PIP4K2B
protein-codingphosphatidylinositol-5-phosphate 4-kinase type 2 beta
Gene summary
The protein encoded by this gene catalyzes the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. The encoded protein sequence does not show similarity to other kinases, but the protein does exhibit kinase activity. Additionally, the encoded protein interacts with p55 TNF receptor. [provided by RefSeq, Jul 2008]
- PIP5K2B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.4 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 PIP4K2B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003559.5. 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 | 1 | 3 | |||
| missense | 31 | 31 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 36 | 1 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003550.1 | 10 | MANE Select | |
| Ensembl | ENSP00000482548.1 | 10 | MANE Select | |
| Ensembl | ENSP00000477549.1 | 3 | Standard | |
| Ensembl | ENSP00000532474.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inositol phosphate metabolism - Homo sapiens (human)
- Regulation of actin cytoskeleton - Homo sapiens (human)
- Phosphatidylinositol signaling system - Homo sapiens (human)
- Regulation of Actin Cytoskeleton
- D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis
Biological Process
- phospholipid metabolic process
- phosphatidylinositol biosynthetic process
- cell surface receptor signaling pathway
- regulation of autophagy
- regulation of phosphatidylinositol 3-kinase signaling
Molecular Function
- protein binding
- ATP binding
- 1-phosphatidylinositol-4-phosphate 5-kinase activity
- 1-phosphatidylinositol-5-phosphate 4-kinase activity
- protein homodimerization activity
Cellular Component
- nucleoplasm
- autophagosome
- endoplasmic reticulum membrane
- cytosol
- plasma membrane
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate. {ECO:0000269|PubMed:9038203}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 50.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |