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    PCMTD1 protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 115294, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PCMTD1provided by HGNC
    Official Full Name
    protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:30483
    See related
    Ensembl:ENSG00000168300 MIM:620091; AllianceGenome:HGNC:30483
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables ubiquitin-like ligase-substrate adaptor activity. Involved in protein ubiquitination. Part of Cul5-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 31.9), fat (RPKM 21.9) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PCMTD1 in Genome Data Viewer
    Location:
    8q11.23
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (51817575..51899186, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (52193558..52274823, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (52730135..52811746, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene peroxidasin like Neighboring gene uncharacterized LOC105375833 Neighboring gene MPRA-validated peak7013 silencer Neighboring gene BTF3 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52721378-52721900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52721901-52722422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27340 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:52837590-52838789 Neighboring gene PCMTD1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27342 Neighboring gene uncharacterized LOC124901944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27343

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Association study in a South Indian population supports rs1015213 as a risk factor for primary angle closure. Duvesh R, et al. Invest Ophthalmol Vis Sci, 2013 Aug 19. PMID 23847314, Free PMC Article
    2. Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky. Liu J, et al. Cancer Epidemiol Biomarkers Prev, 2019 Feb. PMID 30377206, Free PMC Article
    3. Genotype-phenotype correlation analysis for three primary angle closure glaucoma-associated genetic polymorphisms. Wei X, et al. Invest Ophthalmol Vis Sci, 2014 Feb 24. PMID 24474268
    4. [Association of PLEKHA7, COL11A1 and PCMTD1-ST18 gene polymorphisms with primary angle closure glaucoma in ethnic Han Chinese from Sichuan]. Tan C, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2016 Aug. PMID 27455018
    5. Human Protein-l-isoaspartate O-Methyltransferase Domain-Containing Protein 1 (PCMTD1) Associates with Cullin-RING Ligase Proteins. Warmack RA, et al. Biochemistry, 2022 May 17. PMID 35486881, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Human Protein-l-isoaspartate O-Methyltransferase Domain-Containing Protein 1 (PCMTD1) Associates with Cullin-RING Ligase Proteins.
      Title: Human Protein-l-isoaspartate O-Methyltransferase Domain-Containing Protein 1 (PCMTD1) Associates with Cullin-RING Ligase Proteins.
    2. This study has identified an increased percentage of IDH1 and PCMTD1 mutations in Squamous Cell Lung Cancers arising in the Appalachian Kentucky residents versus The Cancer Genome Atlas, with population-specific implications for the personalized treatment of this disease.
      Title: Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky.
    3. In this study, 2 of 8 (primary angle-closure glaucoma) PACG-associated loci were associated significantly with PACS status, the earliest stage in the angle-closure glaucoma disease course. The association of these PACG loci with PACS status suggests that these loci may confer susceptibility to a narrow angle configuration.
      Title: Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci in Patients with Early Stages of Angle-Closure Disease.
    4. No significant association of PLEKHA7 rs11024102, COL11A1 rs3753841 and PCMTD1-ST18 rs1015213 with primary angle closure glaucoma was found among ethnic Han Chinese from Sichuan
      Title: [Association of PLEKHA7, COL11A1 and PCMTD1-ST18 gene polymorphisms with primary angle closure glaucoma in ethnic Han Chinese from Sichuan].
    5. The three genetic susceptibility loci for primary angle-closure glaucoma did not underlie any major phenotypic diversity in terms of disease severity or progression.
      Title: Genotype-phenotype correlation analysis for three primary angle closure glaucoma-associated genetic polymorphisms.
    6. In our study, rs1015213 (located in the intergenic region between PCMTD1 and ST18) was associated significantly with primary angle closure.
      Title: Association study in a South Indian population supports rs1015213 as a risk factor for primary angle closure.
    7. Presence of at least one A allele (AG or AA genotype) for rs1015213 was associated with a shallower anterior chamber depth (-0.07 mm, 95% CI -0.01 to -0.14 mm, p=0.028) after adjusting for age and sex (both p</=0.001).
      Title: Genotype-phenotype analysis of SNPs associated with primary angle closure glaucoma (rs1015213, rs3753841 and rs11024102) and ocular biometry in the EPIC-Norfolk Eye Study.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10883

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables S-adenosylmethionine-dependent methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-L-isoaspartate (D-aspartate) O-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-like ligase-substrate adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul5-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein-L-isoaspartate O-methyltransferase domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001286782.1 → NP_001273711.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC090186, AC103769, BC010693
      Consensus CDS
      CCDS69480.1
      UniProtKB/Swiss-Prot
      Q96MG8
      UniProtKB/TrEMBL
      F5H1M8
      Related
      ENSP00000444026.1, ENST00000544451.2
      Conserved Domains (1) summary
      COG2518
      Location:84 → 144
      Pcm; Protein-L-isoaspartate O-methyltransferase [Posttranslational modification, protein turnover, chaperones]

    2. NM_001286783.2 → NP_001273712.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001273712.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (3) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC090186, AC103769, AK304332
      Conserved Domains (1) summary
      COG2518
      Location:5 → 44
      Pcm; Protein-L-isoaspartate O-methyltransferase [Posttranslational modification, protein turnover, chaperones]

    3. NM_001363193.1 → NP_001350122.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AA521309, AC090186, AK056952
      Conserved Domains (1) summary
      pfam01135
      Location:11 → 219
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)

    4. NM_052937.4 → NP_443169.2  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_443169.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC090186, AK056952
      Consensus CDS
      CCDS6148.1
      UniProtKB/Swiss-Prot
      F5H1M8, Q96FK9, Q96MG8
      Related
      ENSP00000428099.1, ENST00000522514.6
      Conserved Domains (1) summary
      pfam01135
      Location:11 → 219
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      51817575..51899186 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421325.1 → XP_047277281.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform X3

    2. XM_047421323.1 → XP_047277279.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      F5H1M8, Q96FK9, Q96MG8

    3. XM_047421324.1 → XP_047277280.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      52193558..52274823 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359714.1 → XP_054215689.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      B7Z927

    2. XM_054359712.1 → XP_054215687.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform X1

    3. XM_054359713.1 → XP_054215688.1  protein-L-isoaspartate O-methyltransferase domain-containing protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MG8.2 GenPept UniProtKB/Swiss-Prot:Q96MG8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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