PIP5K1B

phosphatidylinositol-4-phosphate 5-kinase type 1 beta

Basic information

Region (hg38): 9:68705239-69009176

Links

ENSG00000107242 ∙ NCBI:8395 ∙ OMIM:602745 ∙ HGNC:8995 ∙ Uniprot:O14986 ∙ 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 PIP5K1B gene.

• Inborn genetic diseases (20 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.

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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4		1	5
Total	0	0	20	0	1

Variants in PIP5K1B

This is a list of pathogenic ClinVar variants found in the PIP5K1B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-68780097-C-G			Benign (Jun 20, 2018)
9-68780196-A-G		not specified	Uncertain significance (Mar 21, 2023)
9-68780211-C-T		not specified	Uncertain significance (Jan 04, 2024)
9-68780349-G-A		not specified	Uncertain significance (Mar 11, 2024)
9-68780360-C-T		not specified	Uncertain significance (Jul 05, 2023)
9-68780535-G-C		not specified	Uncertain significance (Jul 09, 2021)
9-68780541-A-G		not specified	Uncertain significance (Nov 22, 2023)
9-68780561-T-A		not specified	Uncertain significance (Apr 07, 2022)
9-68780562-C-G		not specified	Uncertain significance (Jun 06, 2023)
9-68780870-G-T		not specified	Uncertain significance (Feb 09, 2023)
9-68780882-T-C		not specified	Uncertain significance (Mar 07, 2024)
9-68780909-A-C		not specified	Uncertain significance (Dec 17, 2023)
9-68822643-C-A		not specified	Uncertain significance (Jan 22, 2024)
9-68876678-G-A		not specified	Uncertain significance (Jun 30, 2022)
9-68888996-G-C		not specified	Uncertain significance (Jun 14, 2022)
9-68889048-T-C		not specified	Uncertain significance (Oct 14, 2023)
9-68889077-A-G		not specified	Uncertain significance (Oct 12, 2022)
9-68917631-G-A			Likely benign (Mar 01, 2024)
9-68917668-G-T		not specified	Uncertain significance (Jan 31, 2023)
9-68917672-T-C		not specified	Uncertain significance (Feb 17, 2024)
9-68919513-G-A		not specified	Uncertain significance (Nov 09, 2023)
9-68919520-T-A		not specified	Uncertain significance (Dec 05, 2022)
9-68923342-G-C		not specified	Uncertain significance (Jul 26, 2022)
9-68923375-A-G		not specified	Uncertain significance (Dec 20, 2023)
9-68934916-C-T		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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