Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PCMTD1 Gene

Aliases for PCMTD1 Gene

  • Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase Domain Containing 1 2 3 5
  • Protein-L-Isoaspartate O-Methyltransferase Domain-Containing Protein 1 3

External Ids for PCMTD1 Gene

Previous GeneCards Identifiers for PCMTD1 Gene

  • GC08M052893
  • GC08M052730
  • GC08M048198

Summaries for PCMTD1 Gene

GeneCards Summary for PCMTD1 Gene

PCMTD1 (Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include protein-L-isoaspartate (D-aspartate) O-methyltransferase activity. An important paralog of this gene is PCMTD2.

Additional gene information for PCMTD1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCMTD1 Gene

Genomics for PCMTD1 Gene

GeneHancer (GH) Regulatory Elements for PCMTD1 Gene

Promoters and enhancers for PCMTD1 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
GH08J051896 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 658.2 -0.4 -416 6.4 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF207 ZNF143 PCMTD1 ENSG00000228801 PXDNL LOC102724330 ENSG00000253844 GC08P051948 GC08P051831
GH08J051960 Promoter/Enhancer 1.3 Ensembl ENCODE 15.8 -63.2 -63161 3 PKNOX1 BMI1 KLF5 ZNF335 ZNF548 ATF7 ETV6 IKZF2 RUNX3 CREM ENSG00000253844 PCMTD1 ENSG00000228801 GC08P051958 GC08P051959 ENSG00000254136 LOC102724330
GH08J051884 Enhancer 1 Ensembl ENCODE dbSUPER 7.7 +13.6 13550 3 JUN MAX REST GABPA YY1 SP1 HNF4G HNF4A ZBTB33 PCMTD1 ENSG00000228801 PXDNL ENSG00000253475 GC08P051831
GH08J051869 Enhancer 1 Ensembl ENCODE dbSUPER 7.7 +28.5 28507 2.2 BACH1 MAFG FEZF1 ATF2 ATF4 PRDM6 ZNF316 ZNF629 IKZF1 ATF7 PCMTD1 ENSG00000253475 GC08P051831
GH08J051858 Enhancer 0.8 ENCODE dbSUPER 7.6 +39.9 39918 0.9 FOXA2 RXRA MAX YY1 SP1 POLR2A HNF4G HNF4A ZBTB33 PCMTD1 ENSG00000228801 GC08P051831 ENSG00000253475
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCMTD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCMTD1 gene promoter:
  • CUTL1
  • Sox9
  • STAT5A
  • Sox5
  • POU3F1
  • STAT5B

Genomic Locations for PCMTD1 Gene

Genomic Locations for PCMTD1 Gene
81,612 bases
Minus strand
81,596 bases
Minus strand

Genomic View for PCMTD1 Gene

Genes around PCMTD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCMTD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCMTD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCMTD1 Gene

Proteins for PCMTD1 Gene

  • Protein details for PCMTD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein-L-isoaspartate O-methyltransferase domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • Q96FK9

    Protein attributes for PCMTD1 Gene

    357 amino acids
    Molecular mass:
    40675 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCMTD1 Gene


neXtProt entry for PCMTD1 Gene

Post-translational modifications for PCMTD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PCMTD1 Gene

Domains & Families for PCMTD1 Gene

Gene Families for PCMTD1 Gene

Protein Domains for PCMTD1 Gene

Suggested Antigen Peptide Sequences for PCMTD1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.
  • Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.
genes like me logo Genes that share domains with PCMTD1: view

Function for PCMTD1 Gene

Phenotypes From GWAS Catalog for PCMTD1 Gene

Gene Ontology (GO) - Molecular Function for PCMTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity IBA --
genes like me logo Genes that share ontologies with PCMTD1: view

Phenotypes for PCMTD1 Gene

genes like me logo Genes that share phenotypes with PCMTD1: view

Animal Model Products

miRNA for PCMTD1 Gene

miRTarBase miRNAs that target PCMTD1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCMTD1 Gene

Localization for PCMTD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCMTD1 Gene

Cytoplasm. Membrane; Lipid-anchor.

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 PCMTD1 gene
Compartment Confidence
nucleus 3
cytosol 3
golgi apparatus 3
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCMTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PCMTD1: view

Pathways & Interactions for PCMTD1 Gene

SuperPathways for PCMTD1 Gene

No Data Available

Interacting Proteins for PCMTD1 Gene

Gene Ontology (GO) - Biological Process for PCMTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process IEA --
GO:0006479 protein methylation IEA --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PCMTD1: view

No data available for Pathways by source and SIGNOR curated interactions for PCMTD1 Gene

Drugs & Compounds for PCMTD1 Gene

No Compound Related Data Available

Transcripts for PCMTD1 Gene

Unigene Clusters for PCMTD1 Gene

Protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCMTD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9
SP1: - - - - -
SP2: - -
SP3: - -

Relevant External Links for PCMTD1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCMTD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCMTD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCMTD1 Gene

This gene is overexpressed in Lung (34.7) and Testis (17.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCMTD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCMTD1 Gene:


SOURCE GeneReport for Unigene cluster for PCMTD1 Gene:


Evidence on tissue expression from TISSUES for PCMTD1 Gene

  • Muscle(4.3)
  • Skin(4.3)
  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with PCMTD1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCMTD1 Gene

Orthologs for PCMTD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCMTD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCMTD1 34 33
  • 99.63 (n)
(Canis familiaris)
Mammalia PCMTD1 34 33
  • 95.22 (n)
(Ornithorhynchus anatinus)
Mammalia PCMTD1 34
  • 95 (a)
(Monodelphis domestica)
Mammalia PCMTD1 34
  • 94 (a)
(Mus musculus)
Mammalia Pcmtd1 16 34 33
  • 92.62 (n)
(Rattus norvegicus)
Mammalia Pcmtd1 33
  • 91.88 (n)
(Bos Taurus)
Mammalia PCMTD1 34 33
  • 89.98 (n)
(Gallus gallus)
Aves PCMTD1 34 33
  • 86.27 (n)
(Anolis carolinensis)
Reptilia PCMTD1 34
  • 91 (a)
(Danio rerio)
Actinopterygii pcmtd1 34 33
  • 69.84 (n)
wufi15f10 33
(Caenorhabditis elegans)
Secernentea R119.5 34
  • 12 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
Species where no ortholog for PCMTD1 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for PCMTD1 Gene

Gene Tree for PCMTD1 (if available)
Gene Tree for PCMTD1 (if available)
Evolutionary constrained regions (ECRs) for PCMTD1: view image

Paralogs for PCMTD1 Gene

Paralogs for PCMTD1 Gene

(2) SIMAP similar genes for PCMTD1 Gene using alignment to 4 proteins:

  • F5H1M8_HUMAN
genes like me logo Genes that share paralogs with PCMTD1: view

Variants for PCMTD1 Gene

Sequence variations from dbSNP and Humsavar for PCMTD1 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000005616 -- 51,823,081(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000020008 -- 51,869,804(-) T/A genic_upstream_transcript_variant, intron_variant
rs1000081060 -- 51,898,277(-) C/G genic_upstream_transcript_variant, intron_variant
rs1000114371 -- 51,821,968(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000196532 -- 51,880,094(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCMTD1 Gene

Variant ID Type Subtype PubMed ID
dgv3825n106 CNV deletion 24896259
dgv7215n100 CNV gain 25217958
esv1000050 CNV deletion 20482838
esv1338407 CNV deletion 17803354
esv3543487 CNV deletion 23714750
nsv1075136 CNV deletion 25765185
nsv1078613 CNV duplication 25765185
nsv1110978 OTHER inversion 24896259
nsv1152652 CNV deletion 26484159
nsv526922 CNV loss 19592680
nsv817615 CNV gain 22305530
nsv824630 CNV loss 20364138
nsv824632 CNV gain 20364138
nsv831316 CNV gain 17160897
nsv951429 CNV duplication 24416366
nsv957676 CNV deletion 24416366
nsv967589 CNV duplication 23825009

Variation tolerance for PCMTD1 Gene

Residual Variation Intolerance Score: 81.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.36; 92.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCMTD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCMTD1 Gene

Disorders for PCMTD1 Gene

Additional Disease Information for PCMTD1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PCMTD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCMTD1 Gene

Publications for PCMTD1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. An Interaction Landscape of Ubiquitin Signaling. (PMID: 28190767) Zhang X … Vermeulen M (Molecular cell 2017) 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for PCMTD1 Gene

Sources for PCMTD1 Gene

Loading form....