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PHC1 polyhomeotic homolog 1 [ Homo sapiens (human) ]

Gene ID: 1911, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (8913843..8941467)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (8896088..8923703)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9067105..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_chr12:8942577-8943254 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8941899-8942576 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 ATAC-STARR-seq lymphoblastoid silent region 4221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4222 Neighboring gene VDAC2 pseudogene 2 Neighboring gene long intergenic non-protein coding RNA 612

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. 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 (54) 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
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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)

Genotypes

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 
part_of 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

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581
    Related
    ENSP00000399194.2, ENST00000433083.6

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

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

    Status: REVIEWED

    Source sequence(s)
    AC006581

  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_2023_10

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

  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

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

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

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

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

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

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

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

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

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

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

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