PPIP5K1

diphosphoinositol pentakisphosphate kinase 1

Basic information

Region (hg38): 15:43533461-43590208

Previous symbols: [ "HISPPD2A" ]

Links

ENSG00000168781 ∙ NCBI:9677 ∙ OMIM:610979 ∙ HGNC:29023 ∙ Uniprot:Q6PFW1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in PPIP5K1

This is a list of pathogenic ClinVar variants found in the PPIP5K1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-43534749-C-A		not specified	Uncertain significance (Jun 16, 2024)
15-43534780-G-A		not specified	Uncertain significance (Mar 18, 2024)
15-43534882-A-G		not specified	Likely benign (Jun 18, 2021)
15-43534900-C-G		not specified	Uncertain significance (Nov 07, 2022)
15-43534924-T-A		not specified	Uncertain significance (Apr 23, 2024)
15-43534939-A-G		not specified	Likely benign (Feb 21, 2024)
15-43534960-C-T		not specified	Uncertain significance (Nov 01, 2022)
15-43534979-C-T		not specified	Uncertain significance (Nov 30, 2022)
15-43534998-C-A		not specified	Uncertain significance (Mar 01, 2024)
15-43535099-G-A		not specified	Uncertain significance (Sep 16, 2021)
15-43535105-C-T		not specified	Uncertain significance (Jun 29, 2022)
15-43535140-C-A		not specified	Uncertain significance (Apr 04, 2024)
15-43535140-C-T		not specified	Uncertain significance (Jun 28, 2023)
15-43535155-G-A		not specified	Uncertain significance (Oct 29, 2021)
15-43535207-G-T		not specified	Uncertain significance (Mar 29, 2023)
15-43535222-C-T		not specified	Uncertain significance (Feb 27, 2024)
15-43535252-C-T		not specified	Uncertain significance (Jan 08, 2024)
15-43535302-A-G		not specified	Uncertain significance (Aug 02, 2022)
15-43535314-C-G		not specified	Uncertain significance (Jan 08, 2024)
15-43535321-C-T		not specified	Uncertain significance (Jan 26, 2022)
15-43535426-T-C		not specified	Uncertain significance (Jun 14, 2024)
15-43539526-C-T		not specified	Uncertain significance (Feb 07, 2023)
15-43539529-G-A		not specified	Uncertain significance (Aug 02, 2021)
15-43558827-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-43558843-T-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ppip5k1

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