ITPKA

inositol-trisphosphate 3-kinase A

Basic information

Region (hg38): 15:41493393-41503551

Links

ENSG00000137825 ∙ NCBI:3706 ∙ OMIM:147521 ∙ HGNC:6178 ∙ Uniprot:P23677 ∙ 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 ITPKA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITPKA 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	1
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	1

Variants in ITPKA

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

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

Position	Type	Phenotype	Significance	ClinVar
15-41493946-C-T		not specified	Uncertain significance (Nov 11, 2024)
15-41493956-T-G		not specified	Uncertain significance (Nov 16, 2021)
15-41493971-G-A		not specified	Uncertain significance (May 03, 2023)
15-41493975-G-C			Benign (Dec 18, 2017)
15-41494013-G-C		not specified	Uncertain significance (Mar 20, 2023)
15-41494021-G-C		not specified	Uncertain significance (Jan 10, 2022)
15-41494072-G-A		not specified	Uncertain significance (Jan 18, 2025)
15-41494108-C-G		not specified	Uncertain significance (Aug 10, 2021)
15-41494108-C-T		not specified	Uncertain significance (May 23, 2023)
15-41494141-C-T		not specified	Uncertain significance (Feb 22, 2025)
15-41494262-C-T		not specified	Uncertain significance (Feb 24, 2025)
15-41494283-G-T		not specified	Uncertain significance (Dec 28, 2022)
15-41494307-C-A		not specified	Uncertain significance (Apr 25, 2023)
15-41494357-G-A		not specified	Uncertain significance (Nov 09, 2024)
15-41494372-A-G		not specified	Uncertain significance (Apr 23, 2024)
15-41494376-G-A		not specified	Uncertain significance (Mar 29, 2023)
15-41494391-T-G		not specified	Uncertain significance (Oct 16, 2023)
15-41494397-C-A		not specified	Uncertain significance (Aug 23, 2021)
15-41501480-G-C		not specified	Uncertain significance (Sep 16, 2021)
15-41501530-A-G		not specified	Uncertain significance (Feb 23, 2023)
15-41501661-G-C		not specified	Uncertain significance (Oct 17, 2023)
15-41501682-T-G		not specified	Uncertain significance (Feb 19, 2025)
15-41502055-A-T		not specified	Uncertain significance (May 08, 2023)
15-41502095-C-T		not specified	Uncertain significance (Dec 11, 2024)
15-41502119-C-A		not specified	Uncertain significance (May 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITPKA	protein_coding	protein_coding	ENST00000260386	7	10157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.649	0.351	125649	0	4	125653	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	155	221	0.703	0.0000102	2919
Missense in Polyphen		42	91.283	0.46011		1066
Synonymous	0.673	89	97.5	0.913	0.00000465	987
Loss of Function	3.07	3	16.4	0.183	7.99e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000941	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
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);Inositol Phosphate Metabolism;Inositol Metabolism;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: 0.127

Haploinsufficiency Scores

• pHI: 0.214
• hipred: Y
• hipred_score: 0.809
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.764

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itpka
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: inositol metabolic process;protein phosphorylation;signal transduction;actin cytoskeleton organization;inositol phosphate biosynthetic process;inositol phosphate metabolic process;regulation of synaptic plasticity;positive regulation of dendritic spine morphogenesis;dendritic spine maintenance
• Cellular component: cytosol;dendritic spine
• Molecular function: calmodulin-dependent protein kinase activity;calmodulin binding;ATP binding;inositol-1,4,5-trisphosphate 3-kinase activity;Rac GTPase binding