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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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PIP5K1C
phosphatidylinositol-4-phosphate 5-kinase type 1 gamma
Chromosome 19 Β· 19p13.3
NCBI Gene: 23396Ensembl: ENSG00000186111.12HGNC: HGNC:8996UniProt: O60331
89PubMed Papers
21Diseases
0Drugs
7Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneKinase
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingnucleoplasmcytosolendosome membranelethal congenital contracture syndrome 3Lethal congenital contracture syndrome type 3Neurodevelopmental disordergenetic disorder
✦AI Summary

PIP5K1C (phosphatidylinositol-4-phosphate 5-kinase type 1 gamma) is a lipid kinase that catalyzes phosphorylation of phosphatidylinositol 4-phosphate (PI4P) to generate phosphatidylinositol 4,5-bisphosphate (PIP2), a critical second messenger regulating signal transduction, vesicle trafficking, cytoskeleton dynamics, and cell adhesion 12. PIP5K1C controls the plasma membrane pool of PIP2 essential for synaptic vesicle endocytosis and exocytosis 3, clathrin-coated pit assembly 4, and focal adhesion dynamics by modulating talin targeting to the plasma membrane 1. The enzyme mediates Arf6-driven exocyst recruitment and membrane tethering through rapid PIP2 synthesis 5. PIP5K1C loss in osteocytes impairs bone remodeling through reduced collagen expression and increased sclerostin, with decreased focal adhesion proteins and elevated apoptosis 6. In chondrocytes, PIP5K1C deletion causes age-related osteoarthritis-like lesions with cartilage degradation and impaired chondrocyte adhesion 7. Clinically, PIP5K1C deficiency in cancer cells increases dependence on PIKFYVE, making them sensitive to PIKFYVE inhibitors through disrupted lysosome homeostasis and autophagy 89. Additionally, dual PIP5K1C/PIKfyve inhibition prevents SARS-CoV-2 entry by blocking ACE2-mediated endocytosis and cathepsin L activation 10. PIP5K1C mutations are associated with lethal congenital contracture syndrome 3.

Sources cited
1
PIP5K1C controls the plasma membrane pool of PIP2 essential for synaptic vesicle endocytosis and exocytosis , clathrin-coated pit assembly , and focal adhesion dynamics by modulating talin targeting to the plasma membrane .
PMID: 12847086
2
PIP5K1C controls the plasma membrane pool of PIP2 essential for synaptic vesicle endocytosis and exocytosis , clathrin-coated pit assembly , and focal adhesion dynamics by modulating talin targeting to the plasma membrane .
PMID: 17261850
3
PIP5K1C (phosphatidylinositol-4-phosphate 5-kinase type 1 gamma) is a lipid kinase that catalyzes phosphorylation of phosphatidylinositol 4-phosphate (PI4P) to generate phosphatidylinositol 4,5-bisphosphate (PIP2), a critical second messenger regulating signal transduction, vesicle trafficking, cytoskeleton dynamics, and cell adhesion , .
PMID: 12422219
4
The enzyme mediates Arf6-driven exocyst recruitment and membrane tethering through rapid PIP2 synthesis .
PMID: 35609603
5
PIP5K1C loss in osteocytes impairs bone remodeling through reduced collagen expression and increased sclerostin, with decreased focal adhesion proteins and elevated apoptosis .
PMID: 38495744
6
In chondrocytes, PIP5K1C deletion causes age-related osteoarthritis-like lesions with cartilage degradation and impaired chondrocyte adhesion .
PMID: 37008048
7
Additionally, dual PIP5K1C/PIKfyve inhibition prevents SARS-CoV-2 entry by blocking ACE2-mediated endocytosis and cathepsin L activation .
PMID: 39085352
Disease Associationsβ“˜21
lethal congenital contracture syndrome 3Open Targets
0.67Moderate
Lethal congenital contracture syndrome type 3Open Targets
0.60Moderate
Neurodevelopmental disorderOpen Targets
0.51Moderate
genetic disorderOpen Targets
0.41Moderate
Intellectual disabilityOpen Targets
0.37Weak
epilepsyOpen Targets
0.37Weak
neuroinflammatory disorderOpen Targets
0.36Weak
PIP5K1C-related neurodevelopmental disorderOpen Targets
0.36Weak
neurodegenerative diseaseOpen Targets
0.24Weak
Miyoshi muscular dystrophy 1Open Targets
0.12Weak
Meniere diseaseOpen Targets
0.07Suggestive
Abruptio PlacentaeOpen Targets
0.07Suggestive
hereditary angioedemaOpen Targets
0.06Suggestive
Milroy diseaseOpen Targets
0.06Suggestive
lymphatic malformation 11Open Targets
0.06Suggestive
LipedemaOpen Targets
0.05Suggestive
lymphatic malformation 14Open Targets
0.05Suggestive
hereditary angioedema with normal C1InhOpen Targets
0.04Suggestive
lymphatic malformation 8Open Targets
0.04Suggestive
lymphatic malformation 3Open Targets
0.04Suggestive
Lethal congenital contracture syndrome 3UniProt
Pathogenic Variants7
NM_012398.3(PIP5K1C):c.662A>G (p.Tyr221Cys)Pathogenic
not provided|PIP5K1C-related neurodevelopmental disorder|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 221
NM_012398.3(PIP5K1C):c.700C>T (p.Arg234Cys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 234
NM_012398.3(PIP5K1C):c.777_778dup (p.Lys260fs)Likely pathogenic
Lethal congenital contracture syndrome 3
β˜…β˜†β˜†β˜†2024β†’ Residue 260
NM_012398.3(PIP5K1C):c.625C>T (p.Leu209Phe)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 209
NM_012398.3(PIP5K1C):c.688_689del (p.Gly230fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2020β†’ Residue 230
NM_012398.3(PIP5K1C):c.1127+1G>APathogenic
not provided
β˜…β˜†β˜†β˜†2020
NM_012398.3(PIP5K1C):c.757G>A (p.Asp253Asn)Pathogenic
Lethal congenital contracture syndrome 3
β˜†β˜†β˜†β˜†2007β†’ Residue 253
View on ClinVar β†—
Related Genes
TLN2Protein interaction100%PIK3R3Protein interaction100%PIK3R1Protein interaction100%PIK3CBProtein interaction100%PIK3CAProtein interaction100%ACTG1Protein interaction99%
Tissue Expression6 tissues
Brain
100%
Ovary
100%
Lung
96%
Heart
82%
Liver
41%
Bone Marrow
23%
Gene Interaction Network
Click a node to explore
PIP5K1CTLN2PIK3R3PIK3R1PIK3CBPIK3CAACTG1
PROTEIN STRUCTURE
Preparing viewer…
PDB3H1Z Β· 1.83 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.75LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.58 [0.46–0.75]
RankingsWhere PIP5K1C stands among ~20K protein-coding genes
  • #5,375of 20,598
    Most Researched89
  • #3,192of 5,498
    Most Pathogenic Variants7
  • #5,967of 17,882
    Most Constrained (LOEUF)0.75
Genes detectedPIP5K1C
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
1.00
2
Pip5k1c expression in osteocytes regulates bone remodeling in mice.
PMID: 38495744
J Orthop Translat Β· 2024
0.90
3
Genetic Association and Expression Analyses of the Phosphatidylinositol-4-Phosphate 5-Kinase (PIP5K1C) Gene in Alcohol Use Disorder-Relevance for Pain Signaling and Alcohol Use.
PMID: 29667742
Alcohol Clin Exp Res Β· 2018
0.80
4
PIP5K1C phosphoinositide kinase deficiency distinguishes PIKFYVE-dependent cancer cells from non-malignant cells.
PMID: 36803256
Autophagy Β· 2023
0.70
5
A dual inhibitor of PIP5K1C and PIKfyve prevents SARS-CoV-2 entry into cells.
PMID: 39085352
Exp Mol Med Β· 2024
0.60