PCTP
protein-codingphosphatidylcholine transfer protein, the group of StAR related lipid transfer domain containing
Gene summary
Enables phosphatidylcholine binding activity and phosphatidylcholine intramembrane carrier activity. Involved in phospholipid transport. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~91.8 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 PCTP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021213.4. 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 | 32 | 3 | 35 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 34 | 3 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_067036.2 | 6 | MANE Select | |
| Ensembl | ENSP00000268896.4 | 6 | MANE Select | |
| RefSeq | NP_001095872.1 | 5 | Standard | |
| RefSeq | NP_001317306.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pctp | Danio rerio | Structure: pancreas Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Mitochondrial Fatty Acid Beta-Oxidation
- Metabolism
- Fatty acid metabolism
- Arachidonic acid metabolism
Biological Process
- phosphatidylcholine biosynthetic process
- lipid transport
- phospholipid transport
- negative regulation of cold-induced thermogenesis
Molecular Function
- protein binding
- phospholipid transporter activity
- phosphatidylcholine transporter activity
- phosphatidylcholine binding
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268896
- Coding exons
- 6
- Length
- 91852
- Individuals with no LoFs
- 125655
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 93
- Defined
- 125748
- p
- 0.000370
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.259 | 126 | 118 | 1.07 | 0.00000643 | 1387 |
| Missense (PolyPhen) | 34 | 26.71 | 1.2729 | 316 | ||
| Synonymous | -0.326 | 47 | 44.2 | 1.06 | 0.00000246 | 384 |
| Loss of Function | -0.418 | 16 | 14.3 | 1.12 | 7.93e-7 | 152 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00038 | 0.00037 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0022 | 0.0022 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.00079 | 0.00078 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the transfer of phosphatidylcholine between membranes. Binds a single lipid molecule. {ECO:0000269|PubMed:12055623}.;
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- LoFtool
- 0.594
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.332
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |