2p11.2) / DNAH6 (2p11.2)KCMF1 (2p11.2) / GGCX (2p11.2)
KCMF1 (2p11.2) / KCMF1 (2p11.2)KCMF1 (2p11.2) / KDM4C (9p24.1)KCMF1 (2p11.2) / PRKDC (8q11.21)
ST3GAL5 (2p11.2) / KCMF1 (2p11.2)

DNA/RNA

 
Description DNA size 87.29 kb, mRNA size 7555 bp, 7 exons.

Protein

 
Description 381 amino acids; 41.945 kDa protein.
KCMF1 protein contains ring finger (Zinc finger, ZZ-type) 3-50 (48), zinc finger (C2H2-type) 78-101 (23), nuclear localization signal (NLS) 152-168 (17), and a coiled coil domain 225-257 (33).

Isoforms:
Two isoforms that predicted to encode proteins containing the zinc finger domain have been identified; other isoforms are relatively shorter and not well defined.

  • Isoform bApr07: This partial mRNA is 625 bp long. It is reconstructed from a myeloma cDNA clone. The pre-messenger RNA has 5 exons and covers 74.08 kb. The predicted partial protein has 208 aa (22.9 kDa, pI 5.8) and a very good coding score (7). It contains one Zinc finger, ZZ-type domain, one zinc finger, C2H2-type domain.
  • Isoform dApr07: The dApr07 mRNA variant is 431 bp long. It is reconstructed from a testis cDNA clone. The pre-mRNA has 4 exons and covers 12.72 kb. The predicted partial protein has 143 aa (15.7 kDa, pI 7.2) and a very good coding score (5). It contains one zinc finger, C2H2-type domain.
  • Expression Ubiquitously expressed. High level of expression is in pharynx, thyroid, respiratory tract and larynx; less expressed in female system, uterus and cervix.
    Localisation Nuclear.
    Function KCMF1 is a transcription factor. Basic functions of the KCMF1 gene are (i) early gene up-regulation during growth factor-induced branching tubulogenesis, (ii) ubiquitination through intrinsic E3 ubiquitin ligase activity, and (iii) a possible role in ion channel activity.
    Homology The percent identity below represents identity of KCMF1 over an aligned region in UniGene.
    Pan troglodytes: 97 (Percentage Identity)
    Canis lupas familiaris: 91
    Bos Taurus: 90
    Mus musculus: 96
    Gallus gallus: 93
    Danio rerio: 85.

    Implicated in

    Note
      
    Entity Ewing's sarcoma family of tumors (ESFT)
    Note KCMF1 is down regulated by high constitutive CD99 (a cell surface glycoprotein) expression in ESFT. KCMF1 expression is inversely correlated with CD99 expression, as seen in a series of 22 primary ESFT. High CD99 expression levels contribute to the malignant properties of ESFT by promoting growth and migration of tumor cells.
      
      
    Entity Gastric cancer
    Note KCMF1 (also known as FIGC) encode a RING finger protein, has intrinsic E3 ubiquitin ligase activity and promotes ubiquitination. KCMF1 contains a novel C6H2-type RING finger domain at the NH2-terminal region, consensus sequence CX2C(7-11) CX2CXA5CX2CX(5-9) HX (1-3) H (XA: acidic residues). Using differential display approach with basic fibroblast growth factor (b-FGF) inducible genes in gastric cancer cells, it was observed that FIGC upregulation in response to bFGF in gastric cancer. This suggests that FIGC might be implicated in gastric carcinogenesis through dysregulation of growth modulator.
      

    Bibliography

    FIGC, a novel FGF-induced ubiquitin-protein ligase in gastric cancers.
    Jang JH.
    FEBS Lett. 2004 Dec 3;578(1-2):21-5.
    PMID 15581609
     
    Suppression of KCMF1 by constitutive high CD99 expression is involved in the migratory ability of Ewing's sarcoma cells.
    Kreppel M, Aryee DN, Schaefer KL, Amann G, Kofler R, Poremba C, Kovar H.
    Oncogene. 2006 May 4;25(19):2795-800.
    PMID 16314831
     
    Debt91, a putative zinc finger protein differentially expressed during epithelial morphogenesis.
    Li Z, Stuart RO, Eraly SA, Gittes G, Beier DR, Nigam SK.
    Biochem Biophys Res Commun. 2003 Jul 4;306(3):623-8.
    PMID 12810064
     

    Citation

    This paper should be referenced as such :
    Mandrawalia, R ; Tamuli, R
    KCMF1 (potassium channel modulatory factor 1)
    Atlas Genet Cytogenet Oncol Haematol. 2010;14(6):560-561.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/KCMF1ID46364ch2p11.html


    External links

    Nomenclature
    HGNC (Hugo)KCMF1   20589
    Cards
    AtlasKCMF1ID46364ch2p11
    Entrez_Gene (NCBI)KCMF1  56888  potassium channel modulatory factor 1
    AliasesDEBT91; FIGC; PCMF; ZZZ1
    GeneCards (Weizmann)KCMF1
    Ensembl hg19 (Hinxton)ENSG00000176407 [Gene_View]  chr2:85198231-85286595 [Contig_View]  KCMF1 [Vega]
    Ensembl hg38 (Hinxton)ENSG00000176407 [Gene_View]  chr2:85198231-85286595 [Contig_View]  KCMF1 [Vega]
    ICGC DataPortalENSG00000176407
    TCGA cBioPortalKCMF1
    AceView (NCBI)KCMF1
    Genatlas (Paris)KCMF1
    WikiGenes56888
    SOURCE (Princeton)KCMF1
    Genetics Home Reference (NIH)KCMF1
    Genomic and cartography
    GoldenPath hg19 (UCSC)KCMF1  -     chr2:85198231-85286595 +  2p11.2   [Description]    (hg19-Feb_2009)
    GoldenPath hg38 (UCSC)KCMF1  -     2p11.2   [Description]    (hg38-Dec_2013)
    EnsemblKCMF1 - 2p11.2 [CytoView hg19]  KCMF1 - 2p11.2 [CytoView hg38]
    Mapping of homologs : NCBIKCMF1 [Mapview hg19]  KCMF1 [Mapview hg38]
    OMIM614719   
    Gene and transcription
    Genbank (Entrez)AB083199 AF131740 AF155652 AK023403 AK311099
    RefSeq transcript (Entrez)NM_020122
    RefSeq genomic (Entrez)NC_000002 NC_018913 NT_022184 NW_004929300
    Consensus coding sequences : CCDS (NCBI)KCMF1
    Cluster EST : UnigeneHs.654968 [ NCBI ]
    CGAP (NCI)Hs.654968
    Alternative Splicing GalleryENSG00000176407
    Gene ExpressionKCMF1 [ NCBI-GEO ]   KCMF1 [ EBI - ARRAY_EXPRESS ]   KCMF1 [ SEEK ]   KCMF1 [ MEM ]
    Gene Expression Viewer (FireBrowse)KCMF1 [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)56888
    GTEX Portal (Tissue expression)KCMF1
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ9P0J7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ9P0J7  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ9P0J7
    Splice isoforms : SwissVarQ9P0J7
    Catalytic activity : Enzyme6.3.2.- [ Enzyme-Expasy ]   6.3.2.-6.3.2.- [ IntEnz-EBI ]   6.3.2.- [ BRENDA ]   6.3.2.- [ KEGG ]   
    PhosPhoSitePlusQ9P0J7
    Domaine pattern : Prosite (Expaxy)ZF_ZZ_1 (PS01357)    ZF_ZZ_2 (PS50135)    ZINC_FINGER_C2H2_2 (PS50157)   
    Domains : Interpro (EBI)Di19_Zn_binding_dom    Znf_C2H2    Znf_C2H2-like    Znf_ZZ   
    Domain families : Pfam (Sanger)zf-Di19 (PF05605)    ZZ (PF00569)   
    Domain families : Pfam (NCBI)pfam05605    pfam00569   
    Domain families : Smart (EMBL)ZnF_C2H2 (SM00355)  ZnF_ZZ (SM00291)  
    Conserved Domain (NCBI)KCMF1
    DMDM Disease mutations56888
    Blocks (Seattle)KCMF1
    SuperfamilyQ9P0J7
    Human Protein AtlasENSG00000176407
    Peptide AtlasQ9P0J7
    HPRD13761
    IPIIPI00306661   IPI00926111   IPI00925907   IPI00925692   
    Protein Interaction databases
    DIP (DOE-UCLA)Q9P0J7
    IntAct (EBI)Q9P0J7
    FunCoupENSG00000176407
    BioGRIDKCMF1
    STRING (EMBL)KCMF1
    ZODIACKCMF1
    Ontologies - Pathways
    QuickGOQ9P0J7
    Ontology : AmiGOmetabolic process  zinc ion binding  ligase activity  
    Ontology : EGO-EBImetabolic process  zinc ion binding  ligase activity  
    REACTOMEQ9P0J7 [protein]
    REACTOME Pathways6798695 [pathway]   
    NDEx NetworkKCMF1
    Atlas of Cancer Signalling NetworkKCMF1
    Wikipedia pathwaysKCMF1
    Orthology - Evolution
    OrthoDB56888
    GeneTree (enSembl)ENSG00000176407
    Phylogenetic Trees/Animal Genes : TreeFamKCMF1
    HOVERGENQ9P0J7
    HOGENOMQ9P0J7
    Homologs : HomoloGeneKCMF1
    Homology/Alignments : Family Browser (UCSC)KCMF1
    Gene fusions - Rearrangements
    Fusion : MitelmanAAK1/KCMF1 [2p13.3/2p11.2]  [t(2;2)(p11;p13)]  
    Fusion : MitelmanKCMF1/GGCX [2p11.2/2p11.2]  [t(2;2)(p11;p11)]  
    Fusion : MitelmanKCMF1/PRKDC [2p11.2/8q11.21]  [t(2;8)(p11;q11)]  
    Fusion: TCGAAAK1 2p13.3 KCMF1 2p11.2 PRAD
    Fusion: TCGAKCMF1 2p11.2 GGCX 2p11.2 PRAD
    Fusion: TCGAKCMF1 2p11.2 PRKDC 8q11.21 BRCA
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerKCMF1 [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)KCMF1
    dbVarKCMF1
    ClinVarKCMF1
    1000_GenomesKCMF1 
    Exome Variant ServerKCMF1
    ExAC (Exome Aggregation Consortium)KCMF1 (select the gene name)
    Genetic variants : HAPMAP56888
    Genomic Variants (DGV)KCMF1 [DGVbeta]
    DECIPHER (Syndromes)2:85198231-85286595  ENSG00000176407
    CONAN: Copy Number AnalysisKCMF1 
    Mutations
    ICGC Data PortalKCMF1 
    TCGA Data PortalKCMF1 
    Broad Tumor PortalKCMF1
    OASIS PortalKCMF1 [ Somatic mutations - Copy number]
    Somatic Mutations in Cancer : COSMICKCMF1  [overview]  [genome browser]  [tissue]  [distribution]  
    Mutations and Diseases : HGMDKCMF1
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    BioMutasearch KCMF1
    DgiDB (Drug Gene Interaction Database)KCMF1
    DoCM (Curated mutations)KCMF1 (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)KCMF1 (select a term)
    intoGenKCMF1
    NCG5 (London)KCMF1
    Cancer3DKCMF1(select the gene name)
    Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM614719   
    Orphanet
    MedgenKCMF1
    Genetic Testing Registry KCMF1
    NextProtQ9P0J7 [Medical]
    TSGene56888
    GENETestsKCMF1
    Huge Navigator KCMF1 [HugePedia]
    snp3D : Map Gene to Disease56888
    BioCentury BCIQKCMF1
    ClinGenKCMF1
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD56888
    Chemical/Pharm GKB GenePA134967694
    Clinical trialKCMF1
    Miscellaneous
    canSAR (ICR)KCMF1 (select the gene name)
    Other databaseMod Base
    Other databaseSNP
    Other databaseRNAi
    Other databasePhotosite
    Other databasePharma GKB
    Other databaseHPRD
    Other databaseUniversity of Paris
    Other databaseExon description
    Probes
    Litterature
    PubMed21 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineKCMF1
    EVEXKCMF1
    GoPubMedKCMF1
    iHOPKCMF1
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

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    indexed on : Thu Feb 2 14:03:50 CET 2017

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