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    PPM1M protein phosphatase, Mg2+/Mn2+ dependent 1M [ Homo sapiens (human) ]

    Gene ID: 132160, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PPM1Mprovided by HGNC
    Official Full Name
    protein phosphatase, Mg2+/Mn2+ dependent 1Mprovided by HGNC
    Primary source
    HGNC:HGNC:26506
    See related
    Ensembl:ENSG00000164088 MIM:608979; AllianceGenome:HGNC:26506
    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
    PP2CE; PP2Ceta; PP2C-eta
    Summary
    Predicted to enable [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity and manganese ion binding activity. Predicted to be involved in protein dephosphorylation. Predicted to be located in nucleus. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 16.5), spleen (RPKM 14.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PPM1M in Genome Data Viewer
    Location:
    3p21.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52245759..52250599)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52272420..52283485)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52279775..52284615)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14433 Neighboring gene twinfilin actin binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52270765-52271306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52271307-52271849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19933 Neighboring gene NANOG hESC enhancer GRCh37_chr3:52274848-52275376 Neighboring gene TWF2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19934 Neighboring gene WD repeat domain 82 Neighboring gene microRNA let-7g Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52311392-52312024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52312657-52313288 Neighboring gene uncharacterized LOC107986086 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:52321476-52322675 Neighboring gene glycerate kinase

    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. Exploring the immunological role and prognostic potential of PPM1M in pan-cancer. Zeng R, et al. Medicine (Baltimore), 2023 Mar 24. PMID 36961170, Free PMC Article
    2. Metal-dependent Ser/Thr protein phosphatase PPM family: Evolution, structures, diseases and inhibitors. Kamada R, et al. Pharmacol Ther, 2020 Nov. PMID 32650009
    3. Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis. Velasco HM, et al. Am J Med Genet A, 2020 Oct. PMID 32783359, Free PMC Article
    4. Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder. Chen DT, et al. Mol Psychiatry, 2013 Feb. PMID 22182935
    5. A mechanism for the suppression of interleukin-1-induced nuclear factor kappaB activation by protein phosphatase 2Ceta-2. Henmi T, et al. Biochem J, 2009 Sep 14. PMID 19594441

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exploring the immunological role and prognostic potential of PPM1M in pan-cancer.
      Title: Exploring the immunological role and prognostic potential of PPM1M in pan-cancer.
    2. Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis.
      Title: Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis.
    3. PP2Ceta-2 inhibits the IL-1-NF-kappaB signalling pathway by selectively dephosphorylating IKKbeta.
      Title: A mechanism for the suppression of interleukin-1-induced nuclear factor kappaB activation by protein phosphatase 2Ceta-2.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32332

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    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 manganese ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables myosin phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein dephosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    protein phosphatase 1M
    Names
    protein phosphatase 1M (PP2C domain containing)
    protein phosphatase 2C eta-2
    NP_001116342.1
    NP_653242.3
    XP_005264936.1
    XP_005264937.1
    XP_005264938.1
    XP_047303424.1
    XP_054201258.1
    XP_054201259.1
    XP_054201260.1
    XP_054201261.1
    XP_054201262.1

    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_001122870.3 → NP_001116342.1  protein phosphatase 1M isoform b

      See identical proteins and their annotated locations for NP_001116342.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AA829740, AC006252, BC009644, DA869388
      Consensus CDS
      CCDS46840.1
      UniProtKB/Swiss-Prot
      Q96MI6
      Related
      ENSP00000387046.3, ENST00000409502.7
      Conserved Domains (1) summary
      cd00143
      Location:2 → 237
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    2. NM_144641.4 → NP_653242.3  protein phosphatase 1M isoform a

      See identical proteins and their annotated locations for NP_653242.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AA829740, AB474372, AC006252, BC009644, BF516133, DB479638
      Consensus CDS
      CCDS93282.1
      UniProtKB/Swiss-Prot
      B7XGB9, F8W976, Q8N8J9, Q96DB8, Q96MI6
      Related
      ENSP00000319894.5, ENST00000323588.9
      Conserved Domains (1) summary
      cd00143
      Location:118 → 449
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      52245759..52250599
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005264879.3 → XP_005264936.1  protein phosphatase 1M isoform X1

      Conserved Domains (1) summary
      cd00143
      Location:118 → 410
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    2. XM_047447468.1 → XP_047303424.1  protein phosphatase 1M isoform X3

    3. XM_005264880.4 → XP_005264937.1  protein phosphatase 1M isoform X2

      Conserved Domains (1) summary
      cd00143
      Location:113 → 364
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    4. XM_005264881.2 → XP_005264938.1  protein phosphatase 1M isoform X4

      See identical proteins and their annotated locations for XP_005264938.1

      Conserved Domains (1) summary
      cd00143
      Location:24 → 288
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    RNA

    1. XR_001740024.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52272420..52283485
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345283.1 → XP_054201258.1  protein phosphatase 1M isoform X5

      UniProtKB/Swiss-Prot
      B7XGB9, F8W976, Q8N8J9, Q96DB8, Q96MI6

    2. XM_054345284.1 → XP_054201259.1  protein phosphatase 1M isoform X1

    3. XM_054345286.1 → XP_054201261.1  protein phosphatase 1M isoform X3

    4. XM_054345285.1 → XP_054201260.1  protein phosphatase 1M isoform X2

    5. XM_054345287.1 → XP_054201262.1  protein phosphatase 1M isoform X4

    RNA

    1. XR_008486660.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MI6.2 GenPept UniProtKB/Swiss-Prot:Q96MI6

    Gene LinkOut

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

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