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    PGAM5 PGAM family member 5, mitochondrial serine/threonine protein phosphatase [ Homo sapiens (human) ]

    Gene ID: 192111, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PGAM5provided by HGNC
    Official Full Name
    PGAM family member 5, mitochondrial serine/threonine protein phosphataseprovided by HGNC
    Primary source
    HGNC:HGNC:28763
    See related
    Ensembl:ENSG00000247077 MIM:614939; AllianceGenome:HGNC:28763
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BXLBV68
    Summary
    Enables GTPase activator activity and protein serine/threonine phosphatase activity. Involved in necroptotic process. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in esophagus (RPKM 6.8), testis (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PGAM5 in Genome Data Viewer
    Location:
    12q24.33
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (132710842..132722734)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (132759704..132771989)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (133287428..133299320)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene DNA polymerase epsilon, catalytic subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5123 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_26027 Neighboring gene peroxisomal membrane protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:133280509-133281382 Neighboring gene uncharacterized LOC124903063 Neighboring gene MPRA-validated peak2052 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5125 Neighboring gene RNA, 5S ribosomal pseudogene 379 Neighboring gene ankyrin repeat and LEM domain containing 2 Neighboring gene TPD52 like 2 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Phosphoglycerate mutase family member 5 maintains oocyte quality via mitochondrial dynamic rearrangement during aging. Li CJ, et al. Aging Cell, 2022 Feb. PMID 34995407, Free PMC Article
    2. A regulatory signaling loop comprising the PGAM5 phosphatase and CK2 controls receptor-mediated mitophagy. Chen G, et al. Mol Cell, 2014 May 8. PMID 24746696
    3. PGAM5 expression and macrophage signatures in non-small cell lung cancer associated with chronic obstructive pulmonary disease (COPD). Ng Kee Kwong F, et al. BMC Cancer, 2018 Dec 10. PMID 30526542, Free PMC Article
    4. PGAM5 deacetylation mediated by SIRT2 facilitates lipid metabolism and liver cancer proliferation. Fu G, et al. Acta Biochim Biophys Sin (Shanghai), 2023 Aug 15. PMID 37580952, Free PMC Article
    5. PGAM5 expression levels in heart failure and protection ROS-induced oxidative stress and ferroptosis by Keap1/Nrf2. Li S, et al. Clin Exp Hypertens, 2023 Dec 31. PMID 36780919

    See all (219) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pgam5 aggravates hyperglycemia-induced myocardial dysfunction through disrupting Phb2-dependent mitochondrial dynamics.
      Title: Pgam5 aggravates hyperglycemia-induced myocardial dysfunction through disrupting Phb2-dependent mitochondrial dynamics.
    2. ZBP1 promotes hepatocyte pyroptosis in acute liver injury by regulating the PGAM5/ROS pathway.
      Title: ZBP1 promotes hepatocyte pyroptosis in acute liver injury by regulating the PGAM5/ROS pathway.
    3. Targeted knockdown of PGAM5 in synovial macrophages efficiently alleviates osteoarthritis.
      Title: Targeted knockdown of PGAM5 in synovial macrophages efficiently alleviates osteoarthritis.
    4. The Effect of PGAM5 on Regulating Mitochondrial Dysfunction in Ischemic Stroke.
      Title: The Effect of PGAM5 on Regulating Mitochondrial Dysfunction in Ischemic Stroke.
    5. PGAM5 deacetylation mediated by SIRT2 facilitates lipid metabolism and liver cancer proliferation.
      Title: PGAM5 deacetylation mediated by SIRT2 facilitates lipid metabolism and liver cancer proliferation.
    6. PGAM5 expression levels in heart failure and protection ROS-induced oxidative stress and ferroptosis by Keap1/Nrf2.
      Title: PGAM5 expression levels in heart failure and protection ROS-induced oxidative stress and ferroptosis by Keap1/Nrf2.
    7. Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state.
      Title: Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state.
    8. PGAM5 interacts with Bcl-rambo and regulates apoptosis and mitophagy.
      Title: PGAM5 interacts with Bcl-rambo and regulates apoptosis and mitophagy.
    9. The expression of IFN-beta is suppressed by the viral 3D polymerase via its impact on PGAM5 expression during enterovirus D68 infection.
      Title: The expression of IFN-β is suppressed by the viral 3D polymerase via its impact on PGAM5 expression during enterovirus D68 infection.
    10. Phosphoglycerate mutase family member 5 maintains oocyte quality via mitochondrial dynamic rearrangement during aging.
      Title: Phosphoglycerate mutase family member 5 maintains oocyte quality via mitochondrial dynamic rearrangement during aging.
    Submit: New GeneRIF Correction See all GeneRIFs (34)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC5352

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables MAP kinase serine/threonine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calmodulin-dependent protein phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AXS140 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables myosin phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoprotein phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein serine/threonine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in macroautophagy TAS
    Traceable Author Statement
    more info
    		  
    involved_in necroptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in positive regulation of mitochondrial fission IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial outer membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    serine/threonine-protein phosphatase PGAM5, mitochondrial
    Names
    Bcl-XL-binding protein v68
    PGAM family member 5, serine/threonine protein phosphatase, mitochondrial
    phosphoglycerate mutase family member 5
    NP_001164014.1
    NP_001164015.1
    NP_612642.2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001170543.2 → NP_001164014.1  serine/threonine-protein phosphatase PGAM5, mitochondrial isoform 1

      See identical proteins and their annotated locations for NP_001164014.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC135586, D25830, EU249757
      Consensus CDS
      CCDS53845.1
      UniProtKB/Swiss-Prot
      A9LN06, C9IZY7, Q96HS1, Q96JB0
      Related
      ENSP00000438465.1, ENST00000498926.7
      Conserved Domains (1) summary
      PTZ00122
      Location:58 → 287
      PTZ00122; phosphoglycerate mutase; Provisional

    2. NM_001170544.2 → NP_001164015.1  serine/threonine-protein phosphatase PGAM5, mitochondrial isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC135586, CA307621, D25830, DR155760
      Consensus CDS
      CCDS91784.1
      UniProtKB/TrEMBL
      A0A994J4Y8
      Related
      ENSP00000516057.1, ENST00000704860.1
      Conserved Domains (1) summary
      PTZ00122
      Location:58 → 286
      PTZ00122; phosphoglycerate mutase; Provisional

    3. NM_138575.4 → NP_612642.2  serine/threonine-protein phosphatase PGAM5, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_612642.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and lacks a portion of the 3' coding region compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC135586, BC008196
      Consensus CDS
      CCDS9280.1
      UniProtKB/Swiss-Prot
      Q96HS1
      Related
      ENSP00000321503.2, ENST00000317555.6
      Conserved Domains (1) summary
      cd07067
      Location:99 → 239
      HP_PGM_like; Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      132710842..132722734
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      132759704..132771989
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HS1.2 GenPept UniProtKB/Swiss-Prot:Q96HS1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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