PIP5K1B
Basic information
Region (hg38): 9:68705240-69009176
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (66 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIP5K1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003558.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 43 | 43 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 43 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PIP5K1B | protein_coding | protein_coding | ENST00000265382 | 12 | 303518 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.37e-7 | 0.989 | 125699 | 0 | 49 | 125748 | 0.000195 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.48 | 174 | 294 | 0.592 | 0.0000153 | 3537 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000413 | 0.000413 |
Ashkenazi Jewish | 0.000398 | 0.000397 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.000231 | 0.000231 |
European (Non-Finnish) | 0.000132 | 0.000132 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000197 | 0.000196 |
Other | 0.000490 | 0.000489 |
dbNSFP
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}.;
- Pathway
- 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);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);B Cell Receptor Signaling Pathway;Wnt Signaling Pathway;Regulation of Actin Cytoskeleton;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Signaling by WNT;Signal Transduction;rho cell motility signaling pathway;Metabolism of lipids;Inositol phosphate metabolism;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;BCR;Phosphatidylinositol phosphate metabolism;PIP3 activates AKT signaling;Synthesis of PIPs at the plasma membrane;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Plexin-D1 Signaling;PI Metabolism;Phospholipid metabolism;Intracellular signaling by second messengers;WNT mediated activation of DVL;RAC1 signaling pathway;TCF dependent signaling in response to WNT;Canonical Wnt signaling pathway;RhoA signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.0935
Intolerance Scores
- loftool
- 0.685
- rvis_EVS
- 0.2
- rvis_percentile_EVS
- 67.19
Haploinsufficiency Scores
- pHI
- 0.213
- hipred
- Y
- hipred_score
- 0.746
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.972
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pip5k1b
- Phenotype
- reproductive system phenotype; hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; cellular phenotype;
Gene ontology
- Biological process
- phosphatidylinositol biosynthetic process;regulation of phosphatidylinositol 3-kinase signaling;phosphatidylinositol phosphorylation
- Cellular component
- uropod;cytosol;endomembrane system;membrane
- 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;1-phosphatidylinositol-3-phosphate 4-kinase activity;phosphatidylinositol-3,4-bisphosphate 5-kinase activity