CEPT1

choline/ethanolamine phosphotransferase 1

Basic information

Region (hg38): 1:111139478-111185104

Links

ENSG00000134255 ∙ NCBI:10390 ∙ OMIM:616751 ∙ HGNC:24289 ∙ Uniprot:Q9Y6K0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEPT1 gene.

• Inborn genetic diseases (8 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.

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			8		1	9
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	1

Variants in CEPT1

This is a list of pathogenic ClinVar variants found in the CEPT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-111147833-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-111147848-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-111147881-A-G		not specified	Uncertain significance (Aug 08, 2022)
1-111147997-A-G		not specified	Uncertain significance (Sep 14, 2023)
1-111159398-A-G			Benign (Apr 02, 2018)
1-111161200-A-G		not specified	Uncertain significance (Mar 17, 2023)
1-111174935-T-C		not specified	Uncertain significance (Sep 23, 2023)
1-111182257-G-A		not specified	Uncertain significance (Jun 26, 2023)
1-111182893-A-G		not specified	Uncertain significance (May 05, 2023)
1-111184249-C-G		not specified	Uncertain significance (Jun 14, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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