PEMT

Chr 17

phosphatidylethanolamine N-methyltransferase

Also known as: PEAMT, PEMPT, PEMT2, PLMT

NCBI Gene: 10400 ENSG00000133027 UniProt: Q9UBM1 OMIM: 602391

The enzyme catalyzes the three sequential methylation steps that convert phosphatidylethanolamine to phosphatidylcholine, an essential membrane phospholipid, and is responsible for approximately 30% of hepatic phosphatidylcholine synthesis. Mutations cause autosomal recessive nonalcoholic fatty liver disease, which can present in childhood and may progress to cirrhosis. The gene shows moderate constraint against loss-of-function variants, reflecting its important but non-essential role given alternative phosphatidylcholine synthesis pathways.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.67

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.67LOEUF

pLI 0.235

Z-score 2.35

OE 0.26 (0.12–0.67)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.11Z-score

OE missense 1.03 (0.90–1.18)

142 obs / 138.3 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.26 (0.12–0.67)

0≤0.351.4

Missense OE?1.03 (0.90–1.18)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 3 / 11.6Missense obs/exp: 142 / 138.3Syn Z: -0.19

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PEMT · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox

AI-powered variant curation and clinical analysis

DECIPHER

Genomic variants and phenotypes in rare disease patients

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

Hypertension, Resistant to Conventional Therapy

Antihypertensive Mechanisms of Minocycline in Resistant Hypertension

RECRUITING

NCT06246396Phase PHASE4University of FloridaStarted 2025-01-08

Minocycline HydrochloridePlacebo

Inflammatory Bowel DiseasesCrohn Disease

Predicting IBD Treatment Outcomes With Gut Microbiome Analysis

RECRUITING

NCT06453720University of British ColumbiaStarted 2024-08-01

Colonoscopy

Breast Cancer

Anti-Inflammatory Diet in BRC Patients on Aromatase Inhibitors

RECRUITING

NCT06214598Phase NAUniversity of BelgradeStarted 2024-03-01

SupplementAI dietPlacebo

SpondyloarthritisRuminococcus Gnavus

The Role of Intestinal Microbiota Dysbiosis in the Development of Spondyloarthritis

RECRUITING

NCT04853212Phase NAAssistance Publique - Hôpitaux de ParisStarted 2021-06-14

Biopsy

Type1diabetes

Crosstalk Between Mucosal-Associated Invariant T (MAIT) Cells and the Gut Microbiota and Mucosa in the Development of Type 1 Diabetes in Children

RECRUITING

NCT05054361Institut National de la Santé Et de la Recherche Médicale, FranceStarted 2022-01-01

MAIT cells analysisMAIT cytokines production analysisLactulose/Mannitol Test

COPDChronic Obstructive Pulmonary DiseaseChronic Bronchitis

Study of COPD Subgroups and Biomarkers

ACTIVE NOT RECRUITING

NCT01969344University of North Carolina, Chapel HillStarted 2010-11

Sinusitis, ChronicSinus DiseaseSinus Infection

Microbiota Transfer for Chronic Rhinosinusitis

ACTIVE NOT RECRUITING

NCT05454072Phase NAAmin JaverStarted 2022-06-15

Sinonasal Microbiota TransferSham Sinonasal Microbiota Transfer

Multiple Myeloma

A Clinical Study of TQB2029 for Injection in Subjects With Multiple Myeloma

RECRUITING

NCT06700395Phase PHASE1Chia Tai Tianqing Pharmaceutical Group Nanjing Shunxin Pharmaceutical Co., Ltd.Started 2024-11-28

TQB2029 injection

Anaplastic Large Cell Lymphoma, ALK-NegativeAnaplastic Large Cell Lymphoma, ALK-PositiveApocrine Carcinoma

Talimogene Laherparepvec and Nivolumab in Treating Patients With Refractory Lymphomas or Advanced or Refractory Non-melanoma Skin Cancers

ACTIVE NOT RECRUITING

NCT02978625Phase PHASE2National Cancer Institute (NCI)Started 2017-09-27

Biopsy ProcedureBiospecimen CollectionComputed Tomography

Nonalcoholic Fatty Liver DiseaseNonalcoholic Fatty Liver Disease (NAFLD)MASLD - Metabolic Dysfunction-Associated Steatotic Liver Disease

The Impact of Pectin Supplementation on Systematic Inflammation Pathway, Gut Microbiome, and Metabolic Health in Patients With Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)

RECRUITING

NCT07093346Phase NAUniversity of NottinghamStarted 2025-06-10

PectinCocoa PowderMagnetic Resonance Imaging with Contrast

Infant NeurodevelopmentNutritionMethylation

Maternal Methyl-Nutrient Status and Infant Neurodevelopment Study

RECRUITING

NCT07568561Far Eastern Memorial HospitalStarted 2026-05-27

Functional DyspepsiaGastritisGastritis Chronic

The Prevalence and the Pathophysiological Role of Non-Helicobacter Pylori Helicobacter Spp. in Well-defined Gastric Diseases and (Pre-) Malignancies

RECRUITING

NCT07770126Universiteit AntwerpenStarted 2025-02-24

Clinical Literature