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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
  • EC 4 58
  • PP2C-Kappa 3 4
  • PP2Cm 3 4
  • PTMP 3 4
  • Branched-Chain α-Ketoacid Dehydrogenase Phosphatase 2
  • Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase 3
  • 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
  • PP2Ckappa 3
  • UG0882E07 3
  • MSUDMV 3
  • 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. 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

Regulatory Elements for PPM1K Gene

Enhancers for PPM1K Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04H088318 1.1 Ensembl ENCODE 11.4 -35.5 -35451 3.1 PKNOX1 NFIB SCRT2 ZNF143 ZNF207 FOS ATF7 ETV6 RCOR1 RUNX3 LOC105369192 PPM1K RNU6-112P ENSG00000207480 GC04M088332
GH04H088340 0.9 Ensembl ENCODE 10.7 -56.6 -56624 2.1 ZNF362 FOXA2 JUN FOXA1 JUND PRDM6 IKZF1 SCRT2 FOSL2 FOS LOC105369192 HERC6 PPM1K ENSG00000207480 GC04M088332 LOC105377326
GH04H088608 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.6 -326.8 -326777 6 PKNOX1 TBL1XR1 RB1 BMI1 FEZF1 ZBTB40 BATF ZSCAN5C ATF7 RCOR1 HERC3 LOC100129137 PYURF PIGY NAP1L5 FAM13A-AS1 PPM1K GC04M088591 RNU6-33P GC04M088685
GH04H088244 0.4 Ensembl 11.2 +39.7 39728 1 GABPA LOC105369192 RNU6-112P PPM1K HERC6 RNU6-818P PIGY HERC3 PYURF LOC100129137 PKD2
GH04H088230 0.4 ENCODE 11.1 +53.5 53458 1.8 NFIC LOC105369192 PPM1K RNU6-112P HERC3 LOC100129137 PIGY PYURF RNU6ATAC31P ABCG2 RNU6-1298P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PPM1K on UCSC Golden Path with GeneCards custom track

Promoters for PPM1K Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000170565 531 2601 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A FEZF1 YBX1 YY1 ZNF143

Genomic Locations for PPM1K Gene

Genomic Locations for PPM1K Gene
27,223 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

Selected DME Specific Peptides for PPM1K Gene


Post-translational modifications for PPM1K Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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 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.;
UniProtKB/Swiss-Prot CatalyticActivity:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.
UniProtKB/Swiss-Prot Function:
Regulates the mitochondrial permeability transition pore and is essential for cellular survival and development.

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

Inhibitory RNA Products

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
Manganese Approved Nutra 35
Magnesium Nutra 0
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

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, PaxDb, 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)

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 33 34
  • 99.82 (n)
(Canis familiaris)
Mammalia PPM1K 33 34
  • 92.47 (n)
(Bos Taurus)
Mammalia PPM1K 33 34
  • 91.31 (n)
(Monodelphis domestica)
Mammalia PPM1K 34
  • 90 (a)
(Mus musculus)
Mammalia Ppm1k 33 16 34
  • 87.46 (n)
(Rattus norvegicus)
Mammalia Ppm1k 33
  • 86.92 (n)
(Gallus gallus)
Aves PPM1K 33 34
  • 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)

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 Sequence Context AA Info Type
rs1000128564 -- 88,266,403(+) CAGGT(A/G)ATGCT intron-variant
rs1000199434 -- 88,264,590(+) CTGTA(A/G)CCTCT intron-variant
rs10002084 -- 88,261,699(+) CTTTT(C/T)TTTTT utr-variant-3-prime
rs1000350878 -- 88,273,411(+) CACAA(C/T)GGCTC intron-variant
rs1000502887 -- 88,264,863(+) TGGGG(A/T)AATAA intron-variant

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

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

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)

Relevant External Links for PPM1K Gene

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

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, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
maple syrup urine disease, mild variant
  • maple syrup urine disease mild variant
intermediate maple syrup urine disease
  • intermediate bckd deficiency
maple syrup urine disease, type ii
  • dihydrolipoamide dehydrogenase deficiency
- 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.

Relevant External Links for PPM1K

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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. 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 60
  2. Genome-wide association study identifies multiple loci influencing human serum metabolite levels. (PMID: 22286219) Kettunen J … Ripatti S (Nature genetics 2012) 3 45 60
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  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 45 60
  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 45 60

Products for PPM1K Gene

Sources for PPM1K Gene

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