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    CFDP1 craniofacial development protein 1 [ Homo sapiens (human) ]

    Gene ID: 10428, updated on 14-Nov-2024

    Summary

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    Official Symbol
    CFDP1provided by HGNC
    Official Full Name
    craniofacial development protein 1provided by HGNC
    Primary source
    HGNC:HGNC:1873
    See related
    Ensembl:ENSG00000153774 MIM:608108; AllianceGenome:HGNC:1873
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    p97; BCNT; CP27; SWC5; Yeti; CENP-29; BUCENTAUR
    Summary
    Predicted to be involved in chromatin remodeling. Predicted to act upstream of or within several processes, including cell adhesion; negative regulation of fibroblast apoptotic process; and regulation of cell shape. Predicted to be located in kinetochore. Predicted to be part of Swr1 complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 25.6), kidney (RPKM 23.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CFDP1 in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75293710..75433503, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81340442..81479377, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75327608..75467401, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene BCAR1 scaffold protein, Cas family member Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75289517-75290056 Neighboring gene uncharacterized LOC105371344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75290057-75290597 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75294897-75295696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75297293-75298090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75298091-75298888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75305973-75306511 Neighboring gene RNA, U6 small nuclear 758, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:75339050-75340249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75341536-75342036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11128 Neighboring gene CFDP1 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11129 Neighboring gene small nucleolar RNA SNORA76 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75465381-75465580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7719 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75467440-75468007 Neighboring gene tigger transposable element-derived protein 1-like Neighboring gene transmembrane protein 170A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75490353-75490854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11131 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75498257-75498757

    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 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. The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization. Messina G, et al. Sci Rep, 2017 Apr 3. PMID 28367969, Free PMC Article
    2. Mammalian Bcnt/Cfdp1, a potential epigenetic factor characterized by an acidic stretch in the disordered N-terminal and Ser250 phosphorylation in the conserved C-terminal regions. Iwashita S, et al. Biosci Rep, 2015 Jun 12. PMID 26182435, Free PMC Article
    3. CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway. Zhou Y, et al. Cancer Med, 2023 Jan. PMID 35861040, Free PMC Article
    4. CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity. Formicola D, et al. HGG Adv, 2023 Jan 12. PMID 36425957, Free PMC Article
    5. An Alu-linked repetitive sequence corresponding to 280 amino acids is expressed in a novel bovine protein, but not in its human homologue. Nobukuni T, et al. J Biol Chem, 1997 Jan 31. PMID 9006920

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity.
      Title: CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity.
    2. CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway.
      Title: CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway.
    3. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders.
      Title: The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization.
    4. Overall, these findings highlight unanticipated evidences suggesting that homodimerization mediated by the BCNT domain is integral to the chromatin functions of BCNT proteins.
      Title: Expression of human Cfdp1 gene in Drosophila reveals new insights into the function of the evolutionarily conserved BCNT protein family.
    5. Bcnt/Cfdp1 is acetylated in vitro by CREB-binding protein (CBP) and four lysine residues including Lys(268) in BCNT-C are also acetylated in vivo, revealing a protein regulated at multiple levels.
      Title: Mammalian Bcnt/Cfdp1, a potential epigenetic factor characterized by an acidic stretch in the disordered N-terminal and Ser250 phosphorylation in the conserved C-terminal regions.
    6. This study identified rs4888378 in the BCAR1-CFDP1-TMEM170A locus as a novel genetic determinant of carotid intima-media thickness and coronary artery disease risk.
      Title: Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
    8. includes the region derived from a long interspersed nucleotide
      Title: [A novel type protein, Bcnt, that includes the region derived from a long interspersed nucleotide element].
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in fibroblast apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of fibroblast apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell shape IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Swr1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in kinetochore IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    craniofacial development protein 1
    Names
    centromere protein 29
    phosphoprotein (Bucentaur)

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_006324.3 → NP_006315.1  craniofacial development protein 1

      See identical proteins and their annotated locations for NP_006315.1

      Status: VALIDATED

      Source sequence(s)
      AC009163, AW160432, BC000991, D86549
      Consensus CDS
      CCDS10916.1
      UniProtKB/Swiss-Prot
      O00393, O00404, Q9UEE9, Q9UEF0, Q9UEF1, Q9UEF8
      UniProtKB/TrEMBL
      B2R9W9
      Related
      ENSP00000283882.3, ENST00000283882.4
      Conserved Domains (1) summary
      pfam07572
      Location:222 → 295
      BCNT; Bucentaur or craniofacial development

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      75293710..75433503 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522814.3 → XP_011521116.1  craniofacial development protein 1 isoform X2

      See identical proteins and their annotated locations for XP_011521116.1

      UniProtKB/TrEMBL
      A0A0H5APX3

    2. XM_047433504.1 → XP_047289460.1  craniofacial development protein 1 isoform X1

    3. XM_047433503.1 → XP_047289459.1  craniofacial development protein 1 isoform X1

    4. XM_011522815.3 → XP_011521117.1  craniofacial development protein 1 isoform X3

      See identical proteins and their annotated locations for XP_011521117.1

      UniProtKB/TrEMBL
      A0A0H5AUJ9

    RNA

    1. XR_007064846.1 RNA Sequence

    2. XR_007064847.1 RNA Sequence

    3. XR_007064845.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      81340442..81479377 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379390.1 → XP_054235365.1  craniofacial development protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A0H5APX3

    2. XM_054379389.1 → XP_054235364.1  craniofacial development protein 1 isoform X1

    3. XM_054379388.1 → XP_054235363.1  craniofacial development protein 1 isoform X1

    4. XM_054379387.1 → XP_054235362.1  craniofacial development protein 1 isoform X1

    5. XM_054379391.1 → XP_054235366.1  craniofacial development protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A0H5AUJ9

    RNA

    1. XR_008489043.1 RNA Sequence

    2. XR_008489047.1 RNA Sequence

    3. XR_008489044.1 RNA Sequence

    4. XR_008489046.1 RNA Sequence

    5. XR_008489045.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UEE9.1 GenPept UniProtKB/Swiss-Prot:Q9UEE9

    Gene LinkOut

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

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