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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RPH3A
rabphilin 3A
Chromosome 12 · 12q24.13
NCBI Gene: 22895Ensembl: ENSG00000089169.16HGNC: HGNC:17056UniProt: Q9Y2J0
49PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
FUNCTIONAL ROLE
Transporter
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingcalcium-dependent phospholipid bindingphosphatidylinositol-4,5-bisphosphate bindingzinc ion bindingcoronary artery diseasetype 1 diabetes mellitushypothyroidismthyroid disease
✦AI Summary

RPH3A encodes rabphilin 3A, a synaptic protein with dual presynaptic and postsynaptic functions. Presynaptically, RPH3A is recruited to synaptic vesicle membranes by RAB3A in a GTP-dependent manner to modulate vesicle trafficking and calcium-triggered neurotransmitter release 1. Postsynaptically, RPH3A stabilizes GluN2A-containing NMDA receptors at the cell surface through phase separation mechanisms and forms a ternary complex with GRIN2A and DLG4, which is essential for synaptic plasticity and cognition 2. RPH3A also regulates neutrophil polarization through interaction with phosphatidylinositol-4-phosphate and ARF6, facilitating immune cell adhesion 3. Pathogenic RPH3A missense variants cause neurodevelopmental disorders with variable clinical presentations. Variants exhibit gain-of-function effects, increasing GluN2A-containing NMDA receptors at extrasynaptic sites and altering synaptic function 1. Disease manifestations range from drug-resistant epilepsy with intellectual disability to autism spectrum disorder 1, 4. RPH3A variants impair both presynaptic glutamate release and postsynaptic NMDAR retention, reducing calcium signaling at dendritic spines 4. RPH3A is identified as a congenital myasthenic syndrome gene 5 and represents a therapeutic target for levodopa-induced dyskinesias through modulation of striatal GluN2A composition 6.

Sources cited
1
RPH3A stabilizes GluN2A subunit of NMDA receptors; missense variants increase extrasynaptic GluN2A and cause neurodevelopmental disorders ranging from epilepsy to autism
PMID: 37403762
2
RPH3A undergoes phase separation to promote GluN2A clustering and synaptic localization, essential for synaptic stability and response
PMID: 36693856
3
RPH3A variants reduce presynaptic glutamate release and decrease synaptic retention of GluN2A-containing NMDARs, reducing dendritic spine calcium events
PMID: 40082528
4
RPH3A polarization is directed by phosphatidylinositol-4-phosphate and ARF6, important for neutrophil adhesion during inflammation
PMID: 31924649
5
RPH3A interacts with GluN2A-containing NMDARs at striatal postsynaptic density; increased expression in levodopa-induced dyskinesia; RPH3A/GluN2A complex is a therapeutic target
PMID: 28823933
6
RPH3A is one of 35 genes associated with congenital myasthenic syndromes affecting neuromuscular junction function
PMID: 36835142
7
RPH3A identified as a hub gene in the co-occurrence of Parkinson's disease and major depressive disorder
PMID: 37418066
Disease Associationsⓘ20
coronary artery diseaseOpen Targets
0.41Moderate
type 1 diabetes mellitusOpen Targets
0.39Weak
hypothyroidismOpen Targets
0.38Weak
thyroid diseaseOpen Targets
0.36Weak
myocardial infarctionOpen Targets
0.34Weak
ovarian neoplasmOpen Targets
0.32Weak
acquired thrombocytopeniaOpen Targets
0.31Weak
Alzheimer diseaseOpen Targets
0.31Weak
strokeOpen Targets
0.31Weak
Crohn's diseaseOpen Targets
0.30Weak
Genu valgumOpen Targets
0.30Weak
Genu varumOpen Targets
0.30Weak
goutOpen Targets
0.29Weak
epilepsyOpen Targets
0.27Weak
chronic obstructive pulmonary diseaseOpen Targets
0.26Weak
polyp of colonOpen Targets
0.25Weak
Age-related cataractOpen Targets
0.24Weak
placenta praeviaOpen Targets
0.24Weak
sinoatrial node disorderOpen Targets
0.23Weak
Graves diseaseOpen Targets
0.23Weak
Pathogenic Variants1
NM_001143854.2(RPH3A):c.763G>C (p.Gly255Arg)Pathogenic
not provided
★☆☆☆2019→ Residue 255
View on ClinVar ↗
Related Genes
MYO5AProtein interaction100%RAB3AProtein interaction100%RAB3BProtein interaction100%SNAP25Protein interaction100%RAB8AProtein interaction88%RAB27AProtein interaction83%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
4%
Lung
0%
Liver
0%
Ovary
0%
Heart
0%
Gene Interaction Network
Click a node to explore
RPH3AMYO5ARAB3ARAB3BSNAP25RAB8ARAB27A
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9Y2J0
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.64LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.50 [0.39–0.64]
RankingsWhere RPH3A stands among ~20K protein-coding genes
  • #9,011of 20,598
    Most Researched49
  • #5,107of 5,498
    Most Pathogenic Variants1
  • #4,570of 17,882
    Most Constrained (LOEUF)0.64
Genes detectedRPH3A
Sources retrieved10 papers
Response time—
📄 Sources
10â–¼
1
Clinical and Pathologic Features of Congenital Myasthenic Syndromes Caused by 35 Genes-A Comprehensive Review.
PMID: 36835142
Int J Mol Sci · 2023
1.00
2
Identification and Experimental Validation of Parkinson's Disease with Major Depressive Disorder Common Genes.
PMID: 37418066
Mol Neurobiol · 2023
0.90
3
Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder.
PMID: 37403762
Genet Med · 2023
0.80
4
The choroidal nervous system: a link between mineralocorticoid receptor and pachychoroid.
PMID: 37682293
Acta Neuropathol · 2023
0.70
5
Arg209Lys and Gln508His missense variants in Rabphilin 3A cause pre- and post-synaptic dysfunctions at excitatory glutamatergic synapses.
PMID: 40082528
Sci Rep · 2025
0.60