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.

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.

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				1		1
missense			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	39	1	0

Variants in PI4KB

This is a list of pathogenic ClinVar variants found in the PI4KB region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151292863-C-T		not specified	Uncertain significance (May 27, 2022)
1-151292911-G-A		not specified	Uncertain significance (May 08, 2023)
1-151292964-A-T		PI4KB-related disorder • not specified	Uncertain significance (May 17, 2023)
1-151292971-T-C		not specified	Uncertain significance (Dec 05, 2024)
1-151293000-G-A		not specified	Uncertain significance (Mar 12, 2024)
1-151293003-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-151294026-A-C		Hearing loss, autosomal dominant 87	Pathogenic (Mar 13, 2023)
1-151294128-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-151294513-C-T		Hearing loss, autosomal dominant 87	Pathogenic (Mar 13, 2023)
1-151298938-A-T		not specified	Uncertain significance (Sep 26, 2022)
1-151299009-G-C		not specified	Uncertain significance (Nov 09, 2023)
1-151299013-A-C		not specified	Uncertain significance (Feb 06, 2024)
1-151299022-G-C		not specified	Uncertain significance (Oct 27, 2021)
1-151299052-C-T		not specified	Uncertain significance (Aug 19, 2021)
1-151299054-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-151301885-G-A		not specified	Uncertain significance (May 23, 2023)
1-151302265-C-T			Likely benign (Jun 01, 2025)
1-151303637-T-C		not specified	Uncertain significance (Dec 19, 2023)
1-151303644-C-T		not specified	Uncertain significance (Sep 14, 2021)
1-151306191-T-C		not specified	Uncertain significance (Dec 18, 2023)
1-151306200-A-C		Hearing loss, autosomal dominant 87	Pathogenic (Mar 13, 2023)
1-151306236-A-G		not specified	Uncertain significance (Apr 25, 2023)
1-151306246-C-T		not specified	Uncertain significance (Jan 05, 2022)
1-151306281-C-T		not specified	Uncertain significance (Dec 05, 2024)
1-151306294-T-C		not specified	Uncertain significance (Nov 07, 2023)

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

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