ITPKC

inositol-trisphosphate 3-kinase C

Basic information

Region (hg38): 19:40717112-40740860

Links

ENSG00000086544 ∙ NCBI:80271 ∙ OMIM:606476 ∙ HGNC:14897 ∙ Uniprot:Q96DU7 ∙ 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 ITPKC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITPKC 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				3		3
missense			52	3		55
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				2	1	3
Total	0	0	53	8	1

Variants in ITPKC

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

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

Position	Type	Phenotype	Significance	ClinVar
19-40717208-G-A		not specified	Uncertain significance (Sep 23, 2023)
19-40717264-G-T		ITPKC-related disorder	Likely benign (Apr 16, 2020)
19-40717277-G-T		not specified	Uncertain significance (Aug 17, 2022)
19-40717287-G-A		not specified	Uncertain significance (Jun 17, 2024)
19-40717296-A-C		not specified	Uncertain significance (Dec 16, 2022)
19-40717376-G-T		not specified	Uncertain significance (Aug 30, 2022)
19-40717411-C-G		not specified	Uncertain significance (Aug 16, 2022)
19-40717486-G-C		not specified	Uncertain significance (Jul 14, 2021)
19-40717494-T-G		not specified	Uncertain significance (Oct 13, 2023)
19-40717562-G-A		ITPKC-related disorder	Likely benign (Feb 26, 2020)
19-40717581-C-A		not specified	Uncertain significance (Sep 01, 2021)
19-40717592-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-40717644-A-G		not specified	Uncertain significance (Dec 19, 2023)
19-40717645-TGG-T		ITPKC-related disorder	Uncertain significance (Apr 12, 2023)
19-40717650-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-40717671-A-G		not specified	Uncertain significance (Jul 20, 2022)
19-40717688-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-40717740-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-40717767-C-A		not specified	Uncertain significance (Jun 10, 2024)
19-40717829-A-G		not specified	Uncertain significance (Oct 02, 2023)
19-40717864-G-T		not specified	Uncertain significance (Dec 18, 2023)
19-40717872-C-G		not specified	Uncertain significance (Nov 17, 2023)
19-40717890-A-C		not specified	Uncertain significance (Mar 11, 2022)
19-40717892-C-A		not specified	Uncertain significance (Jun 06, 2023)
19-40717893-A-G		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITPKC	protein_coding	protein_coding	ENST00000263370	7	23758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.152	0.848	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.532	343	372	0.922	0.0000203	4418
Missense in Polyphen		80	125.35	0.63823		1468
Synonymous	0.768	139	151	0.921	0.00000856	1390
Loss of Function	3.66	7	27.8	0.252	0.00000137	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000667	0.0000653
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can phosphorylate inositol 2,4,5-triphosphate to inositol 2,4,5,6-tetraphosphate. {ECO:0000250}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Integrated Breast Cancer Pathway;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);Metabolism;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• loftool: 0.176
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.520
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.648

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itpkc
• Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: phosphorylation;inositol phosphate biosynthetic process;inositol phosphate metabolic process
• Cellular component: cytosol;nuclear speck
• Molecular function: calmodulin binding;ATP binding;inositol-1,4,5-trisphosphate 3-kinase activity