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Aliases for PHC1 Gene

Aliases for PHC1 Gene

  • Polyhomeotic Homolog 1 2 3 5
  • Early Development Regulator 1 (Homolog Of Polyhomeotic 1) 2 3
  • Early Development Regulatory Protein 1 3 4
  • HPH1 3 4
  • EDR1 3 4
  • Polyhomeotic Homolog 1 (Drosophila) 2
  • Polyhomeotic-Like 1 (Drosophila) 2
  • Polyhomeotic-Like Protein 1 3
  • Polyhomeotic-Like 1 3
  • MCPH11 3
  • RAE28 3
  • PH1 4

External Ids for PHC1 Gene

Previous HGNC Symbols for PHC1 Gene

  • EDR1

Previous GeneCards Identifiers for PHC1 Gene

  • GC12P009215
  • GC12P008967
  • GC12P008958
  • GC12P009067

Summaries for PHC1 Gene

Entrez Gene Summary for PHC1 Gene

  • 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]

GeneCards Summary for PHC1 Gene

PHC1 (Polyhomeotic Homolog 1) is a Protein Coding gene. Diseases associated with PHC1 include Microcephaly 11, Primary, Autosomal Recessive and Autosomal Recessive Primary Microcephaly. Among its related pathways are Cellular Senescence and Metabolism of proteins. GO annotations related to this gene include chromatin binding. An important paralog of this gene is PHC2.

UniProtKB/Swiss-Prot for PHC1 Gene

  • Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility. Required for proper control of cellular levels of GMNN expression.

Gene Wiki entry for PHC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHC1 Gene

Genomics for PHC1 Gene

Regulatory Elements for PHC1 Gene

Enhancers for PHC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G008909 1.8 FANTOM5 Ensembl ENCODE dbSUPER 27.4 -1.0 -1035 7.1 HDGF HNRNPUL1 PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 FEZF1 ZNF2 PHC1 KLRG1 M6PR MFAP5 ENSG00000255829 FAM66C A2ML1 A2ML1-AS2 A2ML1-AS1
GH12G009701 1.5 FANTOM5 Ensembl ENCODE dbSUPER 23 +788.7 788652 2.2 ZFP64 ZNF426 ZNF394 ZNF781 ZNF518A ZNF697 ZFHX2 ZNF555 ZNF34 EGR2 CLECL1 PHC1 CLEC2D KLRB1 ENSG00000213443 ENSG00000257027 LOC255308 LOC374443 DDX12P CD69
GH12G008947 1.7 FANTOM5 ENCODE dbSUPER 17.9 +38.3 38318 8.7 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 YY1 ZNF207 ZNF143 M6PR KLRG1 PHC1 ENSG00000257105
GH12G008241 1 ENCODE 30.4 -670.9 -670892 2.7 HDGF PKNOX1 ATF1 AGO1 ARID4B SIN3A YY1 GLIS2 ZNF143 ZNF207 PHC1 NANOG ENSG00000256552 FAM86FP LINC00612 GC12P008268
GH12G009646 2 FANTOM5 Ensembl ENCODE dbSUPER 11.5 +737.8 737838 10.0 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 SLC30A9 CBX5 ZNF143 ZNF207 CLEC2D LOC374443 KLRB1 CLECL1 CLEC12A ENSG00000214776 PHC1 CD69 CLEC7A DDX12P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHC1 on UCSC Golden Path with GeneCards custom track

Promoters for PHC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000048571 704 2001 HDGF PKNOX1 ARNT SIN3A ARID4B FEZF1 ZNF2 ZNF48 GLIS2 PAF1

Genomic Location for PHC1 Gene

Chromosome:
12
Start:
8,913,896 bp from pter
End:
8,941,467 bp from pter
Size:
27,572 bases
Orientation:
Plus strand

Genomic View for PHC1 Gene

Genes around PHC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHC1 Gene

Proteins for PHC1 Gene

  • Protein details for PHC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78364-PHC1_HUMAN
    Recommended name:
    Polyhomeotic-like protein 1
    Protein Accession:
    P78364
    Secondary Accessions:
    • D3DUV4
    • Q8WVM3
    • Q9BU63

    Protein attributes for PHC1 Gene

    Size:
    1004 amino acids
    Molecular mass:
    105534 Da
    Quaternary structure:
    • Homodimer. Component of a PRC1-like complex.
    Miscellaneous:
    • The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different PRC1-like complexes.
    SequenceCaution:
    • Sequence=AAH17748.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHC1 Gene

neXtProt entry for PHC1 Gene

Post-translational modifications for PHC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PHC1 (PHC1)
  • Santa Cruz Biotechnology (SCBT) Antibodies for PHC1

No data available for DME Specific Peptides for PHC1 Gene

Domains & Families for PHC1 Gene

Gene Families for PHC1 Gene

Protein Domains for PHC1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PHC1: view

No data available for UniProtKB/Swiss-Prot for PHC1 Gene

Function for PHC1 Gene

Molecular function for PHC1 Gene

UniProtKB/Swiss-Prot Function:
Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility. Required for proper control of cellular levels of GMNN expression.

Gene Ontology (GO) - Molecular Function for PHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHC1: view
genes like me logo Genes that share phenotypes with PHC1: view

Human Phenotype Ontology for PHC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHC1 Gene

MGI Knock Outs for PHC1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PHC1 Gene

Localization for PHC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHC1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHC1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for PHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 21282530
GO:0005654 nucleoplasm TAS --
GO:0031519 PcG protein complex IDA 21282530
GO:0035102 PRC1 complex IDA 12167701
genes like me logo Genes that share ontologies with PHC1: view

Pathways & Interactions for PHC1 Gene

genes like me logo Genes that share pathways with PHC1: view

Pathways by source for PHC1 Gene

Gene Ontology (GO) - Biological Process for PHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0016574 histone ubiquitination IDA 23418308
genes like me logo Genes that share ontologies with PHC1: view

No data available for SIGNOR curated interactions for PHC1 Gene

Transcripts for PHC1 Gene

Unigene Clusters for PHC1 Gene

Polyhomeotic homolog 1 (Drosophila):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHC1 Gene

No ASD Table

Relevant External Links for PHC1 Gene

GeneLoc Exon Structure for
PHC1
ECgene alternative splicing isoforms for
PHC1

Expression for PHC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHC1 Gene

This gene is overexpressed in Fetal testis (22.6), Testis (19.5), Peripheral blood mononuclear cells (12.4), and Blymphocyte (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PHC1 Gene



Protein tissue co-expression partners for PHC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHC1 Gene:

PHC1

SOURCE GeneReport for Unigene cluster for PHC1 Gene:

Hs.744902

Evidence on tissue expression from TISSUES for PHC1 Gene

  • Lung(4.2)
  • Nervous system(3.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PHC1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
  • ureter
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with PHC1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PHC1 Gene

Orthologs for PHC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHC1 34 35
  • 99.24 (n)
dog
(Canis familiaris)
Mammalia PHC1 35
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phc1 34
  • 89.07 (n)
mouse
(Mus musculus)
Mammalia Phc1 34 16 35
  • 88.84 (n)
cow
(Bos Taurus)
Mammalia PHC1 34 35
  • 88.41 (n)
oppossum
(Monodelphis domestica)
Mammalia PHC1 35
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHC1 35
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHC1 34 35
  • 72.79 (n)
lizard
(Anolis carolinensis)
Reptilia PHC1 35
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100488113 34
  • 64.54 (n)
Str.2700 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.16260 34
zebrafish
(Danio rerio)
Actinopterygii phc1 35
  • 35 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta ph-d 35
  • 16 (a)
ManyToMany
ph-p 35
  • 16 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 27 (a)
OneToMany
Species where no ortholog for PHC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PHC1 Gene

ENSEMBL:
Gene Tree for PHC1 (if available)
TreeFam:
Gene Tree for PHC1 (if available)

Paralogs for PHC1 Gene

Paralogs for PHC1 Gene

genes like me logo Genes that share paralogs with PHC1: view

Variants for PHC1 Gene

Sequence variations from dbSNP and Humsavar for PHC1 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs587777036 Pathogenic, Microcephaly 11, primary, autosomal recessive (MCPH11) [MIM:615414] 8,939,418(+) CTGCC(C/T)TCAAG reference, missense
rs878853029 Likely benign 8,933,055(+) CACTC(A/G)ACAGC reference, missense
rs142253130 Uncertain significance 8,922,662(+) GTAAA(C/T)CGAAC reference, synonymous-codon
rs372044180 Uncertain significance 8,937,324(+) GCCAC(C/T)GGGTG reference, missense
rs768095941 Uncertain significance 8,933,342(+) CTGTG(A/C/T)ACTTG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PHC1 Gene

Variant ID Type Subtype PubMed ID
nsv1051530 CNV gain 25217958
nsv52793 CNV deletion 16902084
nsv832327 CNV loss 17160897
nsv973019 CNV duplication 23825009

Variation tolerance for PHC1 Gene

Residual Variation Intolerance Score: 25.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.76; 78.92% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHC1 Gene

Human Gene Mutation Database (HGMD)
PHC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHC1 Gene

Disorders for PHC1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PHC1 Gene - From: OMIM, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PHC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PHC1_HUMAN
  • Microcephaly 11, primary, autosomal recessive (MCPH11) [MIM:615414]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age-related mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. {ECO:0000269 PubMed:23418308}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PHC1

Genetic Association Database (GAD)
PHC1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHC1
genes like me logo Genes that share disorders with PHC1: view

No data available for Genatlas for PHC1 Gene

Publications for PHC1 Gene

  1. Identification and characterization of interactions between the vertebrate polycomb-group protein BMI1 and human homologs of polyhomeotic. (PMID: 9121482) Gunster M.J. … Otte A.P. (Mol. Cell. Biol. 1997) 2 3 4 22 64
  2. RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor. (PMID: 9199346) Satijn D.P.E. … Otte A.P. (Mol. Cell. Biol. 1997) 3 4 22 64
  3. Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis. (PMID: 23418308) Awad S. … Poizat C. (Hum. Mol. Genet. 2013) 3 4 64
  4. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 Complexes in mammalian cells. (PMID: 21282530) Vandamme J. … Angrand P.O. (Mol. Cell. Proteomics 2011) 3 4 64
  5. Several distinct polycomb complexes regulate and co-localize on the INK4a tumor suppressor locus. (PMID: 19636380) Maertens G.N. … Peters G. (PLoS ONE 2009) 3 4 64

Products for PHC1 Gene

Sources for PHC1 Gene

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