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 4

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. Diseases associated with PCMTD1 include Primary Angle-Closure Glaucoma. 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 Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification 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 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 508.1 -0.4 -414 6.4 FOXK2 ZNF217 SIN3A TCF12 NRF1 MYC POLR2G GTF2E2 PHF8 ZFX PCMTD1 LOC102724330 PXDNL ENSG00000253844 piR-41245-273
GH08J051858 Enhancer 0.9 Ensembl ENCODE dbSUPER 20.1 +39.9 39885 2.2 FOXA2 FOS POLR2A ZBTB33 RXRA MAX HNF4A BHLHE40 GATA1 HNF4G lnc-PXDNL-3 PCMTD1 LOC102724330 ENSG00000253475 piR-50437-629
GH08J051960 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas 7.6 -63.2 -63161 3 ZBTB40 SP1 MEF2C TRIM22 NFYB BCL11A TCF12 ZNF316 CBFB MAFF ENSG00000253844 PCMTD1 LOC102724330 ENSG00000254136
GH08J051850 Enhancer 1.1 Ensembl ENCODE dbSUPER 7.6 +48.2 48185 3.2 ZNF217 CTCF REST CUX1 RAD21 TBX3 GATAD2B CTBP1 HES1 FOXA2 PCMTD1 LOC102724330 PXDNL piR-50437-629 lnc-PXDNL-3 piR-52916-033
GH08J051869 Enhancer 0.8 ENCODE dbSUPER 7.7 +28.5 28507 2.2 ATF2 ZNF316 TCF7L2 FOS NFE2 IKZF1 MAFG PRDM6 FEZF1 ATF4 PCMTD1 lnc-PXDNL-3 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCMTD1

Top Transcription factor binding sites by QIAGEN in the PCMTD1 gene promoter:
  • CUTL1
  • POU3F1
  • Sox5
  • Sox9
  • STAT5A
  • 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
    • [Isoform 2]: Incomplete sequence.

    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

Other Protein References for PCMTD1 Gene

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

  • Protein-L-isoaspartate(D-aspartate) O-methyltransferase

Suggested Antigen Peptide Sequences for PCMTD1 Gene

GenScript: Design optimal peptide antigens:
  • Protein-L-isoaspartate O-methyltransferase domain-containing protein 1 (PCMD1_HUMAN)

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 21873635
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

CRISPR 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 2
extracellular 1
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 21873635
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PCMTD1: view

Pathways & Interactions for PCMTD1 Gene

PathCards logo

SuperPathways for PCMTD1 Gene

No Data Available

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

mRNA/cDNA for PCMTD1 Gene

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

CRISPR Products

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

Expression for PCMTD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCMTD1

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 31 30
  • 99.63 (n)
(Canis familiaris)
Mammalia PCMTD1 31 30
  • 95.22 (n)
(Ornithorhynchus anatinus)
Mammalia PCMTD1 31
  • 95 (a)
(Monodelphis domestica)
Mammalia PCMTD1 31
  • 94 (a)
(Mus musculus)
Mammalia Pcmtd1 17 31 30
  • 92.62 (n)
(Rattus norvegicus)
Mammalia Pcmtd1 30
  • 91.88 (n)
(Bos Taurus)
Mammalia PCMTD1 31 30
  • 89.98 (n)
(Gallus gallus)
Aves PCMTD1 31 30
  • 86.27 (n)
(Anolis carolinensis)
Reptilia PCMTD1 31
  • 91 (a)
(Danio rerio)
Actinopterygii pcmtd1 31 30
  • 69.84 (n)
wufi15f10 30
(Caenorhabditis elegans)
Secernentea R119.5 31
  • 12 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCMTD1 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs12335014 - p.Asn312Ile

Additional dbSNP identifiers (rs#s) for PCMTD1 Gene

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

MalaCards: The human disease database

(1) MalaCards diseases for PCMTD1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
primary angle-closure glaucoma
  • primary angle closure glaucoma
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCMTD1

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 PCMTD1: view

No data available for 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 41 54
  2. 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 54
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  4. Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci in Patients with Early Stages of Angle-Closure Disease. (PMID: 29310965) Nongpiur ME … Vithana EN (Ophthalmology 2018) 3 54
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54

Products for PCMTD1 Gene

Sources for PCMTD1 Gene