ITPKB

inositol-trisphosphate 3-kinase B

Basic information

Region (hg38): 1:226631690-226739323

Links

ENSG00000143772 ∙ NCBI:3707 ∙ OMIM:147522 ∙ HGNC:6179 ∙ Uniprot:P27987 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ITPKB deficiency (Limited), mode of inheritance: AR
• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

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

• not_specified (125 variants)
• not_provided (7 variants)
• ITPKB-related_disorder (4 variants)
• Myeloproliferative_neoplasm,_unclassifiable (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITPKB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002221.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	3	2	8
missense			113	14	1	128
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	118	17	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITPKB	protein_coding	protein_coding	ENST00000429204	7	107634

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.636	546	589	0.926	0.0000348	6103
Missense in Polyphen		108	187.79	0.57511		2008
Synonymous	-1.02	271	250	1.08	0.0000156	1980
Loss of Function	5.08	1	32.1	0.0312	0.00000149	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000185	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);D-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;Metabolism;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.123
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.97

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: MAPK cascade;regulation of protein phosphorylation;myeloid cell homeostasis;signal transduction;cell surface receptor signaling pathway;inositol trisphosphate metabolic process;inositol phosphate biosynthetic process;negative regulation of neutrophil apoptotic process;common myeloid progenitor cell proliferation;inositol phosphate metabolic process;positive thymic T cell selection;negative regulation of myeloid cell differentiation;positive regulation of Ras protein signal transduction;positive regulation of alpha-beta T cell differentiation;cellular response to calcium ion
• Cellular component: nucleus;cytosol;membrane
• Molecular function: protein binding;calmodulin binding;ATP binding;inositol-1,4,5-trisphosphate 3-kinase activity