CEPT1
protein-codingcholine/ethanolamine phosphotransferase 1
Gene summary
This gene codes for a choline/ethanolaminephosphotransferase, which functions in the synthesis of choline- or ethanolamine- containing phospholipids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~45.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CEPT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006090.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 28 | 1 | 29 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 30 | 0 | 1 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006081.1 | 8 | MANE Select | |
| Ensembl | ENSP00000349696.4 | 8 | MANE Select | |
| RefSeq | NP_001007795.1 | 8 | Standard | |
| RefSeq | NP_001317672.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ether lipid metabolism - Homo sapiens (human)
- Glycerophospholipid metabolism - Homo sapiens (human)
- Phosphonate and phosphinate metabolism - Homo sapiens (human)
- Plasmalogen Synthesis
- Kennedy pathway from Sphingolipids
Biological Process
- lipid metabolic process
- phosphatidylethanolamine biosynthetic process
- phosphatidylcholine biosynthetic process
- CDP-choline pathway
Molecular Function
- diacylglycerol cholinephosphotransferase activity
- ethanolaminephosphotransferase activity
- phosphotransferase activity, for other substituted phosphate groups
- metal ion binding
Cellular Component
- endoplasmic reticulum membrane
- Golgi apparatus
- integral component of membrane
- nuclear membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000545121
- Coding exons
- 8
- Length
- 45476
- Individuals with no LoFs
- 125743
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125746
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.50 | 121 | 227 | 0.533 | 0.0000113 | 2722 |
| Missense (PolyPhen) | 45 | 116.46 | 0.38639 | 1433 | ||
| Synonymous | 0.496 | 74 | 79.6 | 0.929 | 0.00000400 | 813 |
| Loss of Function | 3.87 | 1 | 19.4 | 0.0515 | 9.66e-7 | 236 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000061 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes both phosphatidylcholine and phosphatidylethanolamine biosynthesis from CDP-choline and CDP- ethanolamine, respectively. Involved in protein-dependent process of phospholipid transport to distribute phosphatidyl choline to the lumenal surface. Has a higher cholinephosphotransferase activity than ethanolaminephosphotransferase activity. {ECO:0000269|PubMed:10191259, ECO:0000269|PubMed:10893425}.;
Recessive Scores
- pRec
- 0.254
Intolerance Scores
- LoFtool
- 0.148
- RVIS EVS
- 0.31
- RVIS percentile EVS
- 72.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.659
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |