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

Gene ID: 192111, updated on 7-Apr-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 mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in esophagus (RPKM 6.8), testis (RPKM 6.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q24.33
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (132710842..132722734)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (132759704..132771989)
105.20220307 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
  • 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. 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
  2. PGAM5 interacts with Bcl-rambo and regulates apoptosis and mitophagy. Hashino T, et al. Exp Cell Res, 2022 Nov 1. PMID 36075447
  3. DHEA restores mitochondrial dynamics of cumulus cells by regulating PGAM5 expression in poor ovarian responders. Hou YL, et al. Taiwan J Obstet Gynecol, 2022 Mar. PMID 35361380
  4. 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
  5. The expression of IFN-β is suppressed by the viral 3D polymerase via its impact on PGAM5 expression during enterovirus D68 infection. Yang Z, et al. Virus Res, 2021 Oct 15. PMID 34425164

See all (186) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Targeted knockdown of PGAM5 in synovial macrophages efficiently alleviates osteoarthritis.
    Title: Targeted knockdown of PGAM5 in synovial macrophages efficiently alleviates osteoarthritis.
  2. The Effect of PGAM5 on Regulating Mitochondrial Dysfunction in Ischemic Stroke.
    Title: The Effect of PGAM5 on Regulating Mitochondrial Dysfunction in Ischemic Stroke.
  3. 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.
  4. 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.
  5. 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.
  6. PGAM5 interacts with Bcl-rambo and regulates apoptosis and mitophagy.
    Title: PGAM5 interacts with Bcl-rambo and regulates apoptosis and mitophagy.
  7. 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.
  8. 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.
  9. DHEA restores mitochondrial dynamics of cumulus cells by regulating PGAM5 expression in poor ovarian responders.
    Title: DHEA restores mitochondrial dynamics of cumulus cells by regulating PGAM5 expression in poor ovarian responders.
  10. Cleaved PGAM5 dephosphorylates nuclear serine/arginine-rich proteins during mitophagy.
    Title: Cleaved PGAM5 dephosphorylates nuclear serine/arginine-rich proteins during mitophagy.
Submit: New GeneRIF Correction See all GeneRIFs (32)

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)

Genotypes

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 myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables 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 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 peptidyl-threonine dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of mitochondrial fission IBA
Inferred from Biological aspect of Ancestor
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
  
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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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_2023_10

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

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