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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 (NCBI)DEBT91
DKFZP434L1021
FIGC
PCMF
ZZZ1
HGNC (Hugo) KCMF1
HGNC Alias symbDEBT91
PCMF
DKFZP434L1021
ZZZ1
LocusID (NCBI) 56888
Atlas_Id 46364
Location 2p11.2  [Link to chromosome band 2p11]
Location_base_pair Starts at 84971161 and ends at 85059472 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping KCMF1.png]
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
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 ]

    External links

    Nomenclature
    HGNC (Hugo)KCMF1   20589
    Cards
    AtlasKCMF1ID46364ch2p11
    Entrez_Gene (NCBI)KCMF1    potassium channel modulatory factor 1
    AliasesDEBT91; FIGC; PCMF; ZZZ1
    GeneCards (Weizmann)KCMF1
    Ensembl hg19 (Hinxton)ENSG00000176407 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000176407 [Gene_View]  ENSG00000176407 [Sequence]  chr2:84971161-85059472 [Contig_View]  KCMF1 [Vega]
    ICGC DataPortalENSG00000176407
    TCGA cBioPortalKCMF1
    AceView (NCBI)KCMF1
    Genatlas (Paris)KCMF1
    SOURCE (Princeton)KCMF1
    Genetics Home Reference (NIH)KCMF1
    Genomic and cartography
    GoldenPath hg38 (UCSC)KCMF1  -     chr2:84971161-85059472 +  2p11.2   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)KCMF1  -     2p11.2   [Description]    (hg19-Feb_2009)
    GoldenPathKCMF1 - 2p11.2 [CytoView hg19]  KCMF1 - 2p11.2 [CytoView hg38]
    ImmunoBaseENSG00000176407
    genome Data Viewer NCBIKCMF1 [Mapview hg19]  
    OMIM614719   
    Gene and transcription
    Genbank (Entrez)AB083199 AF131740 AF155652 AK023403 AK311099
    RefSeq transcript (Entrez)NM_020122
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)KCMF1
    Alternative Splicing GalleryENSG00000176407
    Gene ExpressionKCMF1 [ NCBI-GEO ]   KCMF1 [ EBI - ARRAY_EXPRESS ]   KCMF1 [ SEEK ]   KCMF1 [ MEM ]
    Gene Expression Viewer (FireBrowse)KCMF1 [ Firebrowse - Broad ]
    GenevisibleExpression of KCMF1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)56888
    GTEX Portal (Tissue expression)KCMF1
    Human Protein AtlasENSG00000176407-KCMF1 [pathology]   [cell]   [tissue]
    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 : Enzyme2.3.2.27 [ Enzyme-Expasy ]   2.3.2.272.3.2.27 [ IntEnz-EBI ]   2.3.2.27 [ BRENDA ]   2.3.2.27 [ KEGG ]   [ MEROPS ]
    PhosPhoSitePlusQ9P0J7
    Domaine pattern : Prosite (Expaxy)ZF_ZZ_1 (PS01357)    ZF_ZZ_2 (PS50135)    ZINC_FINGER_C2H2_2 (PS50157)   
    Domains : Interpro (EBI)Di19_Zn-bd    KCMF1    Znf_C2H2_type    Znf_ZZ    Znf_ZZ_sf   
    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
    Blocks (Seattle)KCMF1
    SuperfamilyQ9P0J7
    Human Protein Atlas [tissue]ENSG00000176407-KCMF1 [tissue]
    Peptide AtlasQ9P0J7
    HPRD13761
    IPIIPI00306661   IPI00926111   IPI00925907   IPI00925692   
    Protein Interaction databases
    DIP (DOE-UCLA)Q9P0J7
    IntAct (EBI)Q9P0J7
    BioGRIDKCMF1
    STRING (EMBL)KCMF1
    ZODIACKCMF1
    Ontologies - Pathways
    QuickGOQ9P0J7
    Ontology : AmiGOextracellular region  cytosol  plasma membrane  zinc ion binding  protein ubiquitination  neutrophil degranulation  synapse  ubiquitin protein ligase activity  synaptic signaling  ficolin-1-rich granule lumen  
    Ontology : EGO-EBIextracellular region  cytosol  plasma membrane  zinc ion binding  protein ubiquitination  neutrophil degranulation  synapse  ubiquitin protein ligase activity  synaptic signaling  ficolin-1-rich granule lumen  
    REACTOMEQ9P0J7 [protein]
    REACTOME PathwaysR-HSA-6798695 [pathway]   
    NDEx NetworkKCMF1
    Atlas of Cancer Signalling NetworkKCMF1
    Wikipedia pathwaysKCMF1
    Orthology - Evolution
    OrthoDB56888
    GeneTree (enSembl)ENSG00000176407
    Phylogenetic Trees/Animal Genes : TreeFamKCMF1
    HOGENOMQ9P0J7
    Homologs : HomoloGeneKCMF1
    Homology/Alignments : Family Browser (UCSC)KCMF1
    Gene fusions - Rearrangements
    Fusion : MitelmanAAK1/KCMF1 [2p13.3/2p11.2]  
    Fusion : MitelmanKCMF1/GGCX [2p11.2/2p11.2]  
    Fusion : MitelmanKCMF1/PRKDC [2p11.2/8q11.21]  
    Fusion PortalAAK1 2p13.3 KCMF1 2p11.2 PRAD
    Fusion PortalKCMF1 2p11.2 GGCX 2p11.2 PRAD
    Fusion PortalKCMF1 2p11.2 PRKDC 8q11.21 BRCA
    Fusion : Fusion_HubAAK1--KCMF1    BAZ2B--KCMF1    DONSON--KCMF1    EXOC6B--KCMF1    IMMT--KCMF1    INADL--KCMF1    KCMF1--AFTPH    KCMF1--ATAD2    KCMF1--B4GALT1    KCMF1--CAB39    KCMF1--CDCP1    KCMF1--DAPL1    KCMF1--DNAH6    KCMF1--GGCX    KCMF1--KCMF1   
    KCMF1--KDM4C    KCMF1--LPP    KCMF1--PRKDC    KCMF1--SUCLG1    LDB2--KCMF1    NR1D1--KCMF1    OCRL--KCMF1    PTPN11--KCMF1    PTPN4--KCMF1    RBMS2--KCMF1    ST3GAL5--KCMF1    TCF7L1--KCMF1    TET3--KCMF1    TLK1--KCMF1   
    Fusion : QuiverKCMF1
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerKCMF1 [hg38]
    dbVarKCMF1
    ClinVarKCMF1
    MonarchKCMF1
    1000_GenomesKCMF1 
    Exome Variant ServerKCMF1
    GNOMAD BrowserENSG00000176407
    Varsome BrowserKCMF1
    Genomic Variants (DGV)KCMF1 [DGVbeta]
    DECIPHERKCMF1 [patients]   [syndromes]   [variants]   [genes]  
    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]  
    Somatic Mutations in Cancer : COSMIC3DKCMF1
    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
    NCG6 (London) select KCMF1
    Cancer3DKCMF1(select the gene name)
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM614719   
    Orphanet
    DisGeNETKCMF1
    MedgenKCMF1
    Genetic Testing Registry KCMF1
    NextProtQ9P0J7 [Medical]
    GENETestsKCMF1
    Target ValidationKCMF1
    Huge Navigator KCMF1 [HugePedia]
    ClinGenKCMF1
    Clinical trials, drugs, therapy
    MyCancerGenomeKCMF1
    Protein Interactions : CTD
    Pharm GKB GenePA134967694
    PharosQ9P0J7
    Clinical trialKCMF1
    Miscellaneous
    canSAR (ICR)KCMF1 (select the gene name)
    HarmonizomeKCMF1
    DataMed IndexKCMF1
    Other databaseMod Base
    Other databaseSNP
    Other databaseRNAi
    Other databasePhotosite
    Other databasePharma GKB
    Other databaseHPRD
    Other databaseUniversity of Paris
    Other databaseExon description
    Probes
    Litterature
    PubMed37 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    EVEXKCMF1
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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    indexed on : Thu Mar 25 20:02:56 CET 2021
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