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

Gene ID: 115294, updated on 26-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
  • 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 Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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