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GCM1 Gene(Protein Coding)

Glial Cells Missing Homolog 1

GCID:
GC06M053099
GIFtS:
43
Genes Participants
UDN Logo

Aliases for GCM1 Gene

Aliases for GCM1 Gene

  • Glial Cells Missing Homolog 1 2 3 4 5
  • GCM Motif Protein 1 3 4
  • HGCMa 3 4
  • GCMA 3 4
  • Glial Cells Missing (Drosophila) Homolog A 2
  • Glial Cells Missing Homolog 1 (Drosophila) 2
  • Chorion-Specific Transcription Factor GCMa 3

External Ids for GCM1 Gene

Previous HGNC Symbols for GCM1 Gene

  • GCMA

Previous GeneCards Identifiers for GCM1 Gene

  • GC06M052993
  • GC06M053039
  • GC06M052991
  • GC06M052823

Summaries for GCM1 Gene

Entrez Gene Summary for GCM1 Gene

  • This gene encodes a DNA-binding protein with a gcm-motif (glial cell missing motif). The encoded protein is a homolog of the Drosophila glial cells missing gene (gcm). This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for GCM1 Gene

GCM1 (Glial Cells Missing Homolog 1) is a Protein Coding gene. Among its related pathways are Human Early Embryo Development. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is GCM2.

UniProtKB/Swiss-Prot for GCM1 Gene

  • Transcription factor involved in the control of expression of placental growth factor (PGF) and other placenta-specific genes (PubMed:10542267, PubMed:18160678). Binds to the trophoblast-specific element 2 (TSE2) of the aromatase gene enhancer (PubMed:10542267). Binds to the SYDE1 promoter (PubMed:27917469). Has a central role in mediating the differentiation of trophoblast cells along both the villous and extravillous pathways in placental development (PubMed:19219068).

Gene Wiki entry for GCM1 Gene

Additional gene information for GCM1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GCM1 Gene

Genomics for GCM1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for GCM1 Gene

Promoters and enhancers for GCM1 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
GH06I053148 Promoter 0.7 EPDnew 550.8 0.0 -21 0.1 NFIC NFIA ZNF189 GCM1 GC06M053154 RNU6-464P
GH06I053147 Promoter 0.5 EPDnew 550.8 +0.9 878 0.1 GCM1 ENSG00000261745
GH06I053119 Enhancer 1.1 Ensembl ENCODE 12.3 +28.9 28891 1.8 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 ETS1 TCF12 SLC30A9 FOS GCM1 RNU6-464P ENSG00000218713 ICK ENSG00000261745 PIR53393
GH06I053213 Enhancer 0.4 dbSUPER 12.9 -67.3 -67284 4.4 NCOA3 GATA3 ELF1 ENSG00000218713 GCM1 GC06P053222 GC06P053224 PIR36996
GH06I053218 Enhancer 0.2 dbSUPER 12.2 -71.3 -71292 2.6 GC06P053222 GC06P053224 RNU1-136P ENSG00000218713 GCM1 GC06M053235
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GCM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GCM1 gene promoter:

Genomic Locations for GCM1 Gene

Genomic Locations for GCM1 Gene
chr6:53,126,961-53,148,829
(GRCh38/hg38)
Size:
21,869 bases
Orientation:
Minus strand
chr6:52,991,759-53,013,627
(GRCh37/hg19)

Genomic View for GCM1 Gene

Genes around GCM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GCM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GCM1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GCM1 Gene

Proteins for GCM1 Gene

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  2. Protein
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  • Protein details for GCM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NP62-GCM1_HUMAN
    Recommended name:
    Chorion-specific transcription factor GCMa
    Protein Accession:
    Q9NP62
    Secondary Accessions:
    • Q4VAQ7
    • Q5T0X0
    • Q99468
    • Q9P1X3

    Protein attributes for GCM1 Gene

    Size:
    436 amino acids
    Molecular mass:
    49268 Da
    Quaternary structure:
    No Data Available

neXtProt entry for GCM1 Gene

Protein Expression for GCM1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for GCM1 Gene

  • Polyubiquitinated in the presence of UBE2D2 and FBXW2 (in vitro).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for GCM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GCM1 Gene

Domains & Families for GCM1 Gene

Gene Families for GCM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for GCM1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GCM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with GCM1: view

No data available for UniProtKB/Swiss-Prot for GCM1 Gene

Function for GCM1 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for GCM1 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor involved in the control of expression of placental growth factor (PGF) and other placenta-specific genes (PubMed:10542267, PubMed:18160678). Binds to the trophoblast-specific element 2 (TSE2) of the aromatase gene enhancer (PubMed:10542267). Binds to the SYDE1 promoter (PubMed:27917469). Has a central role in mediating the differentiation of trophoblast cells along both the villous and extravillous pathways in placental development (PubMed:19219068).

Phenotypes From GWAS Catalog for GCM1 Gene

Gene Ontology (GO) - Molecular Function for GCM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 15385555
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IDA 23867755
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 15385555
GO:0003677 DNA binding TAS 8962155
GO:0003700 DNA binding transcription factor activity IDA 15385555
genes like me logo Genes that share ontologies with GCM1: view
genes like me logo Genes that share phenotypes with GCM1: view

Animal Models for GCM1 Gene

MGI Knock Outs for GCM1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GCM1 Gene

Localization for GCM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GCM1 Gene

Nucleus.

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 GCM1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GCM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 23867755
GO:0005667 transcription factor complex IDA 15385555
genes like me logo Genes that share ontologies with GCM1: view

Pathways & Interactions for GCM1 Gene

genes like me logo Genes that share pathways with GCM1: view

Pathways by source for GCM1 Gene

1 Qiagen pathway for GCM1 Gene

Gene Ontology (GO) - Biological Process for GCM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IDA 15385555
GO:0006366 transcription by RNA polymerase II IDA 23867755
GO:0007275 multicellular organism development IEA --
GO:0009653 anatomical structure morphogenesis TAS 8962155
genes like me logo Genes that share ontologies with GCM1: view

No data available for SIGNOR curated interactions for GCM1 Gene

Drugs & Compounds for GCM1 Gene

Products:

  1. Drug

(1) Drugs for GCM1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with GCM1: view

Transcripts for GCM1 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for GCM1 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(26) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for GCM1 Gene

Glial cells missing homolog 1 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GCM1 Gene

No ASD Table

Relevant External Links for GCM1 Gene

GeneLoc Exon Structure for
GCM1
ECgene alternative splicing isoforms for
GCM1

Expression for GCM1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GCM1 Gene

mRNA expression in normal human tissues for GCM1 Gene
mRNA expression by BioGPS for GCM1 GenemRNA expression by GTEx for GCM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GCM1 Gene

This gene is overexpressed in Whole Blood (x20.6), Testis (x6.3), and Kidney - Cortex (x5.6).

Protein differential expression in normal tissues from HIPED for GCM1 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for GCM1 Gene



Protein tissue co-expression partners for GCM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of GCM1 Gene:

GCM1

SOURCE GeneReport for Unigene cluster for GCM1 Gene:

Hs.28346

mRNA Expression by UniProt/SwissProt for GCM1 Gene:

Q9NP62-GCM1_HUMAN
Tissue specificity: Higly expressed in the placenta (PubMed:10542267). Expressed in trophoblast cells of the villi (PubMed:27917469).

Evidence on tissue expression from TISSUES for GCM1 Gene

  • Liver(4)
genes like me logo Genes that share expression patterns with GCM1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GCM1 Gene

Orthologs for GCM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for GCM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia GCM1 34 33
  • 99.77 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia GCM1 34 33
  • 86.05 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Gcm1 34 16 33
  • 78.9 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Gcm1 33
  • 77.91 (n)
cow
(Bos Taurus)
 Mammalia GCM-1 34
  • 75 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia GCM1 34
  • 66 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia GCM1 34
  • 37 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves GCM1 34 33
  • 59.29 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia GCM1 34
  • 65 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia gcm1 33
  • 56.23 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.16562 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP007782 33
  • 61.31 (n)
fruit fly
(Drosophila melanogaster)
 Insecta gcm 34
  • 23 (a)
 ManyToMany
gcm2 34
  • 19 (a)
 ManyToMany
Species where no ortholog for GCM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • zebrafish (Danio rerio)

Evolution for GCM1 Gene

ENSEMBL:
Gene Tree for GCM1 (if available)
TreeFam:
Gene Tree for GCM1 (if available)

Paralogs for GCM1 Gene

Paralogs for GCM1 Gene

(1) SIMAP similar genes for GCM1 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for GCM1 Gene

genes like me logo Genes that share paralogs with GCM1: view

Variants for GCM1 Gene

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Sequence variations from dbSNP and Humsavar for GCM1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000017172 -- 53,256,623(-) A/T genic_upstream_transcript_variant, intron_variant
rs1000024893 -- 53,126,575(-) T/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs1000038607 -- 53,198,027(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000046027 -- 53,239,428(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000053844 -- 53,139,150(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for GCM1 Gene

Variant ID Type Subtype PubMed ID
nsv1124063 CNV deletion 24896259

Variation tolerance for GCM1 Gene

Residual Variation Intolerance Score: 53.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.29; 25.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GCM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GCM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GCM1 Gene

Disorders for GCM1 Gene

Additional Disease Information for GCM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for GCM1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GCM1 Gene

Publications for GCM1 Gene

  1. Parallel genotyping of 10,204 single nucleotide polymorphisms to screen for susceptible genes for IgA nephropathy. (PMID: 19890582) Woo KT … Chan CM (Annals of the Academy of Medicine, Singapore 2009) 3 22 44 58
  2. Glial cell missing 1 regulates placental growth factor (PGF) gene transcription in human trophoblast. (PMID: 18160678) Chang M … Torry DS (Biology of reproduction 2008) 3 4 22 58
  3. Ubiquitin-conjugating enzyme UBE2D2 is responsible for FBXW2 (F-box and WD repeat domain containing 2)-mediated human GCM1 (glial cell missing homolog 1) ubiquitination and degradation. (PMID: 18703417) Chiang MH … Chen H (Biology of reproduction 2008) 3 4 22 58
  4. Genomic organization, chromosomal localization, and the complete 22 kb DNA sequence of the human GCMa/GCM1, a placenta-specific transcription factor gene. (PMID: 11071865) Yamada K … Okazaki T (Biochemical and biophysical research communications 2000) 3 4 22 58
  5. The gcm-motif: a novel DNA-binding motif conserved in Drosophila and mammals. (PMID: 8962155) Akiyama Y … Hotta Y (Proceedings of the National Academy of Sciences of the United States of America 1996) 2 3 4 58

Products for GCM1 Gene

Sources for GCM1 Gene

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