PI4KB

protein-coding

phosphatidylinositol 4-kinase beta

Gene summary

Enables 1-phosphatidylinositol 4-kinase activity and 14-3-3 protein binding activity. Involved in inner ear development and phosphatidylinositol phosphate biosynthetic process. Acts upstream of or within lysosome organization. Located in Golgi membrane. Is active in cytoplasmic side of trans-Golgi network membrane. Implicated in autosomal dominant nonsyndromic deafness 87. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PIK4CB

MANE transcript

NM_001369623.2

Inheritance

ClinVar variants

P:4U:81B:12

Top phenotype

Deafness, autosomal dominant 87

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr1:151,291,797-151,327,715

External References & Databases

Ensembl (ENSG00000143393)

Transcript & Mutation Effects

hg38 • Region Span ~35.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hearing loss, autosomal dominant 87LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0859525

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Deafness, autosomal dominant 87AD

Manifestation: Audiologic/Otolaryngologic

Intervention: Audiologic/Otolaryngologic

Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development

Refs: 33358777

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PI4KB variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 62

PI4KB-related disorderTotal: 19

not providedTotal: 7

Hearing loss, autosomal dominant 87Total: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001369623.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	9 clinvar		12
missense	4 clinvar		72 clinvar	1 clinvar	1 clinvar	78
nonsense			4 clinvar	1 clinvar		5
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	4	0	81	11	1	97

Highest pathogenic variant AF is 0.0000020522812

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 105 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001369623.2	RefSeq	NP_001356552.1	11	MANE Select
ENST00000368873.6	Ensembl	ENSP00000357867.1	11	MANE Select
NM_001198773.3	RefSeq	NP_001185702.1	10	Standard
NM_001198774.2	RefSeq	NP_001185703.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
pi4kb	Danio rerio	Structure: post-vent region Quality: increased curvature abnormal

Gene / Model

Organism

Observed Phenotype

pi4kb

Danio rerio

Structure: post-vent region

Quality: increased curvature

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

phosphatidylinositol biosynthetic process
receptor-mediated endocytosis
signal transduction
phosphatidylinositol phosphorylation
phosphatidylinositol-mediated signaling

Molecular Function

1-phosphatidylinositol 4-kinase activity
protein binding
ATP binding
14-3-3 protein binding

Cellular Component

Golgi membrane
cytoplasm
mitochondrial outer membrane
endosome
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368875
Coding exons: 12
Length: 35919
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.55	268	489	0.548	0.0000288	5420
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.000065	0.000065	rare
Other	0.00034	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.153

Intolerance Scores

LoFtool: 0.212
RVIS EVS: -0.82
RVIS percentile EVS: 11.77

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.982

Gene Damage Prediction

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