This intronless gene appears to have arisen from a retrotransposition event, yet it is thought to be an expressed, protein-coding gene. The encoded protein is a member of the phosphoglycerate mutase family, a set of enzymes that catalyze the transfer of a phosphate group from 3-phosphoglycerate to 2-phosphoglycerate. [provided by RefSeq, May 2010] See more...

Aliases for PGAM4 Gene

Aliases for PGAM4 Gene

  • Phosphoglycerate Mutase Family Member 4 2 3 5
  • PGAM3 2 3 4
  • Probable Phosphoglycerate Mutase 4 3 4
  • DJ1000K24.1 2 3
  • PGAM-B 2 3
  • PGAM1 2 3
  • Phosphoglycerate Mutase Processed Protein 3
  • Phosphoglycerate Mutase Family 4 2
  • Phosphoglycerate Mutase Family 3 3
  • Phosphoglycerate Mutase 4 3
  • EC 5.4.2.11 4
  • EC 5.4.2.1 51
  • EC 5.4.2.4 4
  • PGAM4 5

External Ids for PGAM4 Gene

Previous GeneCards Identifiers for PGAM4 Gene

  • GC0XM9L0730
  • GC0XM077110
  • GC0XM077223
  • GC0XM070810

Summaries for PGAM4 Gene

Entrez Gene Summary for PGAM4 Gene

  • This intronless gene appears to have arisen from a retrotransposition event, yet it is thought to be an expressed, protein-coding gene. The encoded protein is a member of the phosphoglycerate mutase family, a set of enzymes that catalyze the transfer of a phosphate group from 3-phosphoglycerate to 2-phosphoglycerate. [provided by RefSeq, May 2010]

GeneCards Summary for PGAM4 Gene

PGAM4 (Phosphoglycerate Mutase Family Member 4) is a Protein Coding gene. Diseases associated with PGAM4 include Menkes Disease and Myopathy, Congenital, Compton-North. Among its related pathways are Glucose metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include intramolecular transferase activity, phosphotransferases and bisphosphoglycerate 2-phosphatase activity. An important paralog of this gene is PGAM1.

Additional gene information for PGAM4 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PGAM4 Gene

Genomics for PGAM4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PGAM4 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
GH0XJ077970 Enhancer 0.2 FANTOM5 600.7 -1.1 -1143 0 PGAM4 MN298703 RF00017-8545 piR-37184-004 piR-57138-052 lnc-COX7B-6 PGK1 ATP7A TAF9B
GH0XJ077936 Enhancer 1 Ensembl ENCODE 14.3 +28.3 28337 11.8 ETV6 DPF2 SOX6 TCF12 EP300 CBX3 SP1 CEBPB CTBP1 NFE2 PGAM4 TAF9B CYSLTR1 piR-35674-562 RF00017-8540 piR-36393-557 lnc-COX7B-4 ATP7A PGK1 ENSG00000248503
GH0XJ077998 Enhancer 0.2 Ensembl 14 -29.2 -29163 0.8 TAF9B PGAM4 lnc-COX7B-6 piR-57138-052 ATP7A PGK1
GH0XJ077909 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 0.2 +58.1 58137 3.8 GATAD2A PRDM10 REST TFE3 CTCF JUND ETV6 GABPA PRDM1 POLR2A ATP7A ENSG00000248503 PGK1 lnc-COX7B-4 MN298114-321 RF00017-8540 PGAM4
GH0XJ077975 Enhancer 0.6 Ensembl ENCODE 0.4 -6.4 -6435 0.3 CEBPB JUN EP300 STAT3 TCF7L2 RF00017-8545 PGAM4 piR-57138-052 lnc-COX7B-6 PGK1 ATP7A TAF9B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGAM4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PGAM4

Top Transcription factor binding sites by QIAGEN in the PGAM4 gene promoter:
  • AML1a
  • E47
  • GATA-2
  • HFH-1
  • POU2F1
  • POU2F1a
  • PPAR-gamma1
  • PPAR-gamma2
  • S8
  • SRY

Genomic Locations for PGAM4 Gene

Genomic Locations for PGAM4 Gene
chrX:77,967,949-77,969,638
(GRCh38/hg38)
Size:
1,690 bases
Orientation:
Minus strand
chrX:77,223,458-77,225,135
(GRCh37/hg19)
Size:
1,678 bases
Orientation:
Minus strand

Genomic View for PGAM4 Gene

Genes around PGAM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGAM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGAM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGAM4 Gene

Proteins for PGAM4 Gene

  • Protein details for PGAM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N0Y7-PGAM4_HUMAN
    Recommended name:
    Probable phosphoglycerate mutase 4
    Protein Accession:
    Q8N0Y7
    Secondary Accessions:
    • Q5JPN2
    • Q8NI24
    • Q8NI25
    • Q8NI26

    Protein attributes for PGAM4 Gene

    Size:
    254 amino acids
    Molecular mass:
    28777 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • This is the product of a processed gene created by retroposition from mRNA of an expressed gene. This gene seems to be expressed.

neXtProt entry for PGAM4 Gene

Selected DME Specific Peptides for PGAM4 Gene

Q8N0Y7:
  • IWRRSYD
  • GLNKAETA
  • LVLIRHG
  • WRRSYDV
  • VLIAAHGNS
  • LNERHYG

Post-translational modifications for PGAM4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PGAM4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for PGAM4 Gene

Gene Families for PGAM4 Gene

Protein Domains for PGAM4 Gene

InterPro:
Blocks:
  • Phosphoglycerate/bisphosphoglycerate mutase
ProtoNet:

Suggested Antigen Peptide Sequences for PGAM4 Gene

GenScript: Design optimal peptide antigens:
  • Probable phosphoglycerate mutase 4 (PGAM4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N0Y7

UniProtKB/Swiss-Prot:

PGAM4_HUMAN :
  • Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily.
Family:
  • Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily.
genes like me logo Genes that share domains with PGAM4: view

Function for PGAM4 Gene

Molecular function for PGAM4 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate; Xref=Rhea:RHEA:15901, ChEBI:CHEBI:58272, ChEBI:CHEBI:58289; EC=5.4.2.11; Evidence={ECO:0000250|UniProtKB:P18669};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(2R)-3-phospho-glyceroyl phosphate = (2R)-2,3-bisphosphoglycerate + H(+); Xref=Rhea:RHEA:17765, ChEBI:CHEBI:15378, ChEBI:CHEBI:57604, ChEBI:CHEBI:58248; EC=5.4.2.4; Evidence={ECO:0000250|UniProtKB:P18669};.

Enzyme Numbers (IUBMB) for PGAM4 Gene

Gene Ontology (GO) - Molecular Function for PGAM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004082 bisphosphoglycerate mutase activity IEA --
GO:0004619 phosphoglycerate mutase activity NAS 11961099
GO:0016787 hydrolase activity IEA --
GO:0016853 isomerase activity IEA --
genes like me logo Genes that share ontologies with PGAM4: view

Phenotypes for PGAM4 Gene

genes like me logo Genes that share phenotypes with PGAM4: view

Animal Model Products

CRISPR Products

miRNA for PGAM4 Gene

miRTarBase miRNAs that target PGAM4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGAM4

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PGAM4 Gene

Localization for PGAM4 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 PGAM4 gene
Compartment Confidence
extracellular 4
cytosol 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
nucleus 2
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PGAM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070062 extracellular exosome HDA 23533145
GO:0097228 sperm principal piece IDA 22590500
genes like me logo Genes that share ontologies with PGAM4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PGAM4 Gene

Pathways & Interactions for PGAM4 Gene

genes like me logo Genes that share pathways with PGAM4: view

Pathways by source for PGAM4 Gene

1 GeneGo (Thomson Reuters) pathway for PGAM4 Gene
  • Glycolysis and gluconeogenesis (short map)

Gene Ontology (GO) - Biological Process for PGAM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006096 glycolytic process NAS 11961099
GO:1902093 positive regulation of flagellated sperm motility NAS 22590500
genes like me logo Genes that share ontologies with PGAM4: view

No data available for SIGNOR curated interactions for PGAM4 Gene

Drugs & Compounds for PGAM4 Gene

(4) Drugs for PGAM4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
2-phospho-D-glyceric acid Experimental Pharma 0
3-Phosphoglyceric acid Experimental Pharma 0

(3) Additional Compounds for PGAM4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2,3-Diphosphoglyceric acid
  • 2,3-bisphospho-D-Glycerate
  • 2,3-Bisphosphoglyceric acid
  • 2,3-BPG
  • 2,3-disphospho-D-Glycerate
  • D-Greenwald ester
138-81-8
2-Phosphoglyceric acid
  • 3-Hydroxy-2-(phosphonooxy)propanoic acid
  • 3-Hydroxy-2-(phosphonooxy)propanoate
  • 2-Phosphoglycerate
  • 2-(Dihydrogen phosphate)glycerate
  • 2-(Dihydrogen phosphate)glyceric acid
2553-59-5
Glyceric acid 1,3-biphosphate
  • 1,3-Biphosphoglycerate
  • 1,3-Biphosphoglyceric acid
  • 1,3-Bis-phosphoglycerate
  • 1,3-Bisphosphoglycerate
  • 1,3-Diphosphateglycerate
1981-49-3
genes like me logo Genes that share compounds with PGAM4: view

Transcripts for PGAM4 Gene

mRNA/cDNA for PGAM4 Gene

1 REFSEQ mRNAs :
1 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGAM4

Alternative Splicing Database (ASD) splice patterns (SP) for PGAM4 Gene

No ASD Table

Relevant External Links for PGAM4 Gene

GeneLoc Exon Structure for
PGAM4

Expression for PGAM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PGAM4 Gene

Protein differential expression in normal tissues from HIPED for PGAM4 Gene

This gene is overexpressed in Lung (34.4), Lavage (12.2), and Brain (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PGAM4 Gene



Protein tissue co-expression partners for PGAM4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PGAM4

SOURCE GeneReport for Unigene cluster for PGAM4 Gene:

Hs.632822

Evidence on tissue expression from TISSUES for PGAM4 Gene

  • Blood(2.9)
  • Nervous system(2.9)
  • Kidney(2.6)
  • Liver(2.5)
  • Spleen(2.4)
  • Heart(2.3)
  • Skin(2.3)
  • Bone marrow(2.3)
  • Lung(2.2)
  • Lymph node(2.2)
  • Intestine(2.1)
  • Thyroid gland(2.1)
  • Eye(2)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with PGAM4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGAM4 Gene

Orthologs for PGAM4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PGAM4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PGAM4 30
  • 99.34 (n)
Cow
(Bos Taurus)
Mammalia PGAM1 31
  • 96 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia PGAM4 31
  • 95 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Pgam1 31
  • 95 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 93 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 75 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves PGAM1 31
  • 90 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 88 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii pgam1a 31
  • 87 (a)
ManyToMany
pgam1b 31
  • 87 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Pglym78 31
  • 65 (a)
ManyToMany
Pglym87 31
  • 52 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GPM1 31
  • 49 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.4977 31
  • 60 (a)
OneToMany
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gpm1 30
  • 55.09 (n)
Species where no ortholog for PGAM4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PGAM4 Gene

ENSEMBL:
Gene Tree for PGAM4 (if available)
TreeFam:
Gene Tree for PGAM4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGAM4: view image

Paralogs for PGAM4 Gene

Paralogs for PGAM4 Gene

(3) SIMAP similar genes for PGAM4 Gene using alignment to 1 proteins:

  • PGAM4_HUMAN

Pseudogenes.org Pseudogenes for PGAM4 Gene

genes like me logo Genes that share paralogs with PGAM4: view

Variants for PGAM4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGAM4 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
804036 Benign: Menkes kinky-hair syndrome 77,969,382(-) C/T MISSENSE_VARIANT,INTRON_VARIANT
rs376654190 Benign: not provided 77,968,990(-) C/T MISSENSE_VARIANT,INTRON_VARIANT
rs5959129 - p.Arg90Gln
rs782408548 - p.Arg40Cys
VAR_014357 - p.Ile175Thr

Additional dbSNP identifiers (rs#s) for PGAM4 Gene

Structural Variations from Database of Genomic Variants (DGV) for PGAM4 Gene

Variant ID Type Subtype PubMed ID
esv2758874 CNV loss 17122850

Variation tolerance for PGAM4 Gene

Residual Variation Intolerance Score: 85.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.14; 61.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGAM4 Gene

Human Gene Mutation Database (HGMD)
PGAM4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGAM4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGAM4 Gene

Disorders for PGAM4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PGAM4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
menkes disease
  • mnk
myopathy, congenital, compton-north
  • mypcn
myxosarcoma
- elite association - COSMIC cancer census association via MalaCards
Search PGAM4 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with PGAM4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PGAM4 Gene

Publications for PGAM4 Gene

  1. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. (PMID: 11961099) Betrán E … Long M (Molecular biology and evolution 2002) 2 3 4 23
  2. Emergence of young human genes after a burst of retroposition in primates. (PMID: 16201836) Marques AC … Kaessmann H (PLoS biology 2005) 3 4
  3. A phosphoglycerate mutase brain isoform (PGAM 1) pseudogene is localized within the human Menkes disease gene (ATP7 A). (PMID: 9370262) Dierick HA … Glover TW (Gene 1997) 2 3
  4. Assembly of the WHIP-TRIM14-PPP6C Mitochondrial Complex Promotes RIG-I-Mediated Antiviral Signaling. (PMID: 29053956) Tan P … Wang RF (Molecular cell 2017) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for PGAM4 Gene

  • Signalway Proteins for PGAM4

Sources for PGAM4 Gene