PIP5K1B
protein-codingphosphatidylinositol-4-phosphate 5-kinase type 1 beta
Gene summary
Predicted to enable 1-phosphatidylinositol-4-phosphate 5-kinase activity. Predicted to be involved in phosphatidylinositol phosphate biosynthetic process. Predicted to act upstream of or within phosphatidylinositol biosynthetic process. Located in uropod. [provided by Alliance of Genome Resources, Apr 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~303.9 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 PIP5K1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003558.4. 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 | 5 | 2 | 7 | |||
| missense | 1 | 47 | 2 | 50 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 2 | 0 | 56 | 4 | 0 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003549.1 | 13 | MANE Select | |
| Ensembl | ENSP00000265382.2 | 13 | MANE Select | |
| RefSeq | NP_001265182.1 | 12 | Standard | |
| RefSeq | NP_001362965.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fc gamma R-mediated phagocytosis - Homo sapiens (human)
- Inositol phosphate metabolism - Homo sapiens (human)
- Choline metabolism in cancer - Homo sapiens (human)
- Endocytosis - Homo sapiens (human)
- Regulation of actin cytoskeleton - Homo sapiens (human)
Biological Process
- phosphatidylinositol biosynthetic process
- regulation of phosphatidylinositol 3-kinase signaling
- phosphatidylinositol phosphorylation
Molecular Function
- 1-phosphatidylinositol-3-phosphate 5-kinase activity
- protein binding
- ATP binding
- 1-phosphatidylinositol-4-phosphate 5-kinase activity
- 1-phosphatidylinositol-5-kinase activity
Cellular Component
- uropod
- cytosol
- endomembrane system
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000265382
- Coding exons
- 12
- Length
- 303518
- Individuals with no LoFs
- 125699
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 49
- Defined
- 125748
- p
- 0.000195
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.48 | 174 | 294 | 0.592 | 0.0000153 | 3537 |
| Missense (PolyPhen) | 49 | 129.22 | 0.37921 | 1617 | ||
| Synonymous | 0.847 | 99 | 110 | 0.897 | 0.00000616 | 1017 |
| Loss of Function | 2.35 | 16 | 29.9 | 0.536 | 0.00000161 | 373 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate. Mediates RAC1-dependent reorganization of actin filaments. Contributes to the activation of PLD2. Together with PIP5K1A is required after stimulation of G-protein coupled receptors for stable platelet adhesion (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0935
Intolerance Scores
- LoFtool
- 0.685
- RVIS EVS
- 0.2
- RVIS percentile EVS
- 67.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.972
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |