ITPKB

inositol-trisphosphate 3-kinase B

Basic information

Region (hg38): 1:226631689-226739323

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.

• Inborn genetic diseases (41 variants)
• not specified (9 variants)
• Myeloproliferative neoplasm, unclassifiable (6 variants)
• not provided (6 variants)
• ITPKB-related condition (1 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.

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	4	5
missense			36	8	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel		1				1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	1	36	9	8

Highest pathogenic variant AF is 0.277

Variants in ITPKB

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

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

Position	Type	Phenotype	Significance	ClinVar
1-226634679-G-C		ITPKB-related disorder	Likely benign (Feb 01, 2022)
1-226634772-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-226634796-C-G		not specified	Uncertain significance (Nov 17, 2022)
1-226634824-G-A			Likely benign (Jul 01, 2022)
1-226634872-G-C			Benign (Aug 20, 2018)
1-226637640-G-A		not specified	Benign (Jan 24, 2024)
1-226637717-T-C		not specified	Likely benign (Mar 01, 2024)
1-226642049-C-T		not specified	Uncertain significance (Dec 05, 2022)
1-226642103-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-226647287-C-T		not specified	Likely benign (Jul 26, 2021)
1-226648675-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-226735552-G-A		not specified	Uncertain significance (Jun 11, 2021)
1-226735553-T-C		not specified	Uncertain significance (Apr 10, 2023)
1-226735563-G-A		not specified	Benign (Jan 24, 2024)
1-226735627-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-226735642-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-226735660-G-A		not specified	Uncertain significance (Oct 02, 2023)
1-226735683-G-A			Benign (Jun 15, 2018)
1-226735684-T-C		not specified	Likely benign (Aug 17, 2021)
1-226735691-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-226735695-G-A		not specified	Benign (Jan 24, 2024)
1-226735756-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-226735804-G-T		Myeloproliferative neoplasm, unclassifiable • not specified	Conflicting classifications of pathogenicity (Jan 24, 2024)
1-226735813-G-C		not specified	Uncertain significance (Aug 08, 2023)
1-226735825-G-A		not specified	Uncertain significance (Dec 06, 2022)

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-<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

Haploinsufficiency Scores

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

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

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