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Aliases for PGAM5 Gene

Aliases for PGAM5 Gene

  • PGAM Family Member 5, Mitochondrial Serine/Threonine Protein Phosphatase 2 3 5
  • Phosphoglycerate Mutase Family Member 5 2 3 4
  • PGAM Family Member 5, Serine/Threonine Protein Phosphatase, Mitochondrial 2 3
  • Bcl-XL-Binding Protein V68 3 4
  • Serine/Threonine-Protein Phosphatase PGAM5, Mitochondrial 3
  • EC 3.1.3.16 4
  • BXLBV68 3

External Ids for PGAM5 Gene

Previous GeneCards Identifiers for PGAM5 Gene

  • GC12P131797
  • GC12P133265
  • GC12P133287

Summaries for PGAM5 Gene

GeneCards Summary for PGAM5 Gene

PGAM5 (PGAM Family Member 5, Mitochondrial Serine/Threonine Protein Phosphatase) is a Protein Coding gene. Diseases associated with PGAM5 include Caspase 8 Deficiency. Among its related pathways are Mitophagy - animal and TNF signaling pathway. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and phosphatase activity.

UniProtKB/Swiss-Prot for PGAM5 Gene

  • Displays phosphatase activity for serine/threonine residues, and, dephosphorylates and activates MAP3K5 kinase. Has apparently no phosphoglycerate mutase activity. May be regulator of mitochondrial dynamics. Substrate for a KEAP1-dependent ubiquitin ligase complex. Contributes to the repression of NFE2L2-dependent gene expression. Acts as a central mediator for programmed necrosis induced by TNF, by reactive oxygen species and by calcium ionophore.

Additional gene information for PGAM5 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PGAM5 Gene

Genomics for PGAM5 Gene

GeneHancer (GH) Regulatory Elements for PGAM5 Gene

Promoters and enhancers for PGAM5 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
GH12J132709 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.1 63 2.7 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B ZNF213 E2F8 POLE GC12M132706 PGAM5 NOC4L ANKLE2 EP400 ZNF140 ZNF891 GOLGA3 SFSWAP
GH12J132765 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.6 +58.9 58887 9.2 HDGF PKNOX1 ATF1 SIN3A ZNF2 IRF4 POLR2B ZNF143 ATF7 RUNX3 ANKLE2 GOLGA3 PGAM5 CHFR LOC101928530 P2RX2 RPS11P5
GH12J132657 Enhancer 0.6 ENCODE 12.5 -50.1 -50055 6.8 CTCF DACH1 MAX MNT RAD21 GABPA POLR2A NFATC1 ZBTB33 POLE PGAM5 ANKLE2 GC12M132685 PIR54548
GH12J132684 Enhancer 0.2 Ensembl 13.1 -26.3 -26306 0.6 GC12M132685 PGAM5 POLE PIR54548
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGAM5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PGAM5 gene promoter:
  • Nkx2-5
  • Max1
  • c-Myc
  • Max
  • C/EBPalpha
  • AML1a
  • Ik-2

Genomic Locations for PGAM5 Gene

Genomic Locations for PGAM5 Gene
chr12:132,710,807-132,722,737
(GRCh38/hg38)
Size:
11,931 bases
Orientation:
Plus strand
chr12:133,287,393-133,299,323
(GRCh37/hg19)
Size:
11,931 bases
Orientation:
Plus strand

Genomic View for PGAM5 Gene

Genes around PGAM5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGAM5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGAM5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGAM5 Gene

Proteins for PGAM5 Gene

  • Protein details for PGAM5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96HS1-PGAM5_HUMAN
    Recommended name:
    Serine/threonine-protein phosphatase PGAM5, mitochondrial
    Protein Accession:
    Q96HS1
    Secondary Accessions:
    • A9LN06
    • C9IZY7
    • Q96JB0

    Protein attributes for PGAM5 Gene

    Size:
    289 amino acids
    Molecular mass:
    32004 Da
    Quaternary structure:
    • Dimer. Forms a ternary complex with NFE2L2 and KEAP1. Interacts with BCL2L1 and MAP3K5. Upon TNF-induced necrosis, forms in complex with RIPK1, RIPK3 and MLKL; the formation of this complex leads to PGAM5 phosphorylation. Isoform 2, but not isoform 1, interacts with DNM1L; this interaction leads to DNM1L dephosphorylation and activation and eventually to mitochondria fragmentation.

    Three dimensional structures from OCA and Proteopedia for PGAM5 Gene

    Alternative splice isoforms for PGAM5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGAM5 Gene

Post-translational modifications for PGAM5 Gene

  • Both isoform 1 and isoform 2 are phosphorylated by the RIPK1/RIPK3 complex under necrotic conditions. This phosphorylation increases PGAM5 phosphatase activity.
  • Ubiquitination at Lys141 and isoforms=288
  • Modification sites at PhosphoSitePlus

Other Protein References for PGAM5 Gene

No data available for DME Specific Peptides for PGAM5 Gene

Domains & Families for PGAM5 Gene

Gene Families for PGAM5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for PGAM5 Gene

Suggested Antigen Peptide Sequences for PGAM5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96HS1

UniProtKB/Swiss-Prot:

PGAM5_HUMAN :
  • The N-terminal 35 amino acids, including the potential transmembrane alpha-helix, function as a non-cleaved mitochondrial targeting sequence that targets the protein to the cytosolic side of the outer mitochondrial membrane.
  • Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily.
Domain:
  • The N-terminal 35 amino acids, including the potential transmembrane alpha-helix, function as a non-cleaved mitochondrial targeting sequence that targets the protein to the cytosolic side of the outer mitochondrial membrane.
Family:
  • Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily.
genes like me logo Genes that share domains with PGAM5: view

Function for PGAM5 Gene

Molecular function for PGAM5 Gene

UniProtKB/Swiss-Prot Function:
Displays phosphatase activity for serine/threonine residues, and, dephosphorylates and activates MAP3K5 kinase. Has apparently no phosphoglycerate mutase activity. May be regulator of mitochondrial dynamics. Substrate for a KEAP1-dependent ubiquitin ligase complex. Contributes to the repression of NFE2L2-dependent gene expression. Acts as a central mediator for programmed necrosis induced by TNF, by reactive oxygen species and by calcium ionophore.
UniProtKB/Swiss-Prot CatalyticActivity:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.

Enzyme Numbers (IUBMB) for PGAM5 Gene

Phenotypes From GWAS Catalog for PGAM5 Gene

Gene Ontology (GO) - Molecular Function for PGAM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004722 protein serine/threonine phosphatase activity TAS --
GO:0005096 GTPase activator activity IMP 22265414
GO:0005515 protein binding IPI 19590015
GO:0009400 obsolete signal transducer, downstream of receptor, with serine/threonine phosphatase activity IDA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PGAM5: view
genes like me logo Genes that share phenotypes with PGAM5: view

Animal Models for PGAM5 Gene

MGI Knock Outs for PGAM5:
  • Pgam5 Pgam5<tm1b(EUCOMM)Wtsi>
  • Pgam5 Pgam5<tm1a(EUCOMM)Wtsi>
  • Pgam5 Pgam5<tm1d(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for PGAM5

miRNA for PGAM5 Gene

miRTarBase miRNAs that target PGAM5

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PGAM5 Gene

Localization for PGAM5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGAM5 Gene

Mitochondrion outer membrane; Single-pass membrane protein. Note=Isoform 2 overexpression results in the formation of disconnected punctuate mitochondria distributed throughout the cytoplasm. Isoform 1 overexpression results in the clustering of mitochondria around the 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 PGAM5 gene
Compartment Confidence
mitochondrion 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PGAM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA,IEA --
GO:0005741 mitochondrial outer membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PGAM5: view

Pathways & Interactions for PGAM5 Gene

genes like me logo Genes that share pathways with PGAM5: view

Pathways by source for PGAM5 Gene

3 KEGG pathways for PGAM5 Gene

Gene Ontology (GO) - Biological Process for PGAM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0007165 signal transduction IEA --
GO:0012501 programmed cell death IEA --
GO:0016236 macroautophagy TAS --
GO:0016311 dephosphorylation IEA --
genes like me logo Genes that share ontologies with PGAM5: view

No data available for SIGNOR curated interactions for PGAM5 Gene

Drugs & Compounds for PGAM5 Gene

(2) Drugs for PGAM5 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

(1) Additional Compounds for PGAM5 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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
genes like me logo Genes that share compounds with PGAM5: view

Transcripts for PGAM5 Gene

mRNA/cDNA for PGAM5 Gene

Unigene Clusters for PGAM5 Gene

Phosphoglycerate mutase family member 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PGAM5 Gene

No ASD Table

Relevant External Links for PGAM5 Gene

GeneLoc Exon Structure for
PGAM5
ECgene alternative splicing isoforms for
PGAM5

Expression for PGAM5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PGAM5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PGAM5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.0) and Adrenal (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PGAM5 Gene



Protein tissue co-expression partners for PGAM5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PGAM5 Gene:

PGAM5

SOURCE GeneReport for Unigene cluster for PGAM5 Gene:

Hs.102558

Evidence on tissue expression from TISSUES for PGAM5 Gene

  • Kidney(4)
genes like me logo Genes that share expression patterns with PGAM5: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGAM5 Gene

Orthologs for PGAM5 Gene

This gene was present in the common ancestor of animals.

Orthologs for PGAM5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PGAM5 34 33
  • 99.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PGAM5 34 33
  • 88.08 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PGAM5 34 33
  • 87.62 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PGAM5 34
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pgam5 16 34 33
  • 84.79 (n)
rat
(Rattus norvegicus)
Mammalia Pgam5 33
  • 84.67 (n)
oppossum
(Monodelphis domestica)
Mammalia PGAM5 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves PGAM5 34 33
  • 74.17 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PGAM5 34
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pgam5 33
  • 65.71 (n)
Str.1334 33
African clawed frog
(Xenopus laevis)
Amphibia LOC398484 33
zebrafish
(Danio rerio)
Actinopterygii pgam5 34 33
  • 64.4 (n)
OneToOne
Dr.24263 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10049 33
fruit fly
(Drosophila melanogaster)
Insecta Pgam5 34 33
  • 55.14 (n)
OneToMany
Pgam5-2 34
  • 40 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002535 33
  • 54.97 (n)
worm
(Caenorhabditis elegans)
Secernentea pgam-5 34 33
  • 55.31 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3656 34
  • 47 (a)
OneToMany
-- 34
  • 45 (a)
OneToMany
Species where no ortholog for PGAM5 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)
  • 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)

Evolution for PGAM5 Gene

ENSEMBL:
Gene Tree for PGAM5 (if available)
TreeFam:
Gene Tree for PGAM5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGAM5: view image

Paralogs for PGAM5 Gene

Pseudogenes.org Pseudogenes for PGAM5 Gene

genes like me logo Genes that share paralogs with PGAM5: view

No data available for Paralogs for PGAM5 Gene

Variants for PGAM5 Gene

Sequence variations from dbSNP and Humsavar for PGAM5 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000002859 -- 132,713,379(+) C/G intron_variant
rs1000031393 -- 132,722,699(+) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000167188 -- 132,711,287(+) C/T intron_variant
rs1000520795 -- 132,719,639(+) G/A downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000823642 -- 132,719,749(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PGAM5 Gene

Variant ID Type Subtype PubMed ID
esv3631310 CNV loss 21293372
esv3631311 CNV gain 21293372
nsv1037074 CNV gain 25217958
nsv1047500 CNV gain 25217958
nsv561121 CNV gain 21841781
nsv952512 CNV deletion 24416366

Variation tolerance for PGAM5 Gene

Residual Variation Intolerance Score: 66.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.88; 48.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGAM5 Gene

Human Gene Mutation Database (HGMD)
PGAM5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGAM5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGAM5 Gene

Disorders for PGAM5 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PGAM5 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
caspase 8 deficiency
  • ceds
- elite association - COSMIC cancer census association via MalaCards
Search PGAM5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PGAM5

genes like me logo Genes that share disorders with PGAM5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PGAM5 Gene

Publications for PGAM5 Gene

  1. Mitochondrial phosphoglycerate mutase 5 uses alternate catalytic activity as a protein serine/threonine phosphatase to activate ASK1. (PMID: 19590015) Takeda K … Ichijo H (Proceedings of the National Academy of Sciences of the United States of America 2009) 2 3 4 58
  2. PGAM5 tethers a ternary complex containing Keap1 and Nrf2 to mitochondria. (PMID: 18387606) Lo SC … Hannink M (Experimental cell research 2008) 3 4 22 58
  3. PGAM5, a Bcl-XL-interacting protein, is a novel substrate for the redox-regulated Keap1-dependent ubiquitin ligase complex. (PMID: 17046835) Lo SC … Hannink M (The Journal of biological chemistry 2006) 3 4 22 58
  4. In vitro selection and characterization of Bcl-X(L)-binding proteins from a mix of tissue-specific mRNA display libraries. (PMID: 11283018) Hammond PW … Kreider BL (The Journal of biological chemistry 2001) 2 3 4 58
  5. The mitochondrial phosphatase PGAM5 functions at the convergence point of multiple necrotic death pathways. (PMID: 22265414) Wang Z … Wang X (Cell 2012) 3 4 58

Products for PGAM5 Gene

Sources for PGAM5 Gene

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