PIK3C2G

phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma, the group of Phosphatidylinositol 3-kinase subunits

Basic information

Region (hg38): 12:18242960-18648416

Links

ENSG00000139144 ∙ NCBI:5288 ∙ OMIM:609001 ∙ HGNC:8973 ∙ Uniprot:O75747 ∙ 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 PIK3C2G gene.

• Inborn genetic diseases (40 variants)
• not provided (8 variants)
• Premature coronary artery atherosclerosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3C2G 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			41	1	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)			1	1		2
splice region				1		1
non coding						0
Total	0	0	42	3	2

Variants in PIK3C2G

This is a list of pathogenic ClinVar variants found in the PIK3C2G region.

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

Position	Type	Phenotype	Significance	ClinVar
12-18282091-T-C		not specified	Uncertain significance (Aug 13, 2021)
12-18282103-G-T		not specified	Uncertain significance (Feb 28, 2023)
12-18282286-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-18282314-T-C		not specified	Uncertain significance (Mar 16, 2022)
12-18282344-A-G		not specified	Uncertain significance (Jun 28, 2023)
12-18282394-C-A		not specified	Uncertain significance (May 24, 2023)
12-18282464-GCCC-G			Benign (Aug 16, 2019)
12-18282518-C-T			Benign (Aug 16, 2019)
12-18282520-T-C		not specified	Uncertain significance (Oct 20, 2021)
12-18282536-A-G		not specified	Uncertain significance (Oct 25, 2023)
12-18282538-A-G		not specified	Uncertain significance (Dec 01, 2022)
12-18282565-A-C		not specified	Uncertain significance (Jun 01, 2023)
12-18286931-T-C		Tracheoesophageal fistula	Likely pathogenic (Jul 01, 2019)
12-18290961-A-G		not specified	Uncertain significance (Apr 25, 2022)
12-18293984-A-C		not specified	Uncertain significance (Oct 14, 2023)
12-18294012-A-G		not specified	Uncertain significance (Aug 28, 2023)
12-18313998-A-C		not specified	Uncertain significance (Dec 01, 2022)
12-18314004-A-T			Uncertain significance (-)
12-18321001-C-A		not specified	Uncertain significance (Nov 10, 2021)
12-18338432-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-18343327-A-G		not specified	Uncertain significance (Dec 17, 2023)
12-18346659-C-T		not specified	Uncertain significance (Dec 16, 2022)
12-18346716-A-G		not specified	Uncertain significance (Nov 28, 2023)
12-18381779-G-C		not specified	Uncertain significance (Dec 21, 2022)
12-18381829-G-C		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIK3C2G	protein_coding	protein_coding	ENST00000433979	31	400801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.50e-40	0.0000174	123648	2	1005	124655	0.00405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.973	757	685	1.10	0.0000331	9542
Missense in Polyphen		241	209.35	1.1512		3058
Synonymous	-0.177	248	244	1.01	0.0000125	2566
Loss of Function	0.605	63	68.4	0.921	0.00000315	937

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00677	0.00654
Ashkenazi Jewish	0.000108	0.0000993
East Asian	0.00918	0.00917
Finnish	0.00317	0.00288
European (Non-Finnish)	0.00517	0.00450
Middle Eastern	0.00918	0.00917
South Asian	0.00396	0.00354
Other	0.00423	0.00381

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Generates phosphatidylinositol 3-phosphate (PtdIns3P) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) that act as second messengers. May play a role in SDF1A-stimulated chemotaxis (By similarity). {ECO:0000250}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Signaling Pathways in Glioblastoma;Angiopoietin Like Protein 8 Regulatory Pathway;Insulin Signaling;Regulation of Actin Cytoskeleton;DNA Damage Response (only ATM dependent);cxcr4 signaling pathway;phospholipids as signalling intermediaries;ccr3 signaling in eosinophils;Metabolism of lipids;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;fmlp induced chemokine gene expression in hmc-1 cells;Synthesis of PIPs at the Golgi membrane;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.199

Intolerance Scores

• loftool: 0.704
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.79

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.323
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.653

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pik3c2g
• Phenotype: liver/biliary system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: chemotaxis;phosphatidylinositol 3-kinase signaling;cell migration;phosphatidylinositol-3-phosphate biosynthetic process;viral RNA genome replication;phosphatidylinositol phosphorylation;phosphatidylinositol-mediated signaling
• Cellular component: cytoplasm;cytosol;plasma membrane;phosphatidylinositol 3-kinase complex;membrane
• Molecular function: ATP binding;1-phosphatidylinositol-3-kinase activity;phosphatidylinositol phosphate kinase activity;1-phosphatidylinositol-4-phosphate 3-kinase activity;phosphatidylinositol binding