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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 Microcephaly. Among its related pathways are SUMOylation and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is PHC3.

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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for PHC1 Gene

Promoters and enhancers for PHC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I008909 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 562.7 -1.0 -1034 7.1 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A FEZF1 ZNF2 GLIS2 ZNF143 PHC1 KLRG1 M6PR ENSG00000255829 MFAP5 A2ML1 A2ML1-AS2 ENSG00000282022 A2ML1-AS1
GH12I008241 Promoter/Enhancer 1.4 Ensembl ENCODE 41.3 -670.9 -670875 2.8 HDGF PKNOX1 ATF1 SMAD1 ARID4B SIN3A YY1 GLIS2 ZNF207 ATF7 FAM86FP PHC1 NANOG RIMKLB ENSG00000256552 LINC00612 LINC02449 GC12P008268
GH12I008947 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 17.9 +38.3 38317 8.7 CLOCK SMAD1 ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 YY1 POLR2B M6PR KLRG1 LOC642846 LINC00612 PHC1 DDX12P ENSG00000213443 FOXJ2 ENSG00000257105
GH12I009701 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 23 +788.7 788652 2.2 ZFP64 ZC3H11A EBF1 ZNF781 ZNF518A ZNF697 ZNF555 ZFHX2 RUNX3 EGR2 LINC02390 CLECL1 PHC1 CLEC2D KLRA1P LOC642846 KLRB1 DDX12P LINC00612 ENSG00000213443
GH12I009646 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 11.5 +737.8 737837 10 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 IRF4 SLC30A9 ZNF207 ZNF143 LOC105369728 CLEC2D LOC374443 DDX12P KLRB1 CLECL1 CLEC7A M6PR CLEC12A LOC642846
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHC1 gene promoter:

Genomic Locations for PHC1 Gene

Genomic Locations for PHC1 Gene
chr12:8,913,896-8,941,467
(GRCh38/hg38)
Size:
27,572 bases
Orientation:
Plus strand
chr12:9,066,492-9,094,063
(GRCh37/hg19)

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 (PubMed:12167701, PubMed:19636380, PubMed:21282530). Interacts with RNF2 and CBX7 (By similarity). Interacts with PHC2, PHC2 and BMI1 (By similarity).
    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

No Post-translational modifications

No data available for DME Specific Peptides for PHC1 Gene

Domains & Families for PHC1 Gene

Gene Families for PHC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

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.

Phenotypes From GWAS Catalog for PHC1 Gene

Gene Ontology (GO) - Molecular Function for PHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 19636380
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

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,TAS 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
GO:0070317 negative regulation of G0 to G1 transition TAS --
genes like me logo Genes that share ontologies with PHC1: view

No data available for SIGNOR curated interactions for PHC1 Gene

Drugs & Compounds for PHC1 Gene

No Compound Related Data Available

Transcripts for PHC1 Gene

Unigene Clusters for PHC1 Gene

Polyhomeotic homolog 1 (Drosophila):
Representative Sequences:

Clone 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
Regions:
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

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 33 34
  • 99.24 (n)
dog
(Canis familiaris)
Mammalia PHC1 34
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phc1 33
  • 89.07 (n)
mouse
(Mus musculus)
Mammalia Phc1 33 16 34
  • 88.84 (n)
cow
(Bos Taurus)
Mammalia PHC1 33 34
  • 88.41 (n)
oppossum
(Monodelphis domestica)
Mammalia PHC1 34
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHC1 34
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHC1 33 34
  • 72.79 (n)
lizard
(Anolis carolinensis)
Reptilia PHC1 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100488113 33
  • 64.54 (n)
Str.2700 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16260 33
zebrafish
(Danio rerio)
Actinopterygii phc1 34
  • 35 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta ph-d 34
  • 16 (a)
ManyToMany
ph-p 34
  • 16 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs587777036 pathogenic, likely-pathogenic, Primary autosomal recessive microcephaly 11, Intellectual disability, Primary microcephaly, Microcephaly 11, primary, autosomal recessive (MCPH11) [MIM:615414] 8,939,418(+) C/T coding_sequence_variant, missense_variant
rs878853029 likely-benign, not provided 8,933,055(+) G/A coding_sequence_variant, missense_variant
rs140650800 likely-benign, not specified 8,919,803(+) C/T coding_sequence_variant, synonymous_variant
rs144307674 likely-benign, not specified 8,934,335(+) G/A coding_sequence_variant, missense_variant
rs149376854 likely-benign, not specified 8,934,463(+) A/G coding_sequence_variant, synonymous_variant

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

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

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)

Additional Variant Information 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

(2) MalaCards diseases for PHC1 Gene - From: HGMD, OMIM, GTR, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microcephaly 11, primary, autosomal recessive
  • mcph11
microcephaly
  • microcephalus
- 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.

Additional Disease Information for 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 MJ … Otte AP (Molecular and cellular biology 1997) 2 3 4 22 58
  2. RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor. (PMID: 9199346) Satijn DP … Otte AP (Molecular and cellular biology 1997) 3 4 22 58
  3. Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis. (PMID: 23418308) Awad S … Poizat C (Human molecular genetics 2013) 3 4 58
  4. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. (PMID: 21282530) Vandamme J … Angrand PO (Molecular & cellular proteomics : MCP 2011) 3 4 58
  5. Several distinct polycomb complexes regulate and co-localize on the INK4a tumor suppressor locus. (PMID: 19636380) Maertens GN … Peters G (PloS one 2009) 3 4 58

Products for PHC1 Gene

Sources for PHC1 Gene

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