PI4K2B

protein-coding

phosphatidylinositol 4-kinase type 2 beta, the group of Minor histocompatibility antigens

Gene summary

This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]

MANE transcript

NM_018323.4

Inheritance

—

ClinVar variants

U:59B:5

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr4:25,160,663-25,279,204

External References & Databases

Ensembl (ENSG00000038210)

Transcript & Mutation Effects

hg38 • Region Span ~118.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PI4K2B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 56

Abnormality of neuronal migrationTotal: 2

not providedTotal: 1

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018323.4. 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			1 clinvar			1
missense			55 clinvar	3 clinvar	2 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	59	3	2	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018323.4	RefSeq	NP_060793.2	10	MANE Select
ENST00000264864.8	Ensembl	ENSP00000264864.6	10	MANE Select
ENST00000512921.4	Ensembl	ENSP00000423373.1	9	Standard
ENST00000512921.5	Ensembl	ENSP00000423373.1	9	Standard

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
Golgi organization
endosome organization
phosphatidylinositol phosphorylation

Molecular Function

1-phosphatidylinositol 4-kinase activity
ATP binding

Cellular Component

endosome
trans-Golgi network
cytosol
plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264864
Coding exons: 10
Length: 118452
Individuals with no LoFs: 125706
Homozygous LoFs: 1
Heterozygous LoFs: 41
Defined: 125748
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.24	172	224	0.767	0.0000107	3135
Missense (PolyPhen)		54	71.074	0.75977		941
Synonymous	1.14	66	78.9	0.837	0.00000395	877
Loss of Function	1.67	14	22.6	0.620	0.00000104	303

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00040	0.00036	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Together with PI4K2A and the type III PI4Ks (PIK4CA and PIK4CB) it contributes to the overall PI4-kinase activity of the cell. This contribution may be especially significant in plasma membrane, endosomal and Golgi compartments. The phosphorylation of phosphatidylinositol (PI) to PI4P is the first committed step in the generation of phosphatidylinositol 4,5-bisphosphate (PIP2), a precursor of the second messenger inositol 1,4,5-trisphosphate (InsP3). Contributes to the production of InsP3 in stimulated cells and is likely to be involved in the regulation of vesicular trafficking. {ECO:0000269|PubMed:11923287}.;

Intolerance Scores

LoFtool: 0.653
RVIS EVS: -0.54
RVIS percentile EVS: 20.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.626

Gene Damage Prediction

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