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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TCOF1 Gene

protein-coding   GIFtS: 64
GCID: GC05P149717

Treacher Collins-Franceschetti Syndrome 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Treacher Collins-Franceschetti Syndrome 11 2     Nucleolar Trafficking Phosphoprotein2
Treacher Collins Syndrome Protein2 3     treacle2
MFD12 5     Treacle Protein2
TCS12 5     

External Ids:    HGNC: 116541   Entrez Gene: 69492   Ensembl: ENSG000000708147   OMIM: 6068475   UniProtKB: Q134283   

Export aliases for TCOF1 gene to outside databases

Previous GC identifers: GC05P149806 GC05P150198 GC05P149720 GC05P149765 GC05P144885


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TCOF1 Gene:
This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene
transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been
associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple
transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Sep 2008)

GeneCards Summary for TCOF1 Gene: 
TCOF1 (Treacher Collins-Franceschetti syndrome 1) is a protein-coding gene. Diseases associated with TCOF1 include treacher collins syndrome, and cerebro-costo-mandibular syndrome. GO annotations related to this gene include protein binding and transporter activity.

UniProtKB/Swiss-Prot: TCOF_HUMAN, Q13428
Function: May be involved in nucleolar-cytoplasmic transport. May play a fundamental role in early embryonic
development, particularly in development of the craniofacial complex (By similarity). May participate in certain
stages of ribosome biogenesis

Gene Wiki entry for TCOF1 (Treacle protein) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NT_029289.11  NC_018916.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TCOF1 gene promoter:
         Nkx2-2   HNF-3beta   CBF-C   GATA-1   Egr-2   CBF-A   CP1A   CP1C   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTCOF1 promoter sequence
   Search SABiosciences Chromatin IP Primers for TCOF1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TCOF1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q32   Ensembl cytogenetic band:  5q32   HGNC cytogenetic band: 5q32

TCOF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TCOF1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P149717:  view genomic region     (about GC identifiers)

Start:
149,737,202 bp from pter      End:
149,779,871 bp from pter
Size:
42,670 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TCOF_HUMAN, Q13428 (See protein sequence)
Recommended Name: Treacle protein  
Size: 1488 amino acids; 152106 Da
Subunit: Part of a large pre-ribosomal ribonucleoprotein (RNP) complex, that consists of at least 62 ribosomal
proteins, 45 nonribosomal proteins and both pre-rRNA and mature rRNA species. Within this complex directly
interacts with NOP56 in an RNA-independent manner
Subcellular location: Nucleus, nucleolus
Sequence caution: Sequence=AAH16144.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential
poly-A sequence;
Secondary accessions: A0JLU0 B4E111 Q6SC72 Q7Z5W9 Q96A52 Q99408 Q99860
Alternative splicing: 8 isoforms:  Q13428-1   Q13428-2   Q13428-3   Q13428-4   Q13428-5   Q13428-6   Q13428-7   Q13428-8   
(No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TCOF1: NX_Q13428

Explore proteomics data for TCOF1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q13428

  • TCOF1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    TCOF1 Protein Expression
    REFSEQ proteins (6 alternative transcripts): 
    NP_000347.2  NP_001008657.1  NP_001128715.1  NP_001128716.1  NP_001128717.1  NP_001182070.1  

    ENSEMBL proteins: 
     ENSP00000409944   ENSP00000325223   ENSP00000406888   ENSP00000377811   ENSP00000390717  
     ENSP00000421655   ENSP00000427484   ENSP00000426471   ENSP00000426587   ENSP00000422567  
     ENSP00000400939   ENSP00000367028  

    Human Recombinant Protein Products for TCOF1: 
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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for TCOF1 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IDA--
    GO:0005737cytoplasm IDA--

    TCOF1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    3 InterPro protein domains:
     IPR003993 TCS_treacle
     IPR017859 Treacle-like_TCS
     IPR006594 LisH_dimerisation

    Graphical View of Domain Structure for InterPro Entry Q13428

    ProtoNet protein and cluster: Q13428

    2 Blocks protein domains:
    IPB003993 Treacher Collins syndrome protein Treacle signature
    IPB006594 Lissencephaly type-1-like homology motif


    UniProtKB/Swiss-Prot: TCOF_HUMAN, Q13428
    Similarity: Contains 1 LisH domain


    TCOF1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TCOF_HUMAN, Q13428
    Function: May be involved in nucleolar-cytoplasmic transport. May play a fundamental role in early embryonic
    development, particularly in development of the craniofacial complex (By similarity). May participate in certain
    stages of ribosome biogenesis

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005215transporter activity TAS9096354
    GO:0005515protein binding IPI17620599
         
    TCOF1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for TCOF1:
     Synthetic lethal with Ras 

         12 MGI mutant phenotypes (inferred from 1 allele(MGI details for Tcof1):
     cellular  craniofacial  digestive/alimentary  embryogenesis  endocrine/exocrine gland 
     growth/size  hearing/vestibular/ear  mortality/aging  nervous system  respiratory system 
     skeleton  vision/eye 

    TCOF1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Tcof1tm1Mjd for TCOF1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for TCOF1 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for TCOF1 
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    SwitchGear 3'UTR luciferase reporter plasmidTCOF1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TCOF1


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for TCOF1 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1         Kegg Pathway  (Kegg details for TCOF1):
        Ribosome biogenesis in eukaryotes


    TCOF1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for TCOF1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    5/27 Interacting proteins for TCOF1 (Q134281, 3 ENSP000004068884) via UniProtKB, MINT, STRING, and/or I2D (see all 27)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARRB1P494071, 3, ENSP000003771414EBI-396105,EBI-743313 I2D: score=2 STRING: ENSP00000377141
    ARRB2P321211, 3, ENSP000002692604EBI-396105,EBI-714559 I2D: score=2 STRING: ENSP00000269260
    CSNK2A2P197843, ENSP000002625064I2D: score=2 STRING: ENSP00000262506
    PCNAP120043, ENSP000003684384I2D: score=2 STRING: ENSP00000368438
    UBTFP174803, ENSP000003026404I2D: score=2 STRING: ENSP00000302640
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development TAS9096354
    GO:0042790transcription of nuclear large rRNA transcript from RNA polymerase I promoter IEA--

    TCOF1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    TCOF1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TCOF1 (TCOF)

    2 Novoseek inferred chemical compound relationships for TCOF1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    rrna 24.9 1 12777385 (1)
    serine 15.4 2 9299440 (1), 9074926 (1)

    Search CenterWatch for drugs/clinical trials and news about TCOF1 / TCOF

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TCOF1 gene (7 alternative transcripts): 
    NM_000356.3  NM_001008657.2  NM_001135243.1  NM_001135244.1  NM_001135245.1  NM_001195141.1  NM_001008656.2  

    Unigene Cluster for TCOF1:

    Treacher Collins-Franceschetti syndrome 1
    Hs.519672  [show with all ESTs]
    Unigene Representative Sequence: AB209317
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000445265 ENST00000323668 ENST00000439160 ENST00000394269(uc003lrw.3)
    ENST00000427724(uc011dci.1) ENST00000504761 ENST00000513346 ENST00000515516
    ENST00000515035 ENST00000514442 ENST00000506063 ENST00000506767 ENST00000513538
    ENST00000506630 ENST00000451292 ENST00000377797(uc003lry.3 uc003lrz.3 uc011dch.2 uc003lrx.3 uc003lsa.3)

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    hsa-miR-579 hsa-miR-1206 hsa-miR-3152-3p hsa-miR-466 hsa-miR-377 hsa-miR-3919 hsa-miR-1183
    SwitchGear 3'UTR luciferase reporter plasmidTCOF1 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AB209317.1 AK096467.1 AK225284.1 AK296918.1 AK299167.1 AK303611.1 AK307586.1 AL133039.1 
    AY460334.1 BC008331.1 BC011764.2 BC014559.2 BC016144.1 BC027252.1 BC033093.1 U40847.1 
    U76366.1 

    21 DOTS entries:

    DT.91754561  DT.99946398  DT.313465  DT.92365041  DT.91754556  DT.313464  DT.91639367  DT.100810088 
    DT.91754562  DT.99963839  DT.101982234  DT.102828287  DT.120836695  DT.92005727  DT.97862262  DT.100772141 
    DT.100772142  DT.86856410  DT.95178450  DT.120836709  DT.95178449 

    24/298 AceView cDNA sequences (see all 298):

    BQ680644 BM475199 BP355691 AI392723 BQ878420 BQ920719 BM664489 AL710825 
    BM713047 BM802904 BQ052523 BE793163 BE792061 AI474683 BC016144 BX424546 
    AI419459 CA426852 BQ052970 BX425660 BC008331 BU156635 BQ575957 AI638669 

    GeneLoc Exon Structure

    5/15 Alternative Splicing Database (ASD) splice patterns (SP) for TCOF1 (see all 15)    About this scheme

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

    ExUns: 16 ^ 17 ^ 18a · 18b ^ 19a · 19b · 19c ^ 20 ^ 21a · 21b ^ 22a · 22b · 22c ^ 23
    SP1:                                                                                    
    SP2:                                                                                    
    SP3:                                                                                    
    SP4:                                                                                    
    SP5:                                                                                    


    ECgene alternative splicing isoforms for TCOF1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TCOF1 expression in normal human tissues (normalized intensities)      TCOF1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGTCCCCTA
    TCOF1 Expression
    About this image


    TCOF1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/26 selected tissues (see all 26) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Intestine (Gastrointestinal Tract)    fully expand to see all 3 entries
             small intestine ; glandular cells   
             SMALL INTESTINE   
     
     Bone (Muscoskeletal System)    fully expand to see all 3 entries
             Zeugopod Long Bone
             skeleton/pectoral girdle and thoracic body wall/scapula   
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex

    See TCOF1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TCOF1

    SOURCE GeneReport for Unigene cluster: Hs.519672
        SABiosciences Custom PCR Arrays for TCOF1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TCOF1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for TCOF1 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tcof11 , 5 Treacher Collins Franceschetti syndrome 1, homolog1, 5 70.75(n)1
    61.02(a)1
      18 (34.41 cM)5
    214531  NM_011552.31  NP_035682.11 
     608137555 
    chicken
    (Gallus gallus)
    Aves TCOF11 Treacher Collins-Franceschetti syndrome 1 44.61(n)
    32.9(a)
      416276  NM_001012785.2  NP_001012803.2 
    lizard
    (Anolis carolinensis)
    Reptilia TCOF16
    Uncharacterized protein
    25(a)
    1 ↔ 1
    2(138883449-138928021)
    zebrafish
    (Danio rerio)
    Actinopterygii nolc16
    nucleolar and coiled-body phosphoprotein 1
    13(a)
    possible ortholog
    13(4649847-4669031)
    fruit fly
    (Drosophila melanogaster)
    Insecta mxc6
    CG121056
    (see all 5)
    --
    5(a)
    4(a)
    (see all 5)
    possible ortholog
    possible ortholog
    (see all 5)
    X(9130834-9137237)
    3L(1610696-1615801)
    worm
    (Caenorhabditis elegans)
    Secernentea attf-66
    F39C12.16
    (see all 4)
    Protein F39C12.1
    (see all 4)
    5(a)
    3(a)
    (see all 4)
    possible ortholog
    possible ortholog
    (see all 4)
    I(12787943-12806581)
    X(4834870-4853065)


    ENSEMBL Gene Tree for TCOF1 (if available)
    TreeFam Gene Tree for TCOF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TCOF1 gene
    1 SIMAP similar gene for TCOF1 using alignment to 7 protein entries:     TCOF_HUMAN (see all proteins):
    DKFZp434G1035

    TCOF1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1112 SNPs in TCOF1 are shown (see all 1112)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0356664
    A colorectal cancer sample4--see VAR_0356662 R K mis40--------
    VAR_0056304
    Treacher Collins syndrome 1 (TCS1)4--see VAR_0056302 W R mis40--------
    rs412871241,2
    C,Fnon-pathogenic1150023399(+) CATTCA/GTAGAT 6 -- int11Minor allele frequency- G:0.01NA 120
    rs561133661,2
    C,Fnon-pathogenic1150030031(+) GGCCCG/ATCCCC 6 -- int11Minor allele frequency- A:0.12NA 120
    rs1437137141,2
    Cnon-pathogenic1150030477(+) CATGGC/GTGTGG 6 -- int10--------
    rs1124474021,2
    C,Fnon-pathogenic1150038641(+) ACCACA/GTGCTT 6 -- int10--------
    rs1113658351,2
    C,Fnon-pathogenic1150054169(+) CCAGTA/CGGGGG 5 -- int10--------
    rs1513445631,2
    Cprobable-non-pathogenic1150013621(+) GGGAAA/GTGGCG 6 -- ut510--------
    rs1441494851,2
    Cprobable-non-pathogenic1150017061(+) ATTAAC/TTGTGG 6 -- int10--------
    rs1429659981,2
    C,Fprobable-non-pathogenic1150025149(+) TCAGCG/AGGCCA 12 /A syn11Minor allele frequency- A:0.01NA 4550

    HapMap Linkage Disequilibrium report for TCOF1 (149737202 - 149779871 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for TCOF1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2114978CNV Deletion18987734
    esv2649922CNV Deletion19546169
    esv989812CNV Deletion20482838
    esv5186CNV Deletion18987735
    esv2672361CNV Deletion23128226
    esv2730915CNV Deletion23290073
    esv1309088CNV Deletion17803354
    esv6012CNV Loss19470904


    Human Gene Mutation Database (HGMD): TCOF1

    Locus Specific Mutation Databases (LSDB): TCOF1
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing TCOF1
    DNA2.0 Custom Variant and Variant Library Synthesis for TCOF1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 606847   
    OMIM disorders: 154500  
    UniProtKB/Swiss-Prot: TCOF_HUMAN, Q13428
  • Treacher Collins syndrome 1 (TCS1) [MIM:154500]: A form of Treacher Collins syndrome, a disorder of
    craniofacial development. Treacher Collins syndrome is characterized by a combination of bilateral downward
    slanting of the palpebral fissures, colobomas of the lower eyelids with a paucity of eyelashes medial to the
    defect, hypoplasia of the facial bones, cleft palate, malformation of the external ears, atresia of the external
    auditory canals, and bilateral conductive hearing loss. Note=The disease is caused by mutations affecting the
    gene represented in this entry

  • 20/23 diseases for TCOF1 (see all 23):    About MalaCards
    treacher collins syndrome    cerebro-costo-mandibular syndrome    tcof1-related treacher collins syndrome    treacher collins syndrome 3
    choanal atresia    microtia    goldenhar syndrome    esophageal atresia
    dysostosis    cleft palate    congenital heart defect    craniosynostosis
    lissencephaly    coloboma    pharyngitis    sleep apnea
    was-related disorders    microcephaly    esophagitis    mental retardation

    5 diseases from the University of Copenhagen DISEASES database for TCOF1:
    Treacher Collins syndrome     Cleft palate     Goldenhar syndrome     Coloboma
    Choanal atresia

    TCOF1 for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for TCOF1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    treacher collins syndrome 98.4 51 11013442 (2), 12777385 (2), 20340163 (2), 15214011 (2) (see all 39)
    conductive hearing loss 80 2 8488840 (1), 8281138 (1)
    microtia 78.1 2 15770127 (2)
    cleft palate 70.5 6 18688869 (4), 8488840 (1), 8281138 (1)
    congenital malformation 13.2 2 15249688 (1), 10888597 (1)

    Genatlas disease: TCOF1
    Treacher Collins-Franceschetti syndrome,mandibulofacial dysostosis characterized by antimongoloid slant of
    eyes,coloboma of inferior lid,narrowing of the external ears and malformation of the middle ear ossicles which
    may lead to deafness,hypoplasia of the mandible (macrognathia) and cleft palate and macrostomia

    GeneTests: TCOF1
    GeneReviews: TCOF1
    Genetic Association Database (GAD): TCOF1
    Human Genome Epidemiology (HuGE) Navigator: TCOF1 (6 documents)

    Export disorders for TCOF1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for TCOF1 gene, integrated from 9 sources (see all 114):
    (articles sorted by number of sources associating them with TCOF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Excess maternal transmission of markers in TCOF1 among cleft palate case-parent trios from three populations. (PubMed id 18688869)1, 4, 9 Sull J.W....Beaty T.H. (2008)
    2. TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins syndrome throughout its coding region. (PubMed id 9096354)1, 2, 9 Wise C.A.... Jabs E.W. (1997)
    3. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome. (PubMed id 12777385)1, 2, 9 Hayano T....Takahashi N. (2003)
    4. Identification of the complete coding sequence and genomic organization of the Treacher Collins syndrome gene. (PubMed id 9074926)1, 2, 9 Dixon J....Dixon M.J. (1997)
    5. Genotyping in 46 patients with tentative diagnosis of Treacher Collins syndrome revealed unexpected phenotypic variation. (PubMed id 15340364)1, 4, 9 Teber O.A....Wieczorek D. (2004)
    6. The mutational spectrum in Treacher Collins syndrome reveals a predominance of mutations that create a premature-termination codon. (PubMed id 9042910)1, 2, 9 Edwards S.J.... Dixon M.J. (1997)
    7. Maternal genes and facial clefts in offspring: a comp rehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PubMed id 20634891)1, 4 Jugessur A....Murray J.C. (2010)
    8. Investigation of genetic susceptibility factors for h uman longevity - A targeted nonsynonymous SNP study. (PubMed id 20800603)1, 4 Flachsbart F....Nebel A. (2010)
    9. A candidate gene study of obstructive sleep apnea in European Americans and African Americans. (PubMed id 20538960)1, 4 Larkin E.K....Redline S. (2010)
    10. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6949 HGNC: 11654 AceView: TCOF1 Ensembl:ENSG00000070814 euGenes: HUgn6949
    ECgene: TCOF1 Kegg: 6949 H-InvDB: TCOF1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for TCOF1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/TCOF1

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TCOF1 gene:
    Search GeneIP for patents involving TCOF1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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