PEMT
phosphatidylethanolamine N-methyltransferase, the group of Methyltransferase families
Basic information
Region (hg38): 17:17505563-17591708
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEMT gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 2 |
Variants in PEMT
This is a list of pathogenic ClinVar variants found in the PEMT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-17506246-C-T | Benign (Oct 15, 2018) | |||
| 17-17506272-G-A | not specified | Uncertain significance (Jan 17, 2024) | ||
| 17-17509486-C-T | not specified | Uncertain significance (Dec 07, 2023) | ||
| 17-17509534-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 17-17512563-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 17-17522289-C-T | not specified | Uncertain significance (Aug 17, 2021) | ||
| 17-17522319-C-T | not specified | Uncertain significance (May 21, 2024) | ||
| 17-17522370-C-T | Benign (May 30, 2018) | |||
| 17-17522388-C-T | not specified | Uncertain significance (Oct 02, 2023) | ||
| 17-17576928-A-C | not specified | Uncertain significance (Mar 28, 2024) | ||
| 17-17576976-G-A | not specified | Uncertain significance (Mar 11, 2024) | ||
| 17-17577005-C-A | not specified | Uncertain significance (Sep 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PEMT | protein_coding | protein_coding | ENST00000255389 | 7 | 86146 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.235 | 0.759 | 125731 | 0 | 16 | 125747 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.112 | 142 | 138 | 1.03 | 0.00000842 | 1492 |
| Missense in Polyphen | 35 | 40.624 | 0.86155 | 492 | ||
| Synonymous | -0.189 | 68 | 66.0 | 1.03 | 0.00000452 | 495 |
| Loss of Function | 2.35 | 3 | 11.6 | 0.258 | 5.95e-7 | 123 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000180 | 0.000180 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000445 | 0.0000439 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the three sequential steps of the methylation pathway of phosphatidylcholine biosynthesis, the SAM-dependent methylation of phosphatidylethanolamine (PE) to phosphatidylmonomethylethanolamine (PMME), PMME to phosphatidyldimethylethanolamine (PDME), and PDME to phosphatidylcholine (PC). {ECO:0000255|HAMAP-Rule:MF_03216}.;
- Pathway
- Glycerophospholipid metabolism - Homo sapiens (human);Betaine Metabolism;Phospholipid Biosynthesis;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Acetylcholine Synthesis;Metabolism of lipids;Glycine Serine metabolism;Metabolism;Synthesis of PC;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.217
Intolerance Scores
- loftool
- 0.457
- rvis_EVS
- 0.84
- rvis_percentile_EVS
- 88.3
Haploinsufficiency Scores
- pHI
- 0.170
- hipred
- Y
- hipred_score
- 0.712
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.467
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pemt
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype;
Gene ontology
- Biological process
- blastocyst hatching;lipid metabolic process;phosphatidylcholine biosynthetic process;sphingomyelin biosynthetic process;cell population proliferation;negative regulation of cell population proliferation;methylation;response to vitamin;response to amino acid;response to ethanol;S-adenosylhomocysteine metabolic process;S-adenosylmethionine metabolic process;positive regulation of lipoprotein metabolic process;positive regulation of cold-induced thermogenesis
- Cellular component
- endoplasmic reticulum membrane;integral component of membrane;brush border membrane;mitochondrial membrane;sarcolemma
- Molecular function
- phosphatidyl-N-methylethanolamine N-methyltransferase activity;phosphatidylethanolamine N-methyltransferase activity;phosphatidylethanolamine binding;phosphatidyl-N-dimethylethanolamine N-methyltransferase activity