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    HCFC1 host cell factor C1 [ Homo sapiens (human) ]

    Gene ID: 3054, updated on 28-Oct-2024

    Summary

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    Official Symbol
    HCFC1provided by HGNC
    Official Full Name
    host cell factor C1provided by HGNC
    Primary source
    HGNC:HGNC:4839
    See related
    Ensembl:ENSG00000172534 MIM:300019; AllianceGenome:HGNC:4839
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CFF; HCF; HCF1; HFC1; MRX3; VCAF; HCF-1; MAHCX; XLID3; PPP1R89
    Summary
    This gene is a member of the host cell factor family and encodes a protein with five Kelch repeats, a fibronectin-like motif, and six HCF repeats, each of which contains a highly specific cleavage signal. This nuclear coactivator is proteolytically cleaved at one of the six possible sites, resulting in the creation of an N-terminal chain and the corresponding C-terminal chain. The final form of this protein consists of noncovalently bound N- and C-terminal chains. The protein is involved in control of the cell cycle and transcriptional regulation during herpes simplex virus infection. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 11.5), spleen (RPKM 8.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HCFC1 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153947557..153971818, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152221276..152245538, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153213008..153237269, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153200750-153201255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153201256-153201760 Neighboring gene N-alpha-acetyltransferase 10, NatA catalytic subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153204898-153205662 Neighboring gene renin binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153210247-153211010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153213176-153213715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153231131-153231789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153231790-153232449 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153234675-153234853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153235869-153236718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21078 Neighboring gene HCFC1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21079 Neighboring gene transmembrane protein 187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30048 Neighboring gene microRNA 3202-1 Neighboring gene microRNA 3202-2 Neighboring gene CRISPRi-validated cis-regulatory element chrX.2695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153265676-153266176 Neighboring gene NFE2L2 motif-containing MPRA enhancer 190/191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153277410-153278394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153278395-153279378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153285318-153286287 Neighboring gene interleukin 1 receptor associated kinase 1

    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. Host cell factor-1 and E2F4 interact via multiple determinants in each protein. Knez J, et al. Mol Cell Biochem, 2006 Aug. PMID 16633736
    2. Novel exon-skipping variant disrupting the basic domain of HCFC1 causes intellectual disability without metabolic abnormalities in both male and female patients. Wongkittichote P, et al. J Hum Genet, 2021 Jul. PMID 33517344
    3. Heat-Shock Protein 90 Controls the Expression of Cell-Cycle Genes by Stabilizing Metazoan-Specific Host-Cell Factor HCFC1. Antonova A, et al. Cell Rep, 2019 Nov 5. PMID 31693902
    4. The conserved threonine-rich region of the HCF-1(PRO) repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities. Kapuria V, et al. J Biol Chem, 2018 Nov 16. PMID 30224358, Free PMC Article
    5. Multiple congenital anomalies in two boys with mutation in HCFC1 and cobalamin disorder. Gérard M, et al. Eur J Med Genet, 2015 Mar. PMID 25595573

    See all (281) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Variants in HCFC1 and MN1 genes causing intellectual disability in two Pakistani families.
      Title: Variants in HCFC1 and MN1 genes causing intellectual disability in two Pakistani families.
    2. HCFC1 variants in the proteolysis domain are associated with X-linked idiopathic partial epilepsy: Exploring the underlying mechanism.
      Title: HCFC1 variants in the proteolysis domain are associated with X-linked idiopathic partial epilepsy: Exploring the underlying mechanism.
    3. Novel exon-skipping variant disrupting the basic domain of HCFC1 causes intellectual disability without metabolic abnormalities in both male and female patients.
      Title: Novel exon-skipping variant disrupting the basic domain of HCFC1 causes intellectual disability without metabolic abnormalities in both male and female patients.
    4. MLL5, a histone modifying enzyme, regulates androgen receptor activity in prostate cancer cells by recruiting co-regulators, HCF1 and SET1.
      Title: MLL5, a histone modifying enzyme, regulates androgen receptor activity in prostate cancer cells by recruiting co-regulators, HCF1 and SET1.
    5. HCF-1 promotes cell cycle progression by regulating the expression of CDC42.
      Title: HCF-1 promotes cell cycle progression by regulating the expression of CDC42.
    6. Heat-Shock Protein 90 Controls the Expression of Cell-Cycle Genes by Stabilizing Metazoan-Specific Host-Cell Factor HCFC1.
      Title: Heat-Shock Protein 90 Controls the Expression of Cell-Cycle Genes by Stabilizing Metazoan-Specific Host-Cell Factor HCFC1.
    7. Host cell factors stimulate HIV-1 transcription by antagonizing substrate-binding function of Siah1 ubiquitin ligase to stabilize transcription elongation factor ELL2.
      Title: Host cell factors stimulate HIV-1 transcription by antagonizing substrate-binding function of Siah1 ubiquitin ligase to stabilize transcription elongation factor ELL2.
    8. The HCF-1:ChREBP complex resides at lipogenic gene promoters, where HCF-1 regulates H3K4 trimethylation to prime recruitment of the Jumonji C domain-containing histone demethylase PHF2 for epigenetic activation of these promoters.. these findings define HCF-1's interaction with ChREBP as a previously unappreciated mechanism whereby glucose signals are both relayed to ChREBP and transmitted for epigenetic regulation
      Title: HCF-1 Regulates De Novo Lipogenesis through a Nutrient-Sensitive Complex with ChREBP.
    9. The HCF-1PRO repeat possesses an important extended threonine-rich region that is tightly bound by the OGT tetratricopeptide-repeat region. This region confers both glycosylation and proteolytic activities to HCF-1.
      Title: The conserved threonine-rich region of the HCF-1(PRO) repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities.
    10. Data show that Myc boxes (MbIV) is required for the association of MYC with the abundant transcriptional coregulator host cell factor-1 (HCF-1).
      Title: Interaction of MYC with host cell factor-1 is mediated by the evolutionarily conserved Myc box IV motif.
    Submit: New GeneRIF Correction See all GeneRIFs (50)

    Phenotypes

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    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat specifically associates with HCFC1 promoter to downregulate HCFC1 expression in T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC70925

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables cadherin binding HDA PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of cell cycle TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein stabilization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in release from viral latency NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MLL1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of MLL1 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of MLL1/2 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of NSL complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Set1C/COMPASS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Set1C/COMPASS complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of histone acetyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of histone methyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane HDA PubMed 
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    host cell factor 1
    Names
    VP16-accessory protein
    protein phosphatase 1, regulatory subunit 89

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_012513.2 RefSeqGene

      Range
      5000..29261
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001410705.1 → NP_001397634.1  host cell factor 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      U52112
      Consensus CDS
      CCDS94699.1
      UniProtKB/TrEMBL
      A6NEM2
      Related
      ENSP00000359001.4, ENST00000369984.4

    2. NM_005334.3 → NP_005325.2  host cell factor 1 isoform 2

      See identical proteins and their annotated locations for NP_005325.2

      Status: REVIEWED

      Source sequence(s)
      BC010606, BC063435, L20010, U52112
      Consensus CDS
      CCDS44020.1
      UniProtKB/Swiss-Prot
      P51610, Q6P4G5
      UniProtKB/TrEMBL
      A0A223PQH6
      Related
      ENSP00000309555.7, ENST00000310441.12
      Conserved Domains (6) summary
      PLN02153
      Location:12 → 330
      PLN02153; epithiospecifier protein
      cd00063
      Location:1856 → 1885
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00038
      Location:200 → 253
      Kelch; KELCH repeat [structural motif]
      pfam01344
      Location:32 → 69
      Kelch_1; Kelch motif
      pfam13415
      Location:215 → 263
      Kelch_3; Galactose oxidase, central domain
      pfam13854
      Location:134 → 179
      Kelch_5; Kelch motif

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      153947557..153971818 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442060.1 → XP_047298016.1  host cell factor 1 isoform X14

    2. XM_047442059.1 → XP_047298015.1  host cell factor 1 isoform X13

    3. XM_017029471.3 → XP_016884960.1  host cell factor 1 isoform X12

      UniProtKB/TrEMBL
      A0A223PQH6

    4. XM_047442058.1 → XP_047298014.1  host cell factor 1 isoform X11

    5. XM_011531148.4 → XP_011529450.1  host cell factor 1 isoform X9

      UniProtKB/TrEMBL
      A0A223PQH6
      Conserved Domains (6) summary
      PLN02153
      Location:12 → 330
      PLN02153; epithiospecifier protein
      cd00063
      Location:1859 → 1888
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00038
      Location:200 → 253
      Kelch; KELCH repeat [structural motif]
      pfam01344
      Location:32 → 69
      Kelch_1; Kelch motif
      pfam13415
      Location:215 → 263
      Kelch_3; Galactose oxidase, central domain
      pfam13854
      Location:134 → 179
      Kelch_5; Kelch motif

    6. XM_047442057.1 → XP_047298013.1  host cell factor 1 isoform X10

    7. XM_011531147.4 → XP_011529449.1  host cell factor 1 isoform X8

      UniProtKB/TrEMBL
      A0A223PQH6
      Conserved Domains (6) summary
      PLN02153
      Location:12 → 330
      PLN02153; epithiospecifier protein
      cd00063
      Location:1860 → 1889
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00038
      Location:200 → 253
      Kelch; KELCH repeat [structural motif]
      pfam01344
      Location:32 → 69
      Kelch_1; Kelch motif
      pfam13415
      Location:215 → 263
      Kelch_3; Galactose oxidase, central domain
      pfam13854
      Location:134 → 179
      Kelch_5; Kelch motif

    8. XM_047442056.1 → XP_047298012.1  host cell factor 1 isoform X7

    9. XM_047442054.1 → XP_047298010.1  host cell factor 1 isoform X4

    10. XM_047442055.1 → XP_047298011.1  host cell factor 1 isoform X6

    11. XM_047442053.1 → XP_047298009.1  host cell factor 1 isoform X3

    12. XM_006724816.4 → XP_006724879.1  host cell factor 1 isoform X5

      UniProtKB/TrEMBL
      A0A223PQH6
      Conserved Domains (6) summary
      PLN02153
      Location:12 → 330
      PLN02153; epithiospecifier protein
      cd00063
      Location:1900 → 1929
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00038
      Location:200 → 253
      Kelch; KELCH repeat [structural motif]
      pfam01344
      Location:32 → 69
      Kelch_1; Kelch motif
      pfam13415
      Location:215 → 263
      Kelch_3; Galactose oxidase, central domain
      pfam13854
      Location:134 → 179
      Kelch_5; Kelch motif

    13. XM_047442052.1 → XP_047298008.1  host cell factor 1 isoform X2

    14. XM_047442051.1 → XP_047298007.1  host cell factor 1 isoform X1

    15. XM_047442061.1 → XP_047298017.1  host cell factor 1 isoform X15

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152221276..152245538 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326953.1 → XP_054182928.1  host cell factor 1 isoform X14

    2. XM_054326952.1 → XP_054182927.1  host cell factor 1 isoform X13

    3. XM_054326951.1 → XP_054182926.1  host cell factor 1 isoform X12

    4. XM_054326950.1 → XP_054182925.1  host cell factor 1 isoform X11

    5. XM_054326948.1 → XP_054182923.1  host cell factor 1 isoform X9

    6. XM_054326949.1 → XP_054182924.1  host cell factor 1 isoform X10

    7. XM_054326947.1 → XP_054182922.1  host cell factor 1 isoform X8

    8. XM_054326946.1 → XP_054182921.1  host cell factor 1 isoform X7

    9. XM_054326943.1 → XP_054182918.1  host cell factor 1 isoform X4

    10. XM_054326945.1 → XP_054182920.1  host cell factor 1 isoform X6

    11. XM_054326942.1 → XP_054182917.1  host cell factor 1 isoform X3

    12. XM_054326944.1 → XP_054182919.1  host cell factor 1 isoform X5

    13. XM_054326941.1 → XP_054182916.1  host cell factor 1 isoform X2

    14. XM_054326940.1 → XP_054182915.1  host cell factor 1 isoform X1

    15. XM_054326954.1 → XP_054182929.1  host cell factor 1 isoform X15

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51610.2 GenPept UniProtKB/Swiss-Prot:P51610

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