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

Gene ID: 84923, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (73207353..73232394, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (74097081..74122120, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells. Fogeron ML, et al. Nat Commun, 2013. PMID 23443559
  5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Haenig C, et al. Cell Rep, 2020 Aug 18. PMID 32814053

See all (16) 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; protein FAM104A
Names
family with sequence similarity 104 member A

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_2023_10

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 FAM104A isoform X2

  2. XM_024451008.2 → XP_024306776.1  protein FAM104A 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 FAM104A isoform X2

  2. XM_054317581.1 → XP_054173556.1  protein FAM104A isoform X1

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

Gene LinkOut

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