PITPNA
protein-codingphosphatidylinositol transfer protein alpha, the group of Phosphatidylinositol transfer proteins
Gene summary
This gene encodes a member of a family of lipid-binding proteins that transfer molecules of phosphatidylinositol or phosphatidylcholine between membrane surfaces. The protein is implicated in phospholipase C signaling and in the production of phosphatidylinositol 3,4,5-trisphosphate (PIP3) by phosphoinositide-3-kinase.[provided by RefSeq, Sep 2009]
- PITPN
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~45.1 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 PITPNA variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006224.4. 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 | 20 | 1 | 21 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 26 | 1 | 0 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006215.1 | 11 | MANE Select | |
| Ensembl | ENSP00000316809.7 | 11 | MANE Select | |
| Ensembl | ENSP00000461539.1 | 5 | Standard | |
| Ensembl | ENSP00000460771.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pitpnaa | Danio rerio | Structure: CaP motoneuron Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation
- Developmental Biology
- Role of second messengers in netrin-1 signaling
- EGFR1
- Netrin-1 signaling
Biological Process
- lipid metabolic process
- axonogenesis
- visual perception
- phospholipid transport
- interleukin-12-mediated signaling pathway
Molecular Function
- phosphatidylcholine transporter activity
- phosphatidylinositol transporter activity
- phosphatidylcholine binding
- phosphatidylinositol binding
- phosphatidylglycerol binding
Cellular Component
- cytoplasm
- cytosol
- myelin sheath
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000313486
- Coding exons
- 11
- Length
- 45099
- Individuals with no LoFs
- 124631
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 124638
- p
- 0.0000281
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 67 | 152 | 0.442 | 0.00000831 | 1791 |
| Missense (PolyPhen) | 25 | 61.966 | 0.40345 | 757 | ||
| Synonymous | -0.180 | 61 | 59.2 | 1.03 | 0.00000395 | 466 |
| Loss of Function | 3.94 | 3 | 23.7 | 0.127 | 0.00000136 | 244 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the transfer of PtdIns and phosphatidylcholine between membranes.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- RVIS EVS
- -0.3
- RVIS percentile EVS
- 32.62
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.718
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |