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    PHC1 polyhomeotic homolog 1 [ Homo sapiens (human) ]

    Gene ID: 1911, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PHC1provided by HGNC
    Official Full Name
    polyhomeotic homolog 1provided by HGNC
    Primary source
    HGNC:HGNC:3182
    See related
    Ensembl:ENSG00000111752 MIM:602978; AllianceGenome:HGNC:3182
    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
    EDR1; HPH1; RAE28; MCPH11
    Summary
    This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 40.0), endometrium (RPKM 27.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHC1 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (8913843..8941467)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (8896088..8923703)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9066439..9094063)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8940741-8941280 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8941281-8941820 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8941899-8942576 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8942577-8943254 Neighboring gene A2ML1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8947958-8948568 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8957581-8958288 Neighboring gene long intergenic non-protein coding RNA 2972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8958995-8959702 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8962654-8963394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8963395-8964136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8967023-8967549 Neighboring gene Sharpr-MPRA regulatory region 8322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8980966-8981708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8984681-8985424 Neighboring gene alpha-2-macroglobulin like 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9057572-9058228 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:9060851-9061506 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:9064238-9064790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4220 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9101505-9102410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9102411-9103315 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:9108425-9109624 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene killer cell lectin like receptor G1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 34 Neighboring gene VDAC2 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Structure and chromosomal localization of the RAE28/HPH1 gene, a human homologue of the polyhomeotic gene. Ohta H, et al. DNA Seq, 2000. PMID 10902910
    2. Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis. Awad S, et al. Hum Mol Genet, 2013 Jun 1. PMID 23418308
    3. Identification and characterization of interactions between the vertebrate polycomb-group protein BMI1 and human homologs of polyhomeotic. Gunster MJ, et al. Mol Cell Biol, 1997 Apr. PMID 9121482, Free PMC Article
    4. PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Chen L, et al. Nat Commun, 2021 May 14. PMID 33990559, Free PMC Article
    5. Identification of Bmi1-interacting proteins as constituents of a multimeric mammalian polycomb complex. Alkema MJ, et al. Genes Dev, 1997 Jan 15. PMID 9009205

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus.
      Title: PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus.
    2. These findings reveal several cellular defects in cells carrying the PHC1 mutation and highlight the role of chromatin remodeling in the pathogenesis of PM.
      Title: Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis.
    3. PcG complex 1, involving Rae28 and Cdt1, supports the activity of hematopoietic stem cells by enhancing cycling capability and hematopoietic activity through direct regulation of Geminin
      Title: Polycomb-group complex 1 acts as an E3 ubiquitin ligase for Geminin to sustain hematopoietic stem cell activity.
    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

    Associated conditions

    Description Tests
    Microcephaly 11, primary, autosomal recessive
    MedGen: C3809431 OMIM: 615414 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    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)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to leukemia inhibitory factor IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of PRC1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PRC1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of PcG protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in sex chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    polyhomeotic-like protein 1
    Names
    early development regulator 1 (homolog of polyhomeotic 1)
    early development regulatory protein 1
    polyhomeotic-like 1

    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.

    Genomic

    1. NG_042273.1 RefSeqGene

      Range
      4790..31748
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001413738.1 → NP_001400667.1  polyhomeotic-like protein 1 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/Swiss-Prot
      D3DUV4, P78364, Q8WVM3, Q9BU63
      UniProtKB/TrEMBL
      B2RXH1

    2. NM_001413739.1 → NP_001400668.1  polyhomeotic-like protein 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    3. NM_001413740.1 → NP_001400669.1  polyhomeotic-like protein 1 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    4. NM_001413741.1 → NP_001400670.1  polyhomeotic-like protein 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      J3KQH6
      Related
      ENSP00000399194.2, ENST00000433083.6

    5. NM_001413742.1 → NP_001400671.1  polyhomeotic-like protein 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    6. NM_001413743.1 → NP_001400672.1  polyhomeotic-like protein 1 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    7. NM_001413744.1 → NP_001400673.1  polyhomeotic-like protein 1 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    8. NM_001413745.1 → NP_001400674.1  polyhomeotic-like protein 1 isoform h

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    9. NM_001413746.1 → NP_001400675.1  polyhomeotic-like protein 1 isoform i

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    10. NM_001413747.1 → NP_001400676.1  polyhomeotic-like protein 1 isoform j

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    11. NM_001413748.1 → NP_001400677.1  polyhomeotic-like protein 1 isoform k

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    12. NM_001413749.1 → NP_001400678.1  polyhomeotic-like protein 1 isoform k

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    13. NM_001413750.1 → NP_001400679.1  polyhomeotic-like protein 1 isoform l

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    14. NM_001413751.1 → NP_001400680.1  polyhomeotic-like protein 1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    15. NM_001413752.1 → NP_001400681.1  polyhomeotic-like protein 1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      B2RXH1

    16. NM_001413753.1 → NP_001400682.1  polyhomeotic-like protein 1 isoform n

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      J3KQH6

    17. NM_001413754.1 → NP_001400683.1  polyhomeotic-like protein 1 isoform o

      Status: REVIEWED

      Source sequence(s)
      AC006581
      UniProtKB/TrEMBL
      J3KQH6

    18. NM_004426.3 → NP_004417.2  polyhomeotic-like protein 1 isoform a

      See identical proteins and their annotated locations for NP_004417.2

      Status: REVIEWED

      Source sequence(s)
      AC006581, BC073964, BM473731, BX640639, CN388283, CN388285, CN388316, U89277
      Consensus CDS
      CCDS8597.1
      UniProtKB/Swiss-Prot
      D3DUV4, P78364, Q8WVM3, Q9BU63
      UniProtKB/TrEMBL
      B2RXH1
      Related
      ENSP00000437659.1, ENST00000544916.6
      Conserved Domains (4) summary
      cd09577
      Location:935 → 1003
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:937 → 1004
      SAM; Sterile alpha motif
      pfam06467
      Location:792 → 827
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:828 → 934
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    RNA

    1. NR_182209.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC006581

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      8913843..8941467
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520603.3 → XP_011518905.1  polyhomeotic-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011518905.1

      UniProtKB/TrEMBL
      B2RXH1
      Conserved Domains (4) summary
      cd09577
      Location:952 → 1020
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:954 → 1021
      SAM; Sterile alpha motif
      pfam06467
      Location:809 → 844
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:845 → 951
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    2. XM_011520599.3 → XP_011518901.1  polyhomeotic-like protein 1 isoform X2

      UniProtKB/TrEMBL
      B2RXH1
      Conserved Domains (4) summary
      cd09577
      Location:944 → 1012
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:946 → 1013
      SAM; Sterile alpha motif
      pfam06467
      Location:801 → 836
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:837 → 943
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    3. XM_011520600.3 → XP_011518902.1  polyhomeotic-like protein 1 isoform X3

      UniProtKB/TrEMBL
      B2RXH1
      Conserved Domains (4) summary
      cd09577
      Location:902 → 970
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:904 → 971
      SAM; Sterile alpha motif
      pfam06467
      Location:759 → 794
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:795 → 901
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    4. XM_017018957.2 → XP_016874446.1  polyhomeotic-like protein 1 isoform X4

      UniProtKB/TrEMBL
      B2RXH1

    5. XM_047428475.1 → XP_047284431.1  polyhomeotic-like protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RXH1

    6. XM_017018955.3 → XP_016874444.1  polyhomeotic-like protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RXH1
      Conserved Domains (4) summary
      cd09577
      Location:952 → 1020
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:954 → 1021
      SAM; Sterile alpha motif
      pfam06467
      Location:809 → 844
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:845 → 951
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      8896088..8923703
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371354.1 → XP_054227329.1  polyhomeotic-like protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RXH1

    2. XM_054371356.1 → XP_054227331.1  polyhomeotic-like protein 1 isoform X2

      UniProtKB/TrEMBL
      B2RXH1

    3. XM_054371358.1 → XP_054227333.1  polyhomeotic-like protein 1 isoform X3

      UniProtKB/TrEMBL
      B2RXH1

    4. XM_054371360.1 → XP_054227335.1  polyhomeotic-like protein 1 isoform X5

      UniProtKB/TrEMBL
      B2RXH1

    5. XM_054371361.1 → XP_054227336.1  polyhomeotic-like protein 1 isoform X4

      UniProtKB/TrEMBL
      B2RXH1

    6. XM_054371362.1 → XP_054227337.1  polyhomeotic-like protein 1 isoform X6

      UniProtKB/TrEMBL
      B2RXH1

    7. XM_054371353.1 → XP_054227328.1  polyhomeotic-like protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RXH1

    8. XM_054371357.1 → XP_054227332.1  polyhomeotic-like protein 1 isoform X3

      UniProtKB/TrEMBL
      B2RXH1

    9. XM_054371359.1 → XP_054227334.1  polyhomeotic-like protein 1 isoform X5

      UniProtKB/TrEMBL
      B2RXH1

    10. XM_054371355.1 → XP_054227330.1  polyhomeotic-like protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RXH1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78364.3 GenPept UniProtKB/Swiss-Prot:P78364

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