This gene encodes a member of the type II class of protein carboxyl methyltransferase enzymes. The encoded enzyme plays a role in protein repair by recognizing and converting D-aspartyl and L-isoaspartyl residues resulting from spontaneous deamidation back to the normal L-aspartyl form. The encoded protein may play a protective role in the pathogenesis of Alzheimer's disease, a... See more...

Aliases for PCMT1 Gene

Aliases for PCMT1 Gene

  • Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase 2 3 5
  • Protein-L-Isoaspartate(D-Aspartate) O-Methyltransferase 3 4
  • Protein L-Isoaspartyl/D-Aspartyl Methyltransferase 3 4
  • L-Isoaspartyl Protein Carboxyl Methyltransferase 3 4
  • Protein-Beta-Aspartate Methyltransferase 3 4
  • EC 2.1.1.77 4 51
  • PIMT 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • EC 2.1.1 51
  • PCMT1 5

External Ids for PCMT1 Gene

Previous GeneCards Identifiers for PCMT1 Gene

  • GC06P149632
  • GC06P149966
  • GC06P150101
  • GC06P150163
  • GC06P150112
  • GC06P150070
  • GC06P147636

Summaries for PCMT1 Gene

Entrez Gene Summary for PCMT1 Gene

  • This gene encodes a member of the type II class of protein carboxyl methyltransferase enzymes. The encoded enzyme plays a role in protein repair by recognizing and converting D-aspartyl and L-isoaspartyl residues resulting from spontaneous deamidation back to the normal L-aspartyl form. The encoded protein may play a protective role in the pathogenesis of Alzheimer's disease, and single nucleotide polymorphisms in this gene have been associated with spina bifida and premature ovarian failure. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

GeneCards Summary for PCMT1 Gene

PCMT1 (Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase) is a Protein Coding gene. Diseases associated with PCMT1 include Dehydrated Hereditary Stomatocytosis 1 With Or Without Pseudohyperkalemia And/Or Perinatal Edema and Type 1 Diabetes Mellitus 5. Among its related pathways are Protein repair and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include S-adenosylmethionine-dependent methyltransferase activity and protein-L-isoaspartate (D-aspartate) O-methyltransferase activity. An important paralog of this gene is PCMTD1.

UniProtKB/Swiss-Prot Summary for PCMT1 Gene

  • Catalyzes the methyl esterification of L-isoaspartyl and D-aspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. Acts on EIF4EBP2, microtubule-associated protein 2, calreticulin, clathrin light chains a and b, Ubiquitin carboxyl-terminal hydrolase isozyme L1, phosphatidylethanolamine-binding protein 1, stathmin, beta-synuclein and alpha-synuclein.

Gene Wiki entry for PCMT1 Gene

Additional gene information for PCMT1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCMT1 Gene

Genomics for PCMT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCMT1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCMT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCMT1

Genomic Locations for PCMT1 Gene

Genomic Locations for PCMT1 Gene
chr6:149,749,443-149,811,421
(GRCh38/hg38)
Size:
61,979 bases
Orientation:
Plus strand
chr6:150,070,579-150,132,557
(GRCh37/hg19)
Size:
61,979 bases
Orientation:
Plus strand

Genomic View for PCMT1 Gene

Genes around PCMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCMT1 Gene

Proteins for PCMT1 Gene

  • Protein details for PCMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P22061-PIMT_HUMAN
    Recommended name:
    Protein-L-isoaspartate(D-aspartate) O-methyltransferase
    Protein Accession:
    P22061
    Secondary Accessions:
    • A8K109
    • J3KP72
    • Q14661
    • Q16556
    • Q5VYC1
    • Q5VYC2
    • Q93061
    • Q96II9
    • Q99625
    • Q9BQV7
    • Q9BQV8
    • Q9NP03

    Protein attributes for PCMT1 Gene

    Size:
    227 amino acids
    Molecular mass:
    24636 Da
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • Sequence=EAW47786.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCMT1 Gene

    Alternative splice isoforms for PCMT1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCMT1 Gene

Selected DME Specific Peptides for PCMT1 Gene

P22061:
  • GAKALDV
  • LKPGGRL
  • GSGSGIL
  • TISAPHM
  • GKVIGIDHIKELV
  • NLRKNGIIK
  • PYMDSPQSIG
  • PQALIDQL
  • KDDPTLLSSGRV
  • KMKPLMGVIYVPLTDK
  • DQLKPGGRLILPVGPAGGNQMLEQYDKL

Post-translational modifications for PCMT1 Gene

  • Ubiquitination at Lys4, Lys105, and Lys206
  • Modification sites at PhosphoSitePlus

Domains & Families for PCMT1 Gene

Gene Families for PCMT1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PCMT1 Gene

InterPro:
Blocks:
  • Protein-L-isoaspartate(D-aspartate) O-methyltransferase
ProtoNet:

Suggested Antigen Peptide Sequences for PCMT1 Gene

GenScript: Design optimal peptide antigens:
  • Protein-L-isoaspartate O-methyltransferase (B7Z972_HUMAN)
  • Protein-beta-aspartate methyltransferase (PIMT_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P22061

UniProtKB/Swiss-Prot:

PIMT_HUMAN :
  • Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.
Family:
  • Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.
genes like me logo Genes that share domains with PCMT1: view

Function for PCMT1 Gene

Molecular function for PCMT1 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the methyl esterification of L-isoaspartyl and D-aspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. Acts on EIF4EBP2, microtubule-associated protein 2, calreticulin, clathrin light chains a and b, Ubiquitin carboxyl-terminal hydrolase isozyme L1, phosphatidylethanolamine-binding protein 1, stathmin, beta-synuclein and alpha-synuclein.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=[protein]-L-beta-isoaspartate + S-adenosyl-L-methionine = [protein]-L-beta-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:12705, Rhea:RHEA-COMP:12143, Rhea:RHEA-COMP:12144, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:90596, ChEBI:CHEBI:90598; EC=2.1.1.77;.
GENATLAS Biochemistry:
L-isoaspartyl/D-aspartyl methyltransferase,widely expressed

Enzyme Numbers (IUBMB) for PCMT1 Gene

Gene Ontology (GO) - Molecular Function for PCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity IEA,TAS 8074695
GO:0005515 protein binding IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0045296 cadherin binding HDA 25468996
genes like me logo Genes that share ontologies with PCMT1: view
genes like me logo Genes that share phenotypes with PCMT1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCMT1

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCMT1 Gene

Localization for PCMT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCMT1 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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 PCMT1 gene
Compartment Confidence
cytosol 5
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol IDA,TAS --
GO:0070062 extracellular exosome HDA 23533145
GO:1903561 extracellular vesicle HDA 24769233
genes like me logo Genes that share ontologies with PCMT1: view

Pathways & Interactions for PCMT1 Gene

PathCards logo

SuperPathways for PCMT1 Gene

SuperPathway Contained pathways
1 Metabolism of proteins
2 Protein repair
genes like me logo Genes that share pathways with PCMT1: view

Pathways by source for PCMT1 Gene

2 Reactome pathways for PCMT1 Gene

Gene Ontology (GO) - Biological Process for PCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process IEA --
GO:0006479 protein methylation IEA,TAS 3355545
GO:0030091 protein repair TAS 8074695
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PCMT1: view

No data available for SIGNOR curated interactions for PCMT1 Gene

Drugs & Compounds for PCMT1 Gene

(1) Drugs for PCMT1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma Target 0

(2) Additional Compounds for PCMT1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with PCMT1: view

Transcripts for PCMT1 Gene

mRNA/cDNA for PCMT1 Gene

8 REFSEQ mRNAs :
27 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCMT1

Alternative Splicing Database (ASD) splice patterns (SP) for PCMT1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b · 13c ^ 14
SP1: - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - -
SP6: - - - -
SP7: - - - - - -
SP8: - - - - - -
SP9: - - - - - -
SP10: - - - -
SP11: -
SP12: - - - - - - - - - -

Relevant External Links for PCMT1 Gene

GeneLoc Exon Structure for
PCMT1

Expression for PCMT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCMT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCMT1 Gene



Protein tissue co-expression partners for PCMT1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCMT1

SOURCE GeneReport for Unigene cluster for PCMT1 Gene:

Hs.279257

Evidence on tissue expression from TISSUES for PCMT1 Gene

  • Nervous system(5)
  • Skin(4.6)
  • Muscle(4.5)
  • Liver(4.5)
  • Blood(4.4)
  • Heart(2.7)
  • Lung(2.6)
  • Intestine(2.5)
  • Eye(2.4)
  • Kidney(2.4)
genes like me logo Genes that share expression patterns with PCMT1: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCMT1 Gene

Orthologs for PCMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PCMT1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PCMT1 30 31
  • 99.88 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PCMT1 30 31
  • 93.52 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PCMT1 30 31
  • 93.25 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pcmt1 31
  • 93 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PCMT1 31
  • 81 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PCMT1 31
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PCMT1 30 31
  • 86.37 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PCMT1 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pcmt1 30
  • 81.93 (n)
Str.12222 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.6342 30
Zebrafish
(Danio rerio)
Actinopterygii pcmt 30 31
  • 75.85 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1437 30
Fruit Fly
(Drosophila melanogaster)
Insecta Pcmt 30 31 32
  • 56.12 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000457 30
  • 54.45 (n)
Worm
(Caenorhabditis elegans)
Secernentea pcm-1 30 31 32
  • 57.14 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons PIMT1 30
  • 54.81 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.817 30
Rice
(Oryza sativa)
Liliopsida Os08g0557000 30
  • 53.67 (n)
Os.6061 30
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pcm2 30
  • 51.04 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU05078 30
  • 50.23 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.1090 30
Species where no ortholog for PCMT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • 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)

Evolution for PCMT1 Gene

ENSEMBL:
Gene Tree for PCMT1 (if available)
TreeFam:
Gene Tree for PCMT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCMT1: view image

Paralogs for PCMT1 Gene

Paralogs for PCMT1 Gene

genes like me logo Genes that share paralogs with PCMT1: view

Variants for PCMT1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for PCMT1 Gene

PIMT_HUMAN-P22061
The allele frequencies for the polymorphism at codon 120 differ between ethnic groups; in the Caucasian population Ile-120 is present at a frequency of 0.45, while it is found at a frequency of 0.88 and 0.81 in the Asian and the African populations respectively. Val-120 is found at a frequency of 0.55 in the Caucasians, 0.12 and 0.19 in the Asian and African populations respectively. The Ile-120 variant has higher specific activity and thermostability than the Val-120 variant. The Val-120 variant has a higher affinity for protein substrates.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCMT1 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs4816 - p.Val120Ile

Additional dbSNP identifiers (rs#s) for PCMT1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCMT1 Gene

Variant ID Type Subtype PubMed ID
dgv1023e201 CNV deletion 23290073
esv2259693 CNV deletion 18987734
esv2600122 CNV deletion 19546169
esv2678537 CNV deletion 23128226
esv2732861 CNV deletion 23290073
esv2732864 CNV deletion 23290073
nsv1141827 CNV insertion 24896259
nsv1148946 CNV deletion 26484159
nsv349268 CNV deletion 16902084

Variation tolerance for PCMT1 Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.10; 22.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCMT1 Gene

Human Gene Mutation Database (HGMD)
PCMT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCMT1

SNP Genotyping and Copy Number Assay Products

Disorders for PCMT1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PCMT1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
dehydrated hereditary stomatocytosis 1 with or without pseudohyperkalemia and/or perinatal edema
  • dhs1
type 1 diabetes mellitus 5
  • diabetes mellitus, insulin-dependent, 5
neural tube defects
  • neural tube defects, susceptibility to
alzheimer disease
  • ad
- elite association - COSMIC cancer census association via MalaCards
Search PCMT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCMT1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PCMT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCMT1 Gene

Publications for PCMT1 Gene

  1. Association between polymorphisms in the protein L-isoaspartate (D-aspartate) O-methyltransferase gene and premature ovarian failure. (PMID: 18582870) Pyun JA … Kwack K (Fertility and sterility 2009) 3 23 41
  2. A known functional polymorphism (Ile120Val) of the human PCMT1 gene and risk of spina bifida. (PMID: 16256389) Zhu H … Finnell RH (Molecular genetics and metabolism 2006) 3 23 41
  3. Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site. (PMID: 11847284) Smith CD … Chattopadhyay D (Protein science : a publication of the Protein Society 2002) 3 4 23
  4. Polymorphic forms of the protein L-isoaspartate (D-aspartate) O-methyltransferase involved in the repair of age-damaged proteins. (PMID: 10496068) DeVry CG … Clarke S (Journal of human genetics 1999) 3 4 23
  5. Assignment of the protein L-isoaspartate (D-aspartate) O-methyltransferase gene (PCMT1) to human chromosome bands 6q24-->q25 with radiation hybrid mapping. (PMID: 10343128) DeVry CG … Clarke S (Cytogenetics and cell genetics 1999) 2 3 23

Products for PCMT1 Gene

Sources for PCMT1 Gene