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Aliases for PPM1K Gene

Aliases for PPM1K Gene

  • Protein Phosphatase, Mg2+/Mn2+ Dependent 1K 2 3 5
  • PP2C-Type Mitochondrial Phosphoprotein Phosphatase 2 3 4
  • PP2C Domain-Containing Protein Phosphatase 1K 3 4
  • Protein Phosphatase 2C Kappa 2 3
  • PP2C-Kappa 3 4
  • PTMP 3 4
  • Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase 3
  • Branched-Chain I+/--Ketoacid Dehydrogenase Phosphatase 3
  • Branched-Chain α-Ketoacid Dehydrogenase Phosphatase 2
  • Protein Phosphatase 1K (PP2C Domain Containing) 2
  • Protein Phosphatase, Mg2+/Mn2+ Dependent, 1K 2
  • Protein Phosphatase 1K, Mitochondrial 3
  • Protein Phosphatase 2C Isoform Kappa 4
  • PP2C-Like Mitochondrial Protein 4
  • EC 4
  • PP2Ckappa 3
  • UG0882E07 3
  • MSUDMV 3
  • PP2Cm 3
  • PP2CM 4
  • BDP 3

External Ids for PPM1K Gene

Previous GeneCards Identifiers for PPM1K Gene

  • GC04M089541
  • GC04M089402
  • GC04M089178
  • GC04M084932

Summaries for PPM1K Gene

Entrez Gene Summary for PPM1K Gene

  • This gene encodes a member of the PPM family of Mn2+/Mg2+-dependent protein phosphatases. The encoded protein, essential for cell survival and development, is targeted to the mitochondria where it plays a key role in regulation of the mitochondrial permeability transition pore. [provided by RefSeq, Sep 2012]

GeneCards Summary for PPM1K Gene

PPM1K (Protein Phosphatase, Mg2+/Mn2+ Dependent 1K) is a Protein Coding gene. Diseases associated with PPM1K include Maple Syrup Urine Disease, Mild Variant and Intermediate Maple Syrup Urine Disease. Among its related pathways are Metabolism and Viral mRNA Translation. Gene Ontology (GO) annotations related to this gene include protein serine/threonine phosphatase activity. An important paralog of this gene is PPM1F.

UniProtKB/Swiss-Prot for PPM1K Gene

  • Regulates the mitochondrial permeability transition pore and is essential for cellular survival and development.

Gene Wiki entry for PPM1K Gene

Additional gene information for PPM1K Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PPM1K Gene

Genomics for PPM1K Gene

GeneHancer (GH) Regulatory Elements for PPM1K Gene

Promoters and enhancers for PPM1K Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J088279 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.7 1659 6.7 HDGF PKNOX1 FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 YBX1 LOC105369192 PPM1K HERC6 GC04M088276 RNU6-112P
GH04J088348 Promoter 0.5 EPDnew 660.3 -64.1 -64074 0.1 PPM1K LOC105369192 LOC105377326 ENSG00000207480 GC04M088332 GC04M088341
GH04J088230 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 11.1 +53.5 53457 1.8 NFIC ABCG2 LOC105369192 PPM1K RNU6-112P LOC100129137 PIGY PYURF RNU6ATAC31P HERC3 RNU6-1298P
GH04J088318 Enhancer 1 Ensembl ENCODE 11.4 -35.5 -35451 3.1 PKNOX1 CLOCK NFIB NEUROD1 STAT5A IRF4 SCRT2 ZNF207 ZNF143 ATF7 PPM1K LOC105369192 RNU6-112P ENSG00000207480 GC04M088332
GH04J088244 Promoter/Enhancer 1 EPDnew Ensembl 11.2 +39.7 39728 1 USF1 GABPB1 EHMT2 GABPA ABCG2 LOC105369192 RNU6-112P PPM1K HERC6 RNU6-818P LOC100129137 PIGY PYURF HERC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PPM1K on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PPM1K gene promoter:
  • STAT1beta
  • STAT1alpha
  • STAT1
  • CUTL1
  • STAT3
  • LUN-1
  • NCX
  • TBP

Genomic Locations for PPM1K Gene

Genomic Locations for PPM1K Gene
27,223 bases
Minus strand
27,150 bases
Minus strand

Genomic View for PPM1K Gene

Genes around PPM1K on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PPM1K Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PPM1K Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PPM1K Gene

Proteins for PPM1K Gene

  • Protein details for PPM1K Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein phosphatase 1K, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B2RAZ1
    • Q05CT5
    • Q49AB5
    • Q4W5E6
    • Q56AN8
    • Q8IUZ7
    • Q8IXG7
    • Q8ND70
    • Q96NT4

    Protein attributes for PPM1K Gene

    372 amino acids
    Molecular mass:
    40997 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PPM1K Gene

    Alternative splice isoforms for PPM1K Gene


neXtProt entry for PPM1K Gene

Post-translational modifications for PPM1K Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PPM1K Gene

Domains & Families for PPM1K Gene

Gene Families for PPM1K Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PPM1K Gene

Suggested Antigen Peptide Sequences for PPM1K Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PP2C family.
  • Belongs to the PP2C family.
genes like me logo Genes that share domains with PPM1K: view

Function for PPM1K Gene

Molecular function for PPM1K Gene

UniProtKB/Swiss-Prot Function:
Regulates the mitochondrial permeability transition pore and is essential for cellular survival and development.
UniProtKB/Swiss-Prot CatalyticActivity:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=10.7 mM for p-nitrophenylphosphate {ECO:0000269 PubMed:17336929}; Vmax=3.6 umol/min/mg enzyme toward p-nitrophenylphosphate (at 30 degrees Celsius) {ECO:0000269 PubMed:17336929}; Vmax=4 nmol/min/mg enzyme toward branched-chain alpha-ketoacid dehydrogenase complex (at 37 degrees Celsius) {ECO:0000269 PubMed:17336929}; Note=Half maximal activity toward p-nitrophenylphosphate achieved with 3.7 mM of manganese ions.;

Enzyme Numbers (IUBMB) for PPM1K Gene

Phenotypes From GWAS Catalog for PPM1K Gene

Gene Ontology (GO) - Molecular Function for PPM1K Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity TAS,IEA --
GO:0005515 protein binding IPI 25416956
GO:0016787 hydrolase activity IEA --
GO:0043169 cation binding IEA --
genes like me logo Genes that share ontologies with PPM1K: view
genes like me logo Genes that share phenotypes with PPM1K: view

Human Phenotype Ontology for PPM1K Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PPM1K Gene

MGI Knock Outs for PPM1K:

Animal Model Products

CRISPR Products

miRNA for PPM1K Gene

miRTarBase miRNAs that target PPM1K

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PPM1K

No data available for Transcription Factor Targets and HOMER Transcription for PPM1K Gene

Localization for PPM1K Gene

Subcellular locations from UniProtKB/Swiss-Prot for PPM1K Gene

Mitochondrion matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PPM1K gene
Compartment Confidence
mitochondrion 5
peroxisome 2
cytosol 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PPM1K Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with PPM1K: view

Pathways & Interactions for PPM1K Gene

genes like me logo Genes that share pathways with PPM1K: view

Pathways by source for PPM1K Gene

Gene Ontology (GO) - Biological Process for PPM1K Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0009083 branched-chain amino acid catabolic process TAS --
genes like me logo Genes that share ontologies with PPM1K: view

No data available for SIGNOR curated interactions for PPM1K Gene

Drugs & Compounds for PPM1K Gene

(4) Drugs for PPM1K Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Magnesium Approved Nutra 0
Manganese Approved Nutra 37
genes like me logo Genes that share compounds with PPM1K: view

Transcripts for PPM1K Gene

Unigene Clusters for PPM1K Gene

Protein phosphatase, Mg2+/Mn2+ dependent, 1K:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PPM1K

Alternative Splicing Database (ASD) splice patterns (SP) for PPM1K Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b · 3c · 3d · 3e ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b · 11c ^ 12a ·
SP1: - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - -
SP3: - - - -
SP4: -
SP5: - - - - - - - - - - - -
SP6: - - -
SP8: - - - - - - - - -
SP9: - - - -
SP10: - - -
SP12: -

ExUns: 12b

Relevant External Links for PPM1K Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PPM1K Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PPM1K Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PPM1K Gene

This gene is overexpressed in Heart - Left Ventricle (x6.5).

Protein differential expression in normal tissues from HIPED for PPM1K Gene

This gene is overexpressed in Heart (34.4), Pancreas (15.7), and Skin (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PPM1K Gene

NURSA nuclear receptor signaling pathways regulating expression of PPM1K Gene:


SOURCE GeneReport for Unigene cluster for PPM1K Gene:


Evidence on tissue expression from TISSUES for PPM1K Gene

  • Nervous system(4.5)
  • Lymph node(4.2)
  • Pancreas(4.1)
  • Heart(2.2)
  • Muscle(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PPM1K Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
Head and neck:
  • brain
  • ear
  • head
  • diaphragm
  • esophagus
  • heart
  • lung
  • adrenal gland
  • pancreas
  • stomach
  • blood
  • peripheral nerve
  • peripheral nervous system
  • skin
  • sweat gland
  • white blood cell
genes like me logo Genes that share expression patterns with PPM1K: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PPM1K Gene

Orthologs for PPM1K Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PPM1K Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PPM1K 34 33
  • 99.82 (n)
(Canis familiaris)
Mammalia PPM1K 34 33
  • 92.47 (n)
(Bos Taurus)
Mammalia PPM1K 34 33
  • 91.31 (n)
(Monodelphis domestica)
Mammalia PPM1K 34
  • 90 (a)
(Mus musculus)
Mammalia Ppm1k 16 34 33
  • 87.46 (n)
(Rattus norvegicus)
Mammalia Ppm1k 33
  • 86.92 (n)
(Gallus gallus)
Aves PPM1K 34 33
  • 76.97 (n)
(Anolis carolinensis)
Reptilia PPM1K 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487567 33
  • 71.51 (n)
(Danio rerio)
Actinopterygii ppm1k 34
  • 67 (a)
PPM1K (2 of 2) 34
  • 63 (a)
si:ch211-149b19.3 33
  • 62.93 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10186 33
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PTC1 34
  • 31 (a)
PTC6 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G78200 33
  • 48.16 (n)
Species where no ortholog for PPM1K was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PPM1K Gene

Gene Tree for PPM1K (if available)
Gene Tree for PPM1K (if available)
Evolutionary constrained regions (ECRs) for PPM1K: view image

Paralogs for PPM1K Gene

Paralogs for PPM1K Gene

genes like me logo Genes that share paralogs with PPM1K: view

Variants for PPM1K Gene

Sequence variations from dbSNP and Humsavar for PPM1K Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs113436519 benign, Maple syrup urine disease, mild variant 88,277,203(-) T/C 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs116564150 benign, Maple syrup urine disease, mild variant 88,278,245(-) G/A 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, synonymous_variant, upstream_transcript_variant
rs34981823 benign, Maple syrup urine disease, mild variant 88,265,010(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant
rs1000128564 -- 88,266,403(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000199434 -- 88,264,590(-) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PPM1K Gene

Variant ID Type Subtype PubMed ID
esv2759266 CNV gain 17122850
esv3575758 CNV gain 25503493
nsv474553 CNV novel sequence insertion 20440878

Variation tolerance for PPM1K Gene

Residual Variation Intolerance Score: 38% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.75; 46.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PPM1K Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PPM1K Gene

Disorders for PPM1K Gene

MalaCards: The human disease database

(3) MalaCards diseases for PPM1K Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
maple syrup urine disease, mild variant
  • msudmv
intermediate maple syrup urine disease
  • intermediate bckd deficiency
maple syrup urine disease
  • msud
- elite association - COSMIC cancer census association via MalaCards
Search PPM1K in MalaCards View complete list of genes associated with diseases


  • Maple syrup urine disease, mild variant (MSUDMV) [MIM:615135]: A mild form of maple syrup urine disease, a metabolic disorder due to an enzyme defect in the catabolic pathway of the branched-chain amino acids leucine, isoleucine, and valine. Accumulation of these 3 amino acids and their corresponding keto acids leads to encephalopathy and progressive neurodegeneration. Clinical features include mental and physical retardation, feeding problems, and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine. If untreated, maple syrup urine disease can lead to seizures, coma, and death. The disease is often classified by its pattern of signs and symptoms. The most common and severe form of the disease is the classic type, which becomes apparent soon after birth. Variant forms of the disorder become apparent later in infancy or childhood and are typically milder, but they still involve developmental delay and other medical problems if not treated. MSUDMV is characterized by increased plasma levels of branched-chain amino acids (BCAA) apparent at birth. Treatment with a low-protein diet free of BCAA can result in normal psychomotor development and lack of metabolic episodes. {ECO:0000269 PubMed:23086801}. Note=The gene represented in this entry is involved in disease pathogenesis.

Additional Disease Information for PPM1K

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PPM1K: view

No data available for Genatlas for PPM1K Gene

Publications for PPM1K Gene

  1. Genome-wide association study identifies multiple loci influencing human serum metabolite levels. (PMID: 22286219) Kettunen J … Ripatti S (Nature genetics 2012) 3 44 58
  2. Structural and biochemical characterization of human mitochondrial branched-chain α-ketoacid dehydrogenase phosphatase. (PMID: 22291014) Wynn RM … Chuang DT (The Journal of biological chemistry 2012) 2 3 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. Screening for replication of genome-wide SNP associations in sporadic ALS. (PMID: 18987618) Cronin S … Hardiman O (European journal of human genetics : EJHG 2009) 3 44 58
  5. Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan. (PMID: 18846501) Sonuga-Barke EJ … Faraone SV (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 44 58

Products for PPM1K Gene

Sources for PPM1K Gene

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