PPIP5K1

diphosphoinositol pentakisphosphate kinase 1

Basic information

Region (hg38): 15:43533462-43590208

Previous symbols: [ "HISPPD2A" ]

Links

ENSG00000168781NCBI:9677OMIM:610979HGNC:29023Uniprot:Q6PFW1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPIP5K1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
53
clinvar
3
clinvar
56
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 53 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PPIP5K1protein_codingprotein_codingENST00000420765 2956771
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002700.9951257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.571822520.7220.00001259366
Missense in Polyphen1743.1560.393922739
Synonymous1.218297.20.8440.000004892836
Loss of Function2.63821.00.3810.00000111838

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.000.00
East Asian0.00005780.0000544
Finnish0.000.00
European (Non-Finnish)0.0001060.000105
Middle Eastern0.00005780.0000544
South Asian0.00006540.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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