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    VCF1 VCP nuclear cofactor family member 1 [ Homo sapiens (human) ]

    Gene ID: 84923, updated on 10-Oct-2024

    Summary

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    Official Symbol
    VCF1provided by HGNC
    Official Full Name
    VCP nuclear cofactor family member 1provided by HGNC
    Primary source
    HGNC:HGNC:25918
    See related
    Ensembl:ENSG00000133193 AllianceGenome:HGNC:25918
    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
    FAM104A
    Expression
    Broad expression in testis (RPKM 36.2), bone marrow (RPKM 16.4) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VCF1 in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (73207353..73232394, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (74097081..74122120, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (71203492..71228533, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8920 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:71166424-71167002 Neighboring gene RNA polymerase III subunit K pseudogene 2 Neighboring gene somatostatin receptor 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71188421-71189180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8921 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:71195948-71197147 Neighboring gene Sharpr-MPRA regulatory region 2581 Neighboring gene component of oligomeric golgi complex 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71227250-71228026 Neighboring gene mitochondrial nucleoid associated protein 1 Neighboring gene cleavage and polyadenylation specific factor 4 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71280886-71281442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71281998-71282553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71282554-71283108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12695 Neighboring gene Sharpr-MPRA regulatory region 4436 Neighboring gene CDC42 effector protein 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71287907-71288788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8924

    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 FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP. Körner M, et al. Elife, 2023 Sep 15. PMID 37713320, Free PMC Article
    2. Mapping and characterization of novel (CAG)n repeat cDNAs from adult human brain derived by the oligo capture method. Reddy PH, et al. Genomics, 1997 Dec 1. PMID 9417904
    3. AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. Hülsmann J, et al. Mol Cell Proteomics, 2018 Jul. PMID 29599191, Free PMC Article
    4. PTP4A2 promotes lysophagy by dephosphorylation of VCP/p97 at Tyr805. Bai Y, et al. Autophagy, 2023 May. PMID 36300783, Free PMC Article
    5. Systematic proteomics of the VCP-UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis. Raman M, et al. Nat Cell Biol, 2015 Oct. PMID 26389662, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP.
      Title: The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14775

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein VCF1
    Names
    family with sequence similarity 104 member A
    protein FAM104A

    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_001098832.2 → NP_001092302.1  protein VCF1 isoform 1

      See identical proteins and their annotated locations for NP_001092302.1

      Status: VALIDATED

      Source sequence(s)
      AC097641
      Consensus CDS
      CCDS45766.1
      UniProtKB/Swiss-Prot
      Q969W3
      Related
      ENSP00000384832.3, ENST00000405159.8
      Conserved Domains (1) summary
      pfam15434
      Location:79 → 207
      FAM104; Family 104

    2. NM_001289410.1 → NP_001276339.1  protein VCF1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons, which results in a frameshift, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AI926103, AK027681, BC025238, DB265439
      Consensus CDS
      CCDS74143.1
      UniProtKB/TrEMBL
      J3KT76
      Related
      ENSP00000462840.1, ENST00000581110.1

    3. NM_001289411.1 → NP_001276340.1  protein VCF1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site and lacks an alternate exon, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AI926103, AK027681, BC025238, BG773537, DB265439
      Consensus CDS
      CCDS74144.1
      UniProtKB/TrEMBL
      J3KSI9
      Related
      ENSP00000462507.1, ENST00000583024.1

    4. NM_001289412.2 → NP_001276341.1  protein VCF1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK027681, BC025238, HY026689, HY037907
      UniProtKB/TrEMBL
      J3KT52
      Related
      ENSP00000462806.1, ENST00000579872.1
      Conserved Domains (1) summary
      pfam15434
      Location:12 → 140
      FAM104; Family 104

    5. NM_032837.3 → NP_116226.2  protein VCF1 isoform 2

      See identical proteins and their annotated locations for NP_116226.2

      Status: VALIDATED

      Source sequence(s)
      AC097641
      Consensus CDS
      CCDS11693.2
      UniProtKB/Swiss-Prot
      B4E339, Q969W3
      Related
      ENSP00000384648.3, ENST00000403627.7
      Conserved Domains (1) summary
      pfam15434
      Location:79 → 186
      FAM104; Family 104

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      73207353..73232394 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436947.1 → XP_047292903.1  protein VCF1 isoform X2

    2. XM_024451008.2 → XP_024306776.1  protein VCF1 isoform X1

      UniProtKB/TrEMBL
      J3KT52
      Conserved Domains (1) summary
      pfam15434
      Location:4 → 137
      FAM104; Family 104

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      74097081..74122120 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317582.1 → XP_054173557.1  protein VCF1 isoform X2

    2. XM_054317581.1 → XP_054173556.1  protein VCF1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969W3.2 GenPept UniProtKB/Swiss-Prot:Q969W3

    Gene LinkOut

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

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