U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 10400, updated on 3-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
17p11.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17505563..17592142, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17452171..17538580, complement)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. PEMT variants are associated with nonsyndromic cleft lip with or without cleft palate in Chile. Suazo J, et al. Epigenomics, 2022 Sep. PMID 36154674
  2. Hepatic PEMT Expression Decreases with Increasing NAFLD Severity. Piras IS, et al. Int J Mol Sci, 2022 Aug 18. PMID 36012560, Free PMC Article
  3. Dietary Choline Intake during Pregnancy and PEMT rs7946 Polymorphism on Risk of Preterm Birth: A Case-Control Study. Zhu J, et al. Ann Nutr Metab, 2020. PMID 33503637
  4. Importance of polymorphic variants of phosphatidylethanolamine N-methyltransferase (PEMT) gene in the etiology of intrauterine fetal death in the Polish population. Seremak-Mrozikiewicz A, et al. Eur J Obstet Gynecol Reprod Biol, 2018 Dec. PMID 30321787
  5. 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

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. Hepatic PEMT Expression Decreases with Increasing NAFLD Severity.
    Title: Hepatic PEMT Expression Decreases with Increasing NAFLD Severity.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Study found three gene variants (CLOCK-rs4864548, PEMT-rs936108, and GHRELIN-rs696217) that exhibited uncorrected gene-by-sleep duration interactions in relation to BMI z-scores in a cohort of New Zealand European children. However, no interactions were identified in percentage body fat differences. Notably, these interactions are evident without detectable effects on sleep duration.
    Title: Gene-by-environment interactions of the CLOCK, PEMT, and GHRELIN loci with average sleep duration in relation to obesity traits using a cohort of 643 New Zealand European children.
Submit: New GeneRIF Correction See all GeneRIFs (41)

Phenotypes

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC2483

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidyl-N-dimethylethanolamine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
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
  
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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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_2023_10

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

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous