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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PI4KA
phosphatidylinositol 4-kinase alpha
Chromosome 22 Β· 22q11.21
NCBI Gene: 5297Ensembl: ENSG00000241973.12HGNC: HGNC:8983UniProt: A0A140VK35
157PubMed Papers
23Diseases
0Drugs
38Pathogenic Variants
FUNCTIONAL ROLE
Kinase
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytoplasmprotein bindingextracellular exosomecadherin bindingpolymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposisspastic paraplegia 84, autosomal recessivemultiple intestinal atresianeurodegenerative disease
✦AI Summary

PI4KA encodes phosphatidylinositol 4-kinase alpha, an essential lipid kinase that serves as a master regulator of phosphoinositide signaling at the plasma membrane 1. PI4KA produces the predominant pool of phosphatidylinositol 4-phosphate (PI4P) at the plasma membrane, which is crucial for lipid transport and regulation of PLC and PI3K signaling pathways 1. The enzyme functions as a heterotrimeric complex with regulatory proteins TTC7 and FAM126, and is recruited to the plasma membrane by EFR3 proteins 2. PI4KA undergoes multiple levels of regulation, including posttranslational modifications and interaction with calcineurin phosphatase, which dephosphorylates and promotes PI4KA complex activity during signaling 3. Biallelic PI4KA mutations cause severe multisystem disorders including gastrointestinal defects, immunodeficiency, and neurodevelopmental abnormalities 4. These mutations disrupt B-cell metabolism by altering lipid production, impairing mitochondrial function, and hyperactivating the mTOR pathway, resulting in B-cell lymphopenia and hypogammaglobulinemia 4. Clinical manifestations include spastic paraplegia, hypomyelinating leukodystrophy, developmental delay, and recurrent infections 56. The enzyme's conservation across all eukaryotes underscores its fundamental importance in cellular membrane organization and signaling 1.

Sources cited
1
PI4KA is a master regulator of phosphoinositide signaling at the plasma membrane and produces predominant PI4P pool
PMID: 37979461
2
PI4KA functions as heterotrimeric complex with TTC7 and FAM126, recruited by EFR3 proteins
PMID: 39705356
3
PI4KA is regulated by calcineurin phosphatase which promotes complex activity during signaling
PMID: 34663815
4
Biallelic PI4KA mutations disrupt B-cell metabolism and cause immunodeficiency with B-cell lymphopenia
PMID: 39312004
5
PI4KA mutations cause neurodevelopmental disorders including spastic paraplegia and cerebellar atrophy
PMID: 38003592
6
PI4KA mutations cause combined immunodeficiency and gastrointestinal disorders
PMID: 36341355
Disease Associationsβ“˜23
polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposisOpen Targets
0.75Strong
spastic paraplegia 84, autosomal recessiveOpen Targets
0.69Moderate
multiple intestinal atresiaOpen Targets
0.59Moderate
neurodegenerative diseaseOpen Targets
0.49Moderate
heparin cofactor 2 deficiencyOpen Targets
0.48Moderate
CEDNIK syndromeOpen Targets
0.47Moderate
PI4KA-related disorderOpen Targets
0.47Moderate
bilateral perisylvian polymicrogyriaOpen Targets
0.37Weak
gastrointestinal defect and immunodeficiency syndromeOpen Targets
0.37Weak
Pleural MesotheliomaOpen Targets
0.37Weak
hypomyelinating leukodystrophy 2Open Targets
0.33Weak
hemorrhageOpen Targets
0.27Weak
genetic disorderOpen Targets
0.19Weak
tuberous sclerosis 1Open Targets
0.15Weak
phenylketonuriaOpen Targets
0.14Weak
Prolonged QT intervalOpen Targets
0.14Weak
parasitic infectionOpen Targets
0.12Weak
thrombotic diseaseOpen Targets
0.12Weak
Venous thrombosisOpen Targets
0.12Weak
HypercholesterolemiaOpen Targets
0.12Weak
Gastrointestinal defects and immunodeficiency syndrome 2UniProt
Neurodevelopmental disorder with spasticity, hypomyelinating leukodystrophy, and brain abnormalitiesUniProt
Spastic paraplegia 84, autosomal recessiveUniProt
Pathogenic Variants38
NM_058004.4(PI4KA):c.1852C>T (p.Arg618Ter)Likely pathogenic
Spastic paraplegia 84, autosomal recessive|Phenylketonuria|PI4KA-related disorder|not provided|Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis;Gastrointestinal defects and immunodeficiency syndrome 2;Spastic paraplegia 84, autosomal recessive
β˜…β˜…β˜†β˜†2025β†’ Residue 618
NM_058004.4(PI4KA):c.6156_6159del (p.Thr2053fs)Pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis|Spastic paraplegia 84, autosomal recessive|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 2053
NM_058004.4(PI4KA):c.3454G>A (p.Glu1152Lys)Likely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 1152
NM_058004.4(PI4KA):c.5974C>T (p.Pro1992Ser)Likely pathogenic
not provided|Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜…β˜†β˜†2022β†’ Residue 1992
NM_058004.4(PI4KA):c.5833G>A (p.Ala1945Thr)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1945
NM_058004.4(PI4KA):c.2802_2863-40delLikely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜†β˜†β˜†2024
NM_058004.4(PI4KA):c.5362G>T (p.Asp1788Tyr)Likely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜†β˜†β˜†2024β†’ Residue 1788
NM_058004.4(PI4KA):c.1306C>T (p.Gln436Ter)Likely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜†β˜†β˜†2024β†’ Residue 436
NM_058004.4(PI4KA):c.574C>T (p.Arg192Ter)Likely pathogenic
Spastic paraplegia 84, autosomal recessive
β˜…β˜†β˜†β˜†2024β†’ Residue 192
NM_058004.4(PI4KA):c.4156T>G (p.Phe1386Val)Likely pathogenic
Spastic paraplegia 84, autosomal recessive
β˜…β˜†β˜†β˜†2024β†’ Residue 1386
NM_058004.4(PI4KA):c.3976C>T (p.Arg1326Cys)Likely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜†β˜†β˜†2024β†’ Residue 1326
NM_058004.4(PI4KA):c.5821C>T (p.Arg1941Ter)Likely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜†β˜†β˜†2024β†’ Residue 1941
NM_058004.4(PI4KA):c.2988-2A>GLikely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis;Gastrointestinal defects and immunodeficiency syndrome 2;Spastic paraplegia 84, autosomal recessive
β˜…β˜†β˜†β˜†2024
NM_058004.4(PI4KA):c.1080del (p.Ser361fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 361
NM_058004.4(PI4KA):c.2977del (p.Leu993fs)Pathogenic
PI4KA-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 993
NM_058004.4(PI4KA):c.3918dup (p.Glu1307Ter)Likely pathogenic
PI4KA-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 1307
NM_058004.4(PI4KA):c.5456AAG[1] (p.Glu1820del)Pathogenic
Spastic paraplegia 84, autosomal recessive
β˜…β˜†β˜†β˜†2023β†’ Residue 1820
NM_058004.4(PI4KA):c.5159C>T (p.Thr1720Ile)Pathogenic
Spastic paraplegia 84, autosomal recessive
β˜…β˜†β˜†β˜†2023β†’ Residue 1720
NM_058004.4(PI4KA):c.3900+1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_058004.4(PI4KA):c.4901del (p.Thr1634fs)Likely pathogenic
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
β˜…β˜†β˜†β˜†2022β†’ Residue 1634
View on ClinVar β†—
Related Genes
MTM1Protein interaction98%PIK3C3Protein interaction98%CDIPTProtein interaction98%PIKFYVEProtein interaction94%PIP5KL1Protein interaction94%PTENProtein interaction93%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
87%
Ovary
57%
Lung
54%
Heart
40%
Liver
40%
Gene Interaction Network
Click a node to explore
PI4KAMTM1PIK3C3CDIPTPIKFYVEPIP5KL1PTEN
PROTEIN STRUCTURE
Preparing viewer…
PDB9B9G Β· 3.50 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.55Moderately Constrained
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.46 [0.39–0.55]
RankingsWhere PI4KA stands among ~20K protein-coding genes
  • #2,869of 20,598
    Most Researched157 Β· top quartile
  • #1,582of 5,498
    Most Pathogenic Variants38
  • #3,508of 17,882
    Most Constrained (LOEUF)0.55 Β· top quartile
Genes detectedPI4KA
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
Biallelic PI4KA Mutations Disrupt B-Cell Metabolism and Cause B-Cell Lymphopenia and Hypogammaglobulinemia.
PMID: 39312004
J Clin Immunol Β· 2024
1.00
2
PI4KA and PIKfyve: Essential phosphoinositide signaling enzymes involved in myriad human diseases.
PMID: 37453227
Curr Opin Cell Biol Β· 2023
0.90
3
Molecular basis for plasma membrane recruitment of PI4KA by EFR3.
PMID: 39705356
Sci Adv Β· 2024
0.80
4
A synonymous mutation in
PMID: 36341355
Front Immunol Β· 2022
0.70
5
Structural basis for the conserved roles of PI4KA and its regulatory partners and their misregulation in disease.
PMID: 37979461
Adv Biol Regul Β· 2023
0.60