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GeneE
10 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.
PPFIA3
PPFI scaffold protein A3
Chromosome 19 Β· 19q13.33
NCBI Gene: 8541Ensembl: ENSG00000177380.15HGNC: HGNC:9247UniProt: O75145
39PubMed Papers
21Diseases
0Drugs
19Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
acrosomal vesicleprotein bindingregulation of short-term neuronal synaptic plasticitysynapse organizationPPFIA3-related neurodevelopmental disorderneurodegenerative diseaseNeurodevelopmental delaygenetic disorder
✦AI Summary

PPFIA3 encodes a scaffold protein belonging to the LAR protein-tyrosine phosphatase-interacting protein (liprin) family that plays crucial roles in synaptic function and development 1. The protein is involved in synapse formation, synaptic vesicle transport, and presynaptic active zone assembly, with evolutionarily conserved structure and function 12. PPFIA3 functions as a kinesin-cargo linker and may regulate focal adhesion disassembly while localizing receptor-like tyrosine phosphatases at specific plasma membrane sites 3. Disease relevance has emerged through identification of rare heterozygous variants causing a syndromic neurodevelopmental disorder characterized by developmental delay, intellectual disability, hypotonia, autism, and epilepsy 14. Functional studies in Drosophila demonstrate that pathogenic variants act as dominant-negative loss-of-function alleles, with variants in the N-terminal coiled-coil domain showing stronger phenotypic effects than C-terminal variants 12. The variants disrupt multiple developmental processes and synapse formation, leading to seizure-like behaviors, motor defects, and synaptic abnormalities 2. PPFIA3 has also been identified as a novel gene associated with developmental and epileptic encephalopathy with spike-wave activation in sleep, expanding its clinical significance in pediatric neurology 4.

Sources cited
1
PPFIA3 belongs to liprin family involved in synapse formation, vesicle transport, and active zone assembly; rare variants cause neurodevelopmental syndrome
PMID: 38181735
2
14 individuals with rare PPFIA3 variants show developmental delay, intellectual disability, autism, and epilepsy; variants are dominant-negative loss-of-function
PMID: 37034625
3
PPFIA3 identified as novel gene associated with developmental and epileptic encephalopathy with spike-wave activation in sleep
PMID: 39096015
4
PPFIA4 characterized as kinesin-cargo linker, providing context for PPFIA family function
PMID: 14612982
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
PPFIA3-related neurodevelopmental disorderOpen Targets
0.42Moderate
neurodegenerative diseaseOpen Targets
0.36Weak
Neurodevelopmental delayOpen Targets
0.33Weak
genetic disorderOpen Targets
0.19Weak
hypertensionOpen Targets
0.19Weak
Neurodevelopmental disorderOpen Targets
0.19Weak
IrritabilityOpen Targets
0.16Weak
Increased blood pressureOpen Targets
0.12Weak
cardiovascular diseaseOpen Targets
0.12Weak
dislocationOpen Targets
0.10Suggestive
attention deficit hyperactivity disorderOpen Targets
0.06Suggestive
goutOpen Targets
0.05Suggestive
autismOpen Targets
0.05Suggestive
hereditary attention deficit-hyperactivity disorderOpen Targets
0.05Suggestive
alcohol drinkingOpen Targets
0.05Suggestive
Tourette syndromeOpen Targets
0.05Suggestive
attention deficit-hyperactivity disorder 8Open Targets
0.04Suggestive
Potocki-Lupski syndromeOpen Targets
0.04Suggestive
schizophrenia 15Open Targets
0.04Suggestive
peritonitisOpen Targets
0.04Suggestive
Paul-Chao neurodevelopmental syndromeUniProt
Pathogenic Variants19
NM_003660.4(PPFIA3):c.1243C>T (p.Arg415Trp)Pathogenic
not provided|PPFIA3-related disorder|PAUL-CHAO NEURODEVELOPMENTAL SYNDROME
β˜…β˜…β˜†β˜†2025β†’ Residue 415
NM_003660.4(PPFIA3):c.2332C>T (p.Arg778Ter)Pathogenic
not provided|PPFIA3-related neurodevelopmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 778
NM_003660.4(PPFIA3):c.2717C>T (p.Ser906Leu)Pathogenic
Neurodevelopmental delay|not provided|PAUL-CHAO NEURODEVELOPMENTAL SYNDROME
β˜…β˜…β˜†β˜†2024β†’ Residue 906
NM_003660.4(PPFIA3):c.2706dup (p.Ser903fs)Pathogenic
PPFIA3-related disorder|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 903
NM_003660.4(PPFIA3):c.1492C>T (p.Arg498Trp)Likely pathogenic
PPFIA3-related disorder|PAUL-CHAO NEURODEVELOPMENTAL SYNDROME|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 498
NM_003660.4(PPFIA3):c.2609T>A (p.Ile870Asn)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 870
NM_003660.4(PPFIA3):c.3456dup (p.Asn1153fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1153
NM_003660.4(PPFIA3):c.2374del (p.Thr792fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 792
NM_003660.4(PPFIA3):c.241-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_003660.4(PPFIA3):c.586_587del (p.Leu196fs)Pathogenic
PPFIA3-associated neurodevelopmental disorder
β˜…β˜†β˜†β˜†2024β†’ Residue 196
NM_003660.4(PPFIA3):c.115C>T (p.Arg39Cys)Pathogenic
not provided|PAUL-CHAO NEURODEVELOPMENTAL SYNDROME
β˜…β˜†β˜†β˜†2023β†’ Residue 39
NM_003660.4(PPFIA3):c.1638G>T (p.Trp546Cys)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 546
NM_003660.4(PPFIA3):c.3307del (p.Glu1103fs)Likely pathogenic
Neurodevelopmental delay
β˜…β˜†β˜†β˜†2023β†’ Residue 1103
NM_003660.4(PPFIA3):c.118G>A (p.Glu40Lys)Likely pathogenic
PPFIA3-related disorder
β˜†β˜†β˜†β˜†2023β†’ Residue 40
NM_003660.4(PPFIA3):c.240+1G>ALikely pathogenic
PPFIA3-related disorder
β˜†β˜†β˜†β˜†2023
NM_003660.4(PPFIA3):c.943G>T (p.Ala315Ser)Likely pathogenic
PPFIA3-related disorder
β˜†β˜†β˜†β˜†2023β†’ Residue 315
NM_003660.4(PPFIA3):c.1675C>T (p.Arg559Trp)Likely pathogenic
PPFIA3-related disorder
β˜†β˜†β˜†β˜†2023β†’ Residue 559
NM_003660.4(PPFIA3):c.2350C>T (p.Arg784Trp)Pathogenic
PPFIA3-related disorder
β˜†β˜†β˜†β˜†2023β†’ Residue 784
NM_003660.4(PPFIA3):c.1285C>T (p.Arg429Trp)Likely pathogenic
PPFIA3-related disorder
β˜†β˜†β˜†β˜†2023β†’ Residue 429
View on ClinVar β†—
Related Genes
CASKProtein interaction100%RIMS1Protein interaction100%PPP2CAProtein interaction99%UNC13BProtein interaction93%ERC1Protein interaction86%GIT1Protein interaction86%
Tissue Expression6 tissues
Brain
100%
Liver
25%
Heart
18%
Bone Marrow
13%
Lung
12%
Ovary
11%
Gene Interaction Network
Click a node to explore
PPFIA3CASKRIMS1PPP2CAUNC13BERC1GIT1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt O75145
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.26Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.19 [0.14–0.26]
RankingsWhere PPFIA3 stands among ~20K protein-coding genes
  • #10,378of 20,598
    Most Researched39
  • #2,254of 5,498
    Most Pathogenic Variants19
  • #870of 17,882
    Most Constrained (LOEUF)0.26 Β· top 5%
Genes detectedPPFIA3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3.
PMID: 38181735
Am J Hum Genet Β· 2024
1.00
2
Solving the Etiology of Developmental and Epileptic Encephalopathy with Spike-Wave Activation in Sleep (D/EE-SWAS).
PMID: 39096015
Ann Neurol Β· 2024
0.90
3
The epilepsy-autism phenotype associated with developmental and epileptic encephalopathies: New mechanism-based therapeutic options.
PMID: 39985505
Epilepsia Β· 2025
0.80
4
Clinicopathological Significances and Prognostic Value of
PMID: 36605492
J Cancer Β· 2023
0.70
5
Detection of OSR2, VAV3, and PPFIA3 Methylation in the Serum of Patients with Gastric Cancer.
PMID: 27143812
Dis Markers Β· 2016
0.60