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

Gene ID: 132160, updated on 5-Mar-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 manganese ion binding activity and phosphoprotein phosphatase activity. Predicted to be involved in protein dephosphorylation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 16.5), spleen (RPKM 14.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p21.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52245759..52250599)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52272420..52283485)
105.20220307 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)

Genotypes

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 [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
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 protein dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein dephosphorylation ISS
Inferred from Sequence or Structural Similarity
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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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_2023_10

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

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