PI4K2B

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

Basic information

Region (hg38): 4:25160662-25279204

Links

ENSG00000038210 ∙ NCBI:55300 ∙ OMIM:612101 ∙ HGNC:18215 ∙ Uniprot:Q8TCG2 ∙ 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 PI4K2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PI4K2B 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	22	2	0

Variants in PI4K2B

This is a list of pathogenic ClinVar variants found in the PI4K2B region.

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

Position	Type	Phenotype	Significance	ClinVar
4-25160758-G-T			Benign (Jun 28, 2018)
4-25234173-C-A		Abnormality of neuronal migration	Benign (Oct 31, 2014)
4-25234183-C-G		not specified	Uncertain significance (May 17, 2023)
4-25234212-A-T		not specified	Uncertain significance (Mar 07, 2023)
4-25234278-C-G		not specified	Uncertain significance (Sep 17, 2021)
4-25234287-G-T		not specified	Uncertain significance (Oct 22, 2021)
4-25234346-C-G		not specified	Uncertain significance (Aug 02, 2023)
4-25234351-A-C		not specified	Uncertain significance (Jun 12, 2023)
4-25234351-A-G		not specified	Uncertain significance (Aug 17, 2021)
4-25234384-C-T		not specified	Uncertain significance (Sep 15, 2021)
4-25234409-C-G		not specified	Uncertain significance (Sep 27, 2021)
4-25234426-T-C		not specified	Uncertain significance (Aug 02, 2023)
4-25252407-G-A		not specified	Uncertain significance (Jul 12, 2022)
4-25252465-A-T		not specified	Uncertain significance (Mar 29, 2022)
4-25255065-A-G		not specified	Uncertain significance (Mar 16, 2024)
4-25255069-T-C		not specified	Uncertain significance (May 27, 2022)
4-25255086-C-A		not specified	Uncertain significance (Jul 12, 2023)
4-25255248-A-G		not specified	Uncertain significance (Sep 01, 2021)
4-25256574-A-G		not specified	Uncertain significance (Mar 01, 2023)
4-25259085-T-C		not specified	Uncertain significance (Dec 19, 2023)
4-25259087-G-C		Autism	Uncertain significance (Dec 21, 2023)
4-25259141-G-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
4-25260568-T-C		not specified	Uncertain significance (Dec 27, 2023)
4-25260572-A-G		not specified	Likely benign (May 15, 2024)
4-25260610-TTATATATATA-T			Likely benign (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PI4K2B	protein_coding	protein_coding	ENST00000264864	10	118452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-7	0.897	125706	1	41	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	172	224	0.767	0.0000107	3135
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000491	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000491	0.000489
South Asian	0.000403	0.000359
Other	0.000169	0.000163

dbNSFP

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}.
• 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;Synthesis of PIPs at the ER membrane;Synthesis of PIPs at the Golgi membrane;Synthesis of PIPs at the early endosome membrane;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.653
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.146
• hipred: Y
• hipred_score: 0.790
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.626

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pi4k2b

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;Golgi organization;endosome organization;phosphatidylinositol phosphorylation
• Cellular component: endosome;trans-Golgi network;cytosol;plasma membrane;membrane
• Molecular function: 1-phosphatidylinositol 4-kinase activity;ATP binding