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

Summary

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

Location:: 17p11.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (17505563..17592142, complement)
RS_2023_03	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_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Hepatic PEMT Expression Decreases with Increasing NAFLD Severity.
Title: Hepatic PEMT Expression Decreases with Increasing NAFLD Severity.
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.
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.
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.
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.
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.
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.
In genotypic combination analysis considering PEMT -744GG/CHDH +432GG/BHMT +742GG as the reference combination, PEMT -744GC/CHDH +432GG/BHMT +742GG genotypic combination was significantly higher in mothers of a down syndrome child compared with that in control mothers with an odds ratio of 2.061 (95% CI: 1.10-3.86, P=0.0342).
Title: Choline metabolic pathway gene polymorphisms and risk for Down syndrome: An association study in a population with folate-homocysteine metabolic impairment.
Results showed that PEMT mRNA expression in liver tissues of non-alcoholic steatohepatitis (NASH) patients was significantly lower than those with simple steatosis suggesting a distinct clinical entity of lean NASH with insufficiency of PEMT activities.
Title: Insufficiency of phosphatidylethanolamine N-methyltransferase is risk for lean non-alcoholic steatohepatitis.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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 EBI GWAS CatalogPubMed
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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	PubMed
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	PubMed
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

EC 2.1.1.17

EC 2.1.1.71

NP_001254481.1

EC 2.1.1.17

EC 2.1.1.71

NP_009100.2

EC 2.1.1.17

EC 2.1.1.71

NP_680477.1

EC 2.1.1.17

EC 2.1.1.71

NP_680478.1

EC 2.1.1.17

EC 2.1.1.71

XP_006721481.3

EC 2.1.1.17

EC 2.1.1.71

XP_016879505.1

EC 2.1.1.17

EC 2.1.1.71

XP_024306300.1

EC 2.1.1.17

EC 2.1.1.71

XP_054170662.1

EC 2.1.1.17

EC 2.1.1.71

XP_054170663.1

EC 2.1.1.17

EC 2.1.1.71

XP_054170664.1

EC 2.1.1.17

EC 2.1.1.71

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)

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/Swiss-Prot

Q9UBM1

Related

ENSP00000391288.2, ENST00000435340.6

Conserved Domains (1) summary

pfam04191
Location:123 → 206

PEMT; Phospholipid methyltransferase
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/Swiss-Prot

Q9UBM1

Related

ENSP00000379127.2, ENST00000395781.6

Conserved Domains (1) summary

pfam04191
Location:145 → 193

PEMT; Phospholipid methyltransferase
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

Q9UBM1, Q9Y6V9

Related

ENSP00000379129.1, ENST00000395783.5

Conserved Domains (1) summary

pfam04191
Location:108 → 191

PEMT; Phospholipid methyltransferase
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/Swiss-Prot

Q9UBM1

Related

ENSP00000255389.5, ENST00000255389.10

Conserved Domains (1) summary

pfam04191
Location:145 → 228

PEMT; Phospholipid methyltransferase
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

Q9UBM1, Q9Y6V9

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_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

17505563..17592142 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q9Y6V9

Conserved Domains (1) summary

pfam04191
Location:108 → 191

PEMT; Phospholipid methyltransferase
XM_006721418.5 → XP_006721481.3 phosphatidylethanolamine N-methyltransferase isoform X3
XM_017024016.2 → XP_016879505.1 phosphatidylethanolamine N-methyltransferase isoform X1

Related

ENST00000484838.6

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

17452171..17538580 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314689.1 → XP_054170664.1 phosphatidylethanolamine N-methyltransferase isoform X2
XM_054314687.1 → XP_054170662.1 phosphatidylethanolamine N-methyltransferase isoform X4
XM_054314688.1 → XP_054170663.1 phosphatidylethanolamine N-methyltransferase isoform X1