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

Summary

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, Nov 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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis.
Title: Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis.
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 EBI GWAS CatalogPubMed
Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

A002C09 (e-PCR)
- UniSTS:58888

RH12810 (e-PCR)
- UniSTS:59420

MARC_15661-15662:1016643799:1 (e-PCR)
- UniSTS:267857

RH76369 (e-PCR)
- UniSTS:92562

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

EC 3.1.3.16

NP_653242.3

EC 3.1.3.16

XP_005264936.1

EC 3.1.3.16

XP_005264937.1

EC 3.1.3.16

XP_005264938.1

EC 3.1.3.16

XP_047303424.1

EC 3.1.3.16

XP_054201258.1

EC 3.1.3.16

XP_054201259.1

EC 3.1.3.16

XP_054201260.1

EC 3.1.3.16

XP_054201261.1

EC 3.1.3.16

XP_054201262.1

EC 3.1.3.16

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)

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 ...
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

52245759..52250599

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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