CPTP
protein-codingceramide-1-phosphate transfer protein
Gene summary
Enables ceramide 1-phosphate binding activity and ceramide 1-phosphate transfer activity. Involved in several processes, including ceramide 1-phosphate transport; negative regulation of NLRP3 inflammasome complex assembly; and negative regulation of interleukin-1 beta production. Is active in cytosol and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Jun 2026]
- GLTPD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.1 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 CPTP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001029885.2. 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 | 1 | 1 | ||||
| missense | 47 | 8 | 55 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 49 | 9 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001025056.1 | 2 | MANE Select | |
| Ensembl | ENSP00000343890.4 | 2 | MANE Select | |
| Ensembl | ENSP00000462636.1 | 2 | Standard | |
| Ensembl | ENSP00000570337.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Glycosphingolipid metabolism
- Sphingolipid metabolism
Biological Process
- glycosphingolipid metabolic process
- negative regulation of autophagy
- ceramide transport
- glycolipid transport
- negative regulation of interleukin-1 beta secretion
Molecular Function
- phospholipid binding
- phospholipid transporter activity
- lipid binding
- intermembrane lipid transfer activity
- ceramide 1-phosphate binding
Cellular Component
- nuclear outer membrane
- Golgi apparatus
- cytosol
- plasma membrane
- endosome membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000343938
- Coding exons
- 2
- Length
- 4142
- Individuals with no LoFs
- 125497
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125515
- p
- 0.0000717
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0932 | 158 | 155 | 1.02 | 0.0000115 | 1357 |
| Missense (PolyPhen) | 53 | 53.078 | 0.99853 | 511 | ||
| Synonymous | -1.01 | 88 | 76.7 | 1.15 | 0.00000602 | 464 |
| Loss of Function | 0.928 | 3 | 5.31 | 0.565 | 2.26e-7 | 57 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000089 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000038 | 0.000035 | rare |
| South Asian | 0.00030 | 0.00029 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mediates the intracellular transfer of ceramide-1- phosphate (C1P) between organelle membranes and the cell membrane. Required for normal structure of the Golgi stacks. Can bind phosphoceramides with a variety of aliphatic chains, but has a preference for lipids with saturated C16:0 or monounsaturated C18:1 aliphatic chains, and is inefficient with phosphoceramides containing lignoceryl (C24:0). Plays a role in the regulation of the cellular levels of ceramide-1-phosphate, and thereby contributes to the regulation of phospholipase PLA2G4A activity and the release of arachidonic acid. Has no activity with galactosylceramide, lactosylceramide, sphingomyelin, phosphatidylcholine, phosphatidic acid and ceramide. C1P transfer is stimulated by phosphatidylserine in C1P source vesicles (PubMed:28011644). Regulates autophagy, inflammasome mediated IL1B and IL18 processing, and pyroptosis, but not apoptosis (PubMed:29164996). {ECO:0000269|PubMed:23863933, ECO:0000269|PubMed:28011644, ECO:0000269|PubMed:29164996}.;
Intolerance Scores
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 61.73
Essentials
- Essential (gene trap)
- N