PIP4K2B

phosphatidylinositol-5-phosphate 4-kinase type 2 beta

Basic information

Region (hg38): 17:38765691-38800126

Previous symbols: [ "PIP5K2B" ]

Links

ENSG00000276293 ∙ NCBI:8396 ∙ OMIM:603261 ∙ HGNC:8998 ∙ Uniprot:P78356 ∙ 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 PIP4K2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIP4K2B 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in PIP4K2B

This is a list of pathogenic ClinVar variants found in the PIP4K2B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-38769728-T-C		not specified	Uncertain significance (Dec 16, 2022)
17-38771053-C-T		not specified	Uncertain significance (Nov 25, 2024)
17-38771124-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-38771140-C-T		not specified	Uncertain significance (Jun 26, 2024)
17-38771152-C-G		not specified	Uncertain significance (Jun 12, 2023)
17-38771221-C-T		not specified	Uncertain significance (Mar 26, 2024)
17-38771270-G-C		not specified	Uncertain significance (Apr 15, 2024)
17-38777691-A-G		not specified	Uncertain significance (Aug 28, 2023)
17-38777729-C-G		not specified	Uncertain significance (Dec 21, 2023)
17-38777734-C-G		not specified	Uncertain significance (Jul 15, 2021)
17-38777744-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
17-38778345-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-38779408-G-A		not specified	Uncertain significance (May 03, 2023)
17-38780496-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-38780525-C-T		not specified	Uncertain significance (May 23, 2024)
17-38780531-T-G		not specified	Uncertain significance (Oct 12, 2021)
17-38786840-G-T		not specified	Uncertain significance (Nov 30, 2022)
17-38786845-C-G		not specified	Uncertain significance (Sep 16, 2021)
17-38799271-G-T		not specified	Uncertain significance (Oct 01, 2024)
17-38799293-G-C		not specified	Uncertain significance (Aug 14, 2024)
17-38799337-A-G		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate. {ECO:0000269|PubMed:9038203}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Regulation of Actin Cytoskeleton;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Signal Transduction;Gene expression (Transcription);Synthesis of PIPs in the nucleus;Generic Transcription Pathway;Metabolism of lipids;Inositol phosphate metabolism;RNA Polymerase II Transcription;PI5P Regulates TP53 Acetylation;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;BCR;Phosphatidylinositol phosphate metabolism;PIP3 activates AKT signaling;Synthesis of PIPs at the plasma membrane;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;PI Metabolism;Phospholipid metabolism;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pip4k2b
• Phenotype: skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; embryo phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidylinositol biosynthetic process;cell surface receptor signaling pathway;regulation of autophagy;regulation of phosphatidylinositol 3-kinase signaling;phosphatidylinositol phosphorylation;positive regulation of autophagosome assembly
• Cellular component: nucleoplasm;autophagosome;endoplasmic reticulum membrane;cytosol;plasma membrane
• Molecular function: protein binding;ATP binding;1-phosphatidylinositol-4-phosphate 5-kinase activity;1-phosphatidylinositol-5-phosphate 4-kinase activity;protein homodimerization activity;1-phosphatidylinositol-3-phosphate 4-kinase activity