PI4KB

phosphatidylinositol 4-kinase beta

Basic information

Region (hg38): 1:151291797-151327715

Previous symbols: [ "PIK4CB" ]

Links

ENSG00000143393

∙ NCBI:5298 ∙ OMIM:602758 ∙ HGNC:8984 ∙ Uniprot:Q9UBF8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

hearing loss, autosomal dominant 87 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 87	AD	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	33358777

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PI4KB gene.

not_specified (52 variants)
not_provided (5 variants)
Hearing_loss,_autosomal_dominant_87 (4 variants)
PI4KB-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PI4KB gene is commonly pathogenic or not. These statistics are base on transcript: NM_001369623.2. 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				3 clinvar		3
missense	4 clinvar		52 clinvar			56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	4	0	52	3	0

Highest pathogenic variant AF is 0.0000020522812

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PI4KB	protein_coding	protein_coding	ENST00000368875	12	35919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.866	0.134	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.55	268	489	0.548	0.0000288	5420
Missense in Polyphen		67	201.73	0.33212		2218
Synonymous	0.470	188	196	0.957	0.0000115	1673
Loss of Function	4.85	8	41.8	0.191	0.00000280	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000343	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Phosphorylates phosphatidylinositol (PI) in the first committed step in the production of the second messenger inositol- 1,4,5,-trisphosphate (PIP). May regulate Golgi disintegration/reorganization during mitosis, possibly via its phosphorylation. Involved in Golgi-to-plasma membrane trafficking (By similarity). {ECO:0000250, ECO:0000269|PubMed:10559940, ECO:0000269|PubMed:12749687, ECO:0000269|PubMed:9405935}.;
Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Metabolism of lipids;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;Synthesis of PIPs at the Golgi membrane;PI Metabolism;Phospholipid metabolism;Integrins in angiogenesis (Consensus)

Recessive Scores

pRec: 0.153

Intolerance Scores

loftool: 0.212
rvis_EVS: -0.82
rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

pHI: 0.554
hipred: Y
hipred_score: 0.728
ghis: 0.648

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pi4kb
Phenotype

Zebrafish Information Network

Gene name: pi4kb
Affected structure: post-vent region
Phenotype tag: abnormal
Phenotype quality: increased curvature

Gene ontology

Biological process: phosphatidylinositol biosynthetic process;receptor-mediated endocytosis;signal transduction;phosphatidylinositol phosphorylation;phosphatidylinositol-mediated signaling
Cellular component: Golgi membrane;cytoplasm;mitochondrial outer membrane;endosome;cytosol;membrane;rough endoplasmic reticulum membrane;perinuclear region of cytoplasm
Molecular function: 1-phosphatidylinositol 4-kinase activity;protein binding;ATP binding;14-3-3 protein binding