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

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

ClinVar

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

not_specified (111 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	3 clinvar	4
missense			101 clinvar	12 clinvar	2 clinvar	115
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	101	13	5

Loading clinvar variants...

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
1.00	0.0000572	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-myo-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism;1D-myo-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

Haploinsufficiency Scores

pHI: 0.104
hipred: Y
hipred_score: 0.546
ghis: 0.492

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
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

Mouse Genome Informatics

Gene name: Itpkb
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

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