PIP4K2C

phosphatidylinositol-5-phosphate 4-kinase type 2 gamma

Basic information

Region (hg38): 12:57591174-57603418

Previous symbols: [ "PIP5K2C" ]

Links

ENSG00000166908 ∙ NCBI:79837 ∙ OMIM:617104 ∙ HGNC:23786 ∙ Uniprot:Q8TBX8 ∙ 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 PIP4K2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIP4K2C 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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PIP4K2C

This is a list of pathogenic ClinVar variants found in the PIP4K2C region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57591300-C-T		not specified	Uncertain significance (Dec 13, 2023)
12-57591350-G-T		not specified	Uncertain significance (Mar 15, 2024)
12-57591402-T-A		not specified	Uncertain significance (Nov 25, 2024)
12-57594025-A-G		not specified	Uncertain significance (Feb 13, 2025)
12-57594037-A-G		not specified	Uncertain significance (Mar 19, 2024)
12-57594049-C-T		not specified	Uncertain significance (Oct 06, 2024)
12-57594074-A-G		not specified	Uncertain significance (Jun 22, 2021)
12-57594106-A-C		not specified	Uncertain significance (Nov 13, 2024)
12-57595177-C-A		not specified	Uncertain significance (Dec 16, 2023)
12-57595937-G-A		not specified	Uncertain significance (Oct 25, 2024)
12-57595969-A-G		not specified	Uncertain significance (Mar 19, 2024)
12-57596014-C-G		not specified	Uncertain significance (Nov 08, 2024)
12-57599179-C-T		not specified	Uncertain significance (Sep 17, 2021)
12-57599427-G-A		not specified	Uncertain significance (Aug 01, 2024)
12-57600847-C-A		not specified	Uncertain significance (Jun 29, 2022)
12-57600862-G-A		not specified	Uncertain significance (Mar 12, 2024)
12-57600905-G-A		not specified	Uncertain significance (Jan 18, 2025)
12-57600928-G-A		not specified	Uncertain significance (Feb 28, 2025)
12-57600929-G-C		not specified	Uncertain significance (Dec 02, 2022)
12-57601058-A-C		not specified	Uncertain significance (Mar 02, 2023)
12-57601058-A-G		not specified	Uncertain significance (Aug 10, 2024)
12-57601554-C-T		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIP4K2C	protein_coding	protein_coding	ENST00000354947	10	12242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00183	0.994	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	185	251	0.738	0.0000136	2789
Missense in Polyphen		61	100.44	0.60731		1200
Synonymous	0.359	93	97.5	0.954	0.00000526	812
Loss of Function	2.49	8	20.0	0.400	0.00000108	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000546	0.0000544
South Asian	0.000132	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in the production of Phosphatidylinositol bisphosphate (PIP2), in the endoplasmic reticulum. {ECO:0000250}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Regulation of Actin Cytoskeleton;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Signal Transduction;Gene expression (Transcription);Synthesis of PIPs in the nucleus;Generic Transcription Pathway;Metabolism of lipids;Inositol phosphate metabolism;RNA Polymerase II Transcription;PI5P Regulates TP53 Acetylation;Metabolism;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds;BCR;Phosphatidylinositol phosphate metabolism;PIP3 activates AKT signaling;Synthesis of PIPs at the plasma membrane;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;PI Metabolism;Phospholipid metabolism;Intracellular signaling by second messengers (Consensus)

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.694
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pip4k2c
• Phenotype: digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; liver/biliary system phenotype; respiratory system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;regulation of autophagy;regulation of phosphatidylinositol 3-kinase signaling;phosphatidylinositol phosphorylation;positive regulation of autophagosome assembly
• Cellular component: autophagosome;cytosol;membrane;extracellular exosome
• Molecular function: ATP binding;1-phosphatidylinositol-5-phosphate 4-kinase activity;identical protein binding