PITPNB
protein-codingphosphatidylinositol transfer protein beta, the group of Phosphatidylinositol transfer proteins
Gene summary
This gene encodes a cytoplasmic protein that catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes. This transfer activity is required for COPI complex-mediated retrograde transport from the Golgi apparatus to the endoplasmic reticulum. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~68.5 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 PITPNB variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012399.5. 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 | 2 | 2 | ||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 25 | 0 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036531.1 | 11 | MANE Select | |
| Ensembl | ENSP00000334738.5 | 11 | MANE Select | |
| RefSeq | NP_001271206.1 | 11 | Standard | |
| RefSeq | NP_001271207.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pitpnb | Danio rerio | Structure: retinal cone cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- PI and PC transport between ER and Golgi membranes
- PI Metabolism
- Glycerophospholipid biosynthesis
Biological Process
- lipid metabolic process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
- nucleus organization
- phospholipid transport
Molecular Function
- phosphatidylcholine transporter activity
- phosphatidylinositol transporter activity
- phosphatidylcholine binding
- phosphatidylinositol binding
Cellular Component
- Golgi membrane
- cytoplasm
- endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335272
- Coding exons
- 11
- Length
- 68466
- Individuals with no LoFs
- 125736
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125738
- p
- 0.00000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.15 | 49 | 114 | 0.431 | 0.00000548 | 1807 |
| Missense (PolyPhen) | 11 | 51.622 | 0.21309 | 800 | ||
| Synonymous | 0.603 | 35 | 39.8 | 0.879 | 0.00000212 | 458 |
| Loss of Function | 3.54 | 1 | 16.5 | 0.0606 | 6.95e-7 | 251 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the transfer of PtdIns and phosphatidylcholine between membranes.;
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- LoFtool
- 0.199
- RVIS EVS
- 0.12
- RVIS percentile EVS
- 62.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.575
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |