CEPT1
Basic information
Region (hg38): 1:111139479-111185104
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (25 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEPT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006090.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 25 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 0 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CEPT1 | protein_coding | protein_coding | ENST00000545121 | 8 | 45476 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.994 | 0.00649 | 125743 | 0 | 3 | 125746 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.50 | 121 | 227 | 0.533 | 0.0000113 | 2722 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000606 | 0.0000606 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Phosphonate and phosphinate metabolism - Homo sapiens (human);Plasmalogen Synthesis;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;phosphatidylcholine biosynthesis;Metabolism;Synthesis of PC;Synthesis of PE;phosphatidylcholine biosynthesis pathway;Glycerophospholipid metabolism;phosphatidylethanolamine biosynthesis II;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.254
Intolerance Scores
- loftool
- 0.148
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.23
Haploinsufficiency Scores
- pHI
- 0.150
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.524
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.659
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cept1
- Phenotype
- muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- lipid metabolic process;phosphatidylethanolamine biosynthetic process;phosphatidylcholine biosynthetic process;CDP-choline pathway
- Cellular component
- endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane;nuclear membrane
- Molecular function
- diacylglycerol cholinephosphotransferase activity;ethanolaminephosphotransferase activity;phosphotransferase activity, for other substituted phosphate groups;metal ion binding