PPIP5K1
Basic information
Region (hg38): 15:43533462-43590208
Previous symbols: [ "HISPPD2A" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (56 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIP5K1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001394395.1. 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 | 0 | |||||
missense | 53 | 56 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 53 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PPIP5K1 | protein_coding | protein_coding | ENST00000420765 | 29 | 56771 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00270 | 0.995 | 125731 | 0 | 17 | 125748 | 0.0000676 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.57 | 182 | 252 | 0.722 | 0.0000125 | 9366 |
Missense in Polyphen | 17 | 43.156 | 0.39392 | 2739 | ||
Synonymous | 1.21 | 82 | 97.2 | 0.844 | 0.00000489 | 2836 |
Loss of Function | 2.63 | 8 | 21.0 | 0.381 | 0.00000111 | 838 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000904 | 0.0000904 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000578 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000106 | 0.000105 |
Middle Eastern | 0.0000578 | 0.0000544 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis- diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4. Activated when cells are exposed to hyperosmotic stress. {ECO:0000269|PubMed:17412958, ECO:0000269|PubMed:17690096, ECO:0000269|PubMed:17702752}.;
- Pathway
- Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;inositol pyrophosphates biosynthesis;Metabolism;superpathway of inositol phosphate compounds;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism
(Consensus)
Recessive Scores
- pRec
- 0.0945
Haploinsufficiency Scores
- pHI
- 0.267
- hipred
- Y
- hipred_score
- 0.718
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppip5k1
- Phenotype
Gene ontology
- Biological process
- inositol metabolic process;phosphorylation;inositol phosphate biosynthetic process;inositol phosphate metabolic process
- Cellular component
- nucleoplasm;cytosol;plasma membrane
- Molecular function
- inositol-1,3,4,5,6-pentakisphosphate kinase activity;inositol hexakisphosphate kinase activity;inositol heptakisphosphate kinase activity;inositol hexakisphosphate 5-kinase activity;ATP binding;diphosphoinositol-pentakisphosphate kinase activity;inositol hexakisphosphate 1-kinase activity;inositol hexakisphosphate 3-kinase activity;5-diphosphoinositol pentakisphosphate 3-kinase activity