Human Gene PGAM5 (uc009zyv.3) Description and Page Index
  Description: Homo sapiens phosphoglycerate mutase family member 5 (PGAM5), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:133,287,393-133,299,323 Size: 11,931 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr12:133,287,463-133,297,414 Size: 9,952 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:133,287,393-133,299,323)mRNA (may differ from genome)Protein (289 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
ReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Serine/threonine-protein phosphatase PGAM5, mitochondrial; EC=; AltName: Full=Bcl-XL-binding protein v68; AltName: Full=Phosphoglycerate mutase family member 5;
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.
CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.
SUBUNIT: Dimer. Forms a ternary complex with NFE2L2 and KEAP1. Interacts with BCL2L1 and MAP3K5.
SUBCELLULAR LOCATION: Mitochondrion. Mitochondrion outer membrane. Membrane; Single-pass membrane protein (Potential). 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.
DOMAIN: According to PubMed:18387606, may contain a non-cleaved N- terminal mitochondrial targeting sequence that targets PGAM5 to the cytosolic side of the outer mitochondrial membrane, instead of a N-terminal transmembrane.
SIMILARITY: Belongs to the phosphoglycerate mutase family. BPG- dependent PGAM subfamily.

-  MalaCards Disease Associations
  MalaCards Gene Search: PGAM5
Diseases sorted by gene-association score: autoimmune lymphoproliferative syndrome, type iib (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.08 RPKM in Testis
Total median expression: 20.15 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -38.3070-0.547 Picture PostScript Text
3' UTR -899.731909-0.471 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013078 - His_Pase_superF_clade-1

Pfam Domains:
PF00300 - Histidine phosphatase superfamily (branch 1)

SCOP Domains:
53254 - Phosphoglycerate mutase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q96HS1
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004721 phosphoprotein phosphatase activity
GO:0004722 protein serine/threonine phosphatase activity
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0044877 macromolecular complex binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0012501 programmed cell death
GO:0016236 macroautophagy
GO:0016311 dephosphorylation
GO:0043547 positive regulation of GTPase activity
GO:0070266 necroptotic process

Cellular Component:
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  BC047906 - Homo sapiens phosphoglycerate mutase family member 5, mRNA (cDNA clone IMAGE:5503728).
AK301831 - Homo sapiens cDNA FLJ54922 complete cds.
EU249757 - Homo sapiens phosphoglycerate mutase 5, long isoform (PGAM5-L) mRNA, complete cds.
BC008196 - Homo sapiens phosphoglycerate mutase family member 5, mRNA (cDNA clone MGC:5352 IMAGE:3048106), complete cds.
AK097688 - Homo sapiens cDNA FLJ40369 fis, clone TESTI2034847.
AF357523 - Homo sapiens Bcl-XL-binding protein v68 mRNA, partial cds.
JD194965 - Sequence 175989 from Patent EP1572962.
JD194966 - Sequence 175990 from Patent EP1572962.
JD130748 - Sequence 111772 from Patent EP1572962.
JD431392 - Sequence 412416 from Patent EP1572962.
JD268519 - Sequence 249543 from Patent EP1572962.
JD292183 - Sequence 273207 from Patent EP1572962.
JD364950 - Sequence 345974 from Patent EP1572962.
JD364949 - Sequence 345973 from Patent EP1572962.
JD218504 - Sequence 199528 from Patent EP1572962.
JD522077 - Sequence 503101 from Patent EP1572962.
JD107265 - Sequence 88289 from Patent EP1572962.
JD476737 - Sequence 457761 from Patent EP1572962.
JD414850 - Sequence 395874 from Patent EP1572962.
JD379696 - Sequence 360720 from Patent EP1572962.
JD311827 - Sequence 292851 from Patent EP1572962.
JD255951 - Sequence 236975 from Patent EP1572962.
JD426708 - Sequence 407732 from Patent EP1572962.
JD409250 - Sequence 390274 from Patent EP1572962.
JD396146 - Sequence 377170 from Patent EP1572962.
JD264725 - Sequence 245749 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96HS1 (Reactome details) participates in the following event(s):

R-HSA-8948139 p-S13-FUNDC1 is dephosphorylated by PGAM5
R-HSA-8934903 Receptor Mediated Mitophagy
R-HSA-5205647 Mitophagy

-  Other Names for This Gene
  Alternate Gene Symbols: A9LN06, C9IZY7, NM_001170543, NP_001164014, PGAM5_HUMAN, Q96HS1, Q96JB0
UCSC ID: uc009zyv.3
RefSeq Accession: NM_001170543
Protein: Q96HS1 (aka PGAM5_HUMAN)
CCDS: CCDS53845.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001170543.1
exon count: 6CDS single in 3' UTR: no RNA size: 2851
ORF size: 870CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1749.00frame shift in genome: no % Coverage: 99.93
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.