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    PEMT phosphatidylethanolamine N-methyltransferase [ Homo sapiens (human) ]

    Gene ID: 10400, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PEMTprovided by HGNC
    Official Full Name
    phosphatidylethanolamine N-methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:8830
    See related
    Ensembl:ENSG00000133027 MIM:602391; AllianceGenome:HGNC:8830
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PLMT; PNMT; PEAMT; PEMPT; PEMT2
    Summary
    Phosphatidylcholine (PC) is the most abundant mammalian phospholipid. This gene encodes an enzyme which converts phosphatidylethanolamine to phosphatidylcholine by sequential methylation in the liver. Another distinct synthetic pathway in nucleated cells converts intracellular choline to phosphatidylcholine by a three-step process. The protein isoforms encoded by this gene localize to the endoplasmic reticulum and mitochondria-associated membranes. Alternate splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]
    Expression
    Broad expression in liver (RPKM 29.5), fat (RPKM 10.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PEMT in Genome Data Viewer
    Location:
    17p11.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17505563..17592142, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17452171..17538580, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17408877..17495022, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17406686-17407658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17416043-17416912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17416913-17417782 Neighboring gene mediator complex subunit 9 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17418653-17419522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17420393-17421262 Neighboring gene ras related dexamethasone induced 1 Neighboring gene VISTA enhancer hs1917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17448679-17449178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17456297-17457102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17465957-17466820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17470469-17471358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17471359-17472250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17472251-17473140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17479915-17480660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17494467-17495208 Neighboring gene RNA, U6 small nuclear 468, pseudogene Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17506274-17506774 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17516315-17516931 Neighboring gene Sharpr-MPRA regulatory region 11476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17525146-17526020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17526021-17526896 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17529033-17529938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17529939-17530844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17570789-17571290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17571291-17571790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17578718-17579346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17584813-17585414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8249 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17596270-17596984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17596985-17597697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8250 Neighboring gene uncharacterized LOC124903943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17602043-17602561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17602562-17603079 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17603559-17604070 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 2 Neighboring gene Sharpr-MPRA regulatory region 3199 Neighboring gene Sharpr-MPRA regulatory region 10129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17620721-17621465 Neighboring gene retinoic acid induced 1

    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. PEMT G523A (V175M) is associated with sporadic Alzheimer's disease in a Chinese population. Bi XH, et al. J Mol Neurosci, 2012 Mar. PMID 21881829
    2. Phosphatidylethanolamine N-methyltransferase gene rs7946 polymorphism plays a role in risk of nonalcoholic fatty liver disease: evidence from meta-analysis. Tan HL, et al. Pharmacogenet Genomics, 2016 Feb. PMID 26636496
    3. Activity of phosphatidylethanolamine-N-methyltransferase in brain affected by Alzheimer's disease. Guan ZZ, et al. Neurochem Int, 1999 Jan. PMID 10100195
    4. Structure, expression profile and alternative processing of the human phosphatidylethanolamine N-methyltransferase (PEMT) gene. Shields DJ, et al. Biochim Biophys Acta, 2001 May 31. PMID 11420179
    5. Membrane topography of human phosphatidylethanolamine N-methyltransferase. Shields DJ, et al. J Biol Chem, 2003 Jan 31. PMID 12431977

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association between PEMT rs7946 and blood pressure levels in Chinese adolescents.
      Title: Association between PEMT rs7946 and blood pressure levels in Chinese adolescents.
    2. The Role of Phosphatidylethanolamine N-Methyltransferase (PEMT) and Its Waist-Hip-Ratio-Associated Locus rs4646404 in Obesity-Related Metabolic Traits and Liver Disease.
      Title: The Role of Phosphatidylethanolamine N-Methyltransferase (PEMT) and Its Waist-Hip-Ratio-Associated Locus rs4646404 in Obesity-Related Metabolic Traits and Liver Disease.
    3. Dietary Choline Intake during Pregnancy and PEMT rs7946 Polymorphism on Risk of Preterm Birth: A Case-Control Study.
      Title: Dietary Choline Intake during Pregnancy and PEMT rs7946 Polymorphism on Risk of Preterm Birth: A Case-Control Study.
    4. PEMT variants are associated with nonsyndromic cleft lip with or without cleft palate in Chile.
      Title: PEMT variants are associated with nonsyndromic cleft lip with or without cleft palate in Chile.
    5. Hepatic PEMT Expression Decreases with Increasing NAFLD Severity.
      Title: Hepatic PEMT Expression Decreases with Increasing NAFLD Severity.
    6. Associations between folate and choline intake, homocysteine metabolism, and genetic polymorphism of MTHFR, BHMT and PEMT in healthy pregnant Polish women.
      Title: Associations between folate and choline intake, homocysteine metabolism, and genetic polymorphism of MTHFR, BHMT and PEMT in healthy pregnant Polish women.
    7. Total liver phosphatidylcholine content associates with non-alcoholic steatohepatitis and glycine N-methyltransferase expression.
      Title: Total liver phosphatidylcholine content associates with non-alcoholic steatohepatitis and glycine N-methyltransferase expression.
    8. Genetic variations in PEMT and MTHFR were associated with different PUFA levels in erythrocyte membranes and are estimators for PUFA species in erythrocytes. Further research is needed to establish whether these genotype-specific alterations are specific to overweight children.
      Title: Single Nucleotide Polymorphisms in PEMT and MTHFR Genes are Associated with Omega 3 and 6 Fatty Acid Levels in the Red Blood Cells of Children with Obesity.
    9. Our study shows that choline intake in Polish pregnant women is inadequate and that polymorphisms of PEMT rs12325817 and PCYT1A rs7639752 are associated with betaine but not choline concentrations.
      Title: PEMT rs12325817 and PCYT1A rs7639752 polymorphisms are associated with betaine but not choline concentrations in pregnant women.
    10. PEMT polymorphisms may be associated with the susceptibility to intrauterine fetal death in the Polish population
      Title: Importance of polymorphic variants of phosphatidylethanolamine N-methyltransferase (PEMT) gene in the etiology of intrauterine fetal death in the Polish population.
    Submit: New GeneRIF Correction See all GeneRIFs (42)

    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
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    EBI GWAS Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC2483

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidyl-N-methylethanolamine N-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylethanolamine N-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylethanolamine N-methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylcholine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylcholine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylcholine biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in sphingomyelin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrial membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    phosphatidylethanolamine N-methyltransferase
    Names
    phospholipid methyltransferase
    NP_001254480.1
    NP_001254481.1
    NP_009100.2
    NP_680477.1
    NP_680478.1
    XP_006721481.3
    XP_016879505.1
    XP_024306300.1
    XP_054170662.1
    XP_054170663.1
    XP_054170664.1

    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_001267551.2 → NP_001254480.1  phosphatidylethanolamine N-methyltransferase isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 4) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      AC020558, AK302251, BC050593, BM011377
      UniProtKB/TrEMBL
      Q71UY0
      Related
      ENSP00000391288.2, ENST00000435340.6
      Conserved Domains (1) summary
      pfam04191
      Location:123 → 206
      PEMT; Phospholipid methyltransferase

    2. NM_001267552.2 → NP_001254481.1  phosphatidylethanolamine N-methyltransferase isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has an additional exon in the 3' coding region, compared to variant 1, which results in a frameshift and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC020558, AK302251, BC050593
      Consensus CDS
      CCDS58520.1
      UniProtKB/TrEMBL
      D3YTC7
      Related
      ENSP00000379127.2, ENST00000395781.6
      Conserved Domains (1) summary
      pfam04191
      Location:145 → 193
      PEMT; Phospholipid methyltransferase

    3. NM_007169.3 → NP_009100.2  phosphatidylethanolamine N-methyltransferase isoform 2

      See identical proteins and their annotated locations for NP_009100.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream start codon compared to variant 1. Variants 2 and 3 encode the same isoform (2). Isoform 2 localizes to mitochondria-associated membranes.
      Source sequence(s)
      AC020558
      Consensus CDS
      CCDS11187.1
      UniProtKB/Swiss-Prot
      A8MZ66, B4DY41, D3DXC3, Q6IAQ5, Q86VL3, Q9BW86, Q9UBM1, Q9UHY6, Q9Y6V9
      UniProtKB/TrEMBL
      Q71UY0
      Related
      ENSP00000379129.1, ENST00000395783.5
      Conserved Domains (1) summary
      pfam04191
      Location:108 → 191
      PEMT; Phospholipid methyltransferase

    4. NM_148172.3 → NP_680477.1  phosphatidylethanolamine N-methyltransferase isoform 1

      See identical proteins and their annotated locations for NP_680477.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Isoform 1 localizes to the endoplasmic reticulum.
      Source sequence(s)
      AC020558, AF113126, AK302251, BC050593
      Consensus CDS
      CCDS11186.1
      UniProtKB/TrEMBL
      Q71UY0
      Related
      ENSP00000255389.5, ENST00000255389.10
      Conserved Domains (1) summary
      pfam04191
      Location:145 → 228
      PEMT; Phospholipid methyltransferase

    5. NM_148173.2 → NP_680478.1  phosphatidylethanolamine N-methyltransferase isoform 2

      See identical proteins and their annotated locations for NP_680478.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses a downstream start codon compared to variant 1. Variants 2 and 3 encode the same isoform (2). Isoform 2 localizes to mitochondria-associated membranes.
      Source sequence(s)
      AC020558
      Consensus CDS
      CCDS11187.1
      UniProtKB/Swiss-Prot
      A8MZ66, B4DY41, D3DXC3, Q6IAQ5, Q86VL3, Q9BW86, Q9UBM1, Q9UHY6, Q9Y6V9
      UniProtKB/TrEMBL
      Q71UY0
      Related
      ENSP00000379128.1, ENST00000395782.5
      Conserved Domains (1) summary
      pfam04191
      Location:108 → 191
      PEMT; Phospholipid methyltransferase

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      17505563..17592142 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450532.2 → XP_024306300.1  phosphatidylethanolamine N-methyltransferase isoform X2

      UniProtKB/Swiss-Prot
      A8MZ66, B4DY41, D3DXC3, Q6IAQ5, Q86VL3, Q9BW86, Q9UBM1, Q9UHY6, Q9Y6V9
      UniProtKB/TrEMBL
      Q71UY0
      Conserved Domains (1) summary
      pfam04191
      Location:108 → 191
      PEMT; Phospholipid methyltransferase

    2. XM_006721418.5 → XP_006721481.3  phosphatidylethanolamine N-methyltransferase isoform X3

    3. XM_017024016.2 → XP_016879505.1  phosphatidylethanolamine N-methyltransferase isoform X1

      Related
      ENST00000484838.6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      17452171..17538580 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314689.1 → XP_054170664.1  phosphatidylethanolamine N-methyltransferase isoform X2

    2. XM_054314687.1 → XP_054170662.1  phosphatidylethanolamine N-methyltransferase isoform X4

    3. XM_054314688.1 → XP_054170663.1  phosphatidylethanolamine N-methyltransferase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UBM1.4 GenPept UniProtKB/Swiss-Prot:Q9UBM1

    Gene LinkOut

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