RPH3A (rabphilin 3A)

Gene

• Entrez ID: 22895
• Gene name: Rabphilin 3A
• Gene symbol: RPH3A
• Synonyms (NCBI Gene): -
• Chromosome: 12
• Chromosome location: 12q24.13
• Summary: The protein encoded by this gene is thought to be an effector for RAB3A, which is a small G protein that acts in the late stages of neurotransmitter exocytosis. The encoded protein may be involved in neurotransmitter release and synaptic vesicle traffic.

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs779991033	G>C	Pathogenic	Genic upstream transcript variant, missense variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT048316	hsa-miR-106a-5p	CLASH	23622248
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	21572407
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	21572407
MIRT707181	hsa-miR-124-5p	HITS-CLIP	21572407
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	21572407
MIRT654137	hsa-miR-493-5p	HITS-CLIP	21572407
MIRT654136	hsa-miR-574-5p	HITS-CLIP	21572407
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	23313552
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	23313552
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	23313552
MIRT654137	hsa-miR-493-5p	HITS-CLIP	23313552
MIRT654136	hsa-miR-574-5p	HITS-CLIP	23313552
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	23824327
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	23824327
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	23824327
MIRT654137	hsa-miR-493-5p	HITS-CLIP	23824327
MIRT654136	hsa-miR-574-5p	HITS-CLIP	23824327
MIRT570545	hsa-miR-5197-3p	PAR-CLIP	20371350
MIRT570544	hsa-miR-6873-5p	PAR-CLIP	20371350
MIRT570543	hsa-miR-1321	PAR-CLIP	20371350
MIRT570541	hsa-miR-4739	PAR-CLIP	20371350
MIRT570542	hsa-miR-4756-5p	PAR-CLIP	20371350
MIRT570540	hsa-miR-3150b-3p	PAR-CLIP	20371350
MIRT570539	hsa-miR-4784	PAR-CLIP	20371350
MIRT570538	hsa-miR-4419a	PAR-CLIP	20371350
MIRT570537	hsa-miR-4510	PAR-CLIP	20371350
MIRT570536	hsa-miR-6127	PAR-CLIP	20371350
MIRT570535	hsa-miR-6129	PAR-CLIP	20371350
MIRT570534	hsa-miR-6130	PAR-CLIP	20371350
MIRT570533	hsa-miR-6133	PAR-CLIP	20371350
MIRT570532	hsa-miR-765	PAR-CLIP	20371350
MIRT570531	hsa-miR-3153	PAR-CLIP	20371350
MIRT570530	hsa-miR-6733-5p	PAR-CLIP	20371350
MIRT570529	hsa-miR-6739-5p	PAR-CLIP	20371350
MIRT570528	hsa-miR-7106-5p	PAR-CLIP	20371350
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	27418678
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	27418678
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	27418678
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	27418678
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	27418678
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	27418678
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	27418678
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	27418678
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	27418678
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	27418678
MIRT654137	hsa-miR-493-5p	HITS-CLIP	27418678
MIRT654137	hsa-miR-493-5p	HITS-CLIP	27418678
MIRT654137	hsa-miR-493-5p	HITS-CLIP	27418678
MIRT654137	hsa-miR-493-5p	HITS-CLIP	27418678
MIRT654137	hsa-miR-493-5p	HITS-CLIP	27418678
MIRT654136	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT654136	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT654136	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT654136	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT654136	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	21572407
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	21572407
MIRT707181	hsa-miR-124-5p	HITS-CLIP	21572407
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	21572407
MIRT654137	hsa-miR-493-5p	HITS-CLIP	21572407
MIRT654136	hsa-miR-574-5p	HITS-CLIP	21572407
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	23313552
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	23313552
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	23313552
MIRT654137	hsa-miR-493-5p	HITS-CLIP	23313552
MIRT654136	hsa-miR-574-5p	HITS-CLIP	23313552
MIRT654140	hsa-miR-3177-5p	HITS-CLIP	23824327
MIRT654139	hsa-miR-6867-5p	HITS-CLIP	23824327
MIRT654138	hsa-miR-4666a-5p	HITS-CLIP	23824327
MIRT654137	hsa-miR-493-5p	HITS-CLIP	23824327
MIRT654136	hsa-miR-574-5p	HITS-CLIP	23824327
MIRT570545	hsa-miR-5197-3p	PAR-CLIP	20371350
MIRT570544	hsa-miR-6873-5p	PAR-CLIP	20371350
MIRT570543	hsa-miR-1321	PAR-CLIP	20371350
MIRT570541	hsa-miR-4739	PAR-CLIP	20371350
MIRT570542	hsa-miR-4756-5p	PAR-CLIP	20371350
MIRT570540	hsa-miR-3150b-3p	PAR-CLIP	20371350
MIRT570539	hsa-miR-4784	PAR-CLIP	20371350
MIRT570538	hsa-miR-4419a	PAR-CLIP	20371350
MIRT570537	hsa-miR-4510	PAR-CLIP	20371350
MIRT570536	hsa-miR-6127	PAR-CLIP	20371350
MIRT570535	hsa-miR-6129	PAR-CLIP	20371350
MIRT570534	hsa-miR-6130	PAR-CLIP	20371350
MIRT570533	hsa-miR-6133	PAR-CLIP	20371350
MIRT570532	hsa-miR-765	PAR-CLIP	20371350
MIRT570531	hsa-miR-3153	PAR-CLIP	20371350
MIRT570530	hsa-miR-6733-5p	PAR-CLIP	20371350
MIRT570529	hsa-miR-6739-5p	PAR-CLIP	20371350
MIRT570528	hsa-miR-7106-5p	PAR-CLIP	20371350
MIRT1315676	hsa-miR-1303	CLIP-seq
MIRT1315677	hsa-miR-185	CLIP-seq
MIRT1315678	hsa-miR-3125	CLIP-seq
MIRT1315679	hsa-miR-3152-3p	CLIP-seq
MIRT1315680	hsa-miR-3175	CLIP-seq
MIRT1315681	hsa-miR-3189-5p	CLIP-seq
MIRT1315682	hsa-miR-3202	CLIP-seq
MIRT1315683	hsa-miR-342-3p	CLIP-seq
MIRT1315684	hsa-miR-3916	CLIP-seq
MIRT1315685	hsa-miR-3929	CLIP-seq
MIRT1315686	hsa-miR-4270	CLIP-seq
MIRT1315687	hsa-miR-4306	CLIP-seq
MIRT1315688	hsa-miR-4311	CLIP-seq
MIRT1315689	hsa-miR-4419b	CLIP-seq
MIRT1315690	hsa-miR-4428	CLIP-seq
MIRT1315691	hsa-miR-4441	CLIP-seq
MIRT1315692	hsa-miR-4476	CLIP-seq
MIRT1315693	hsa-miR-4478	CLIP-seq
MIRT1315694	hsa-miR-4644	CLIP-seq
MIRT1315695	hsa-miR-4724-5p	CLIP-seq
MIRT1315696	hsa-miR-4728-5p	CLIP-seq
MIRT1315697	hsa-miR-4758-3p	CLIP-seq
MIRT1315698	hsa-miR-4768-5p	CLIP-seq
MIRT1315699	hsa-miR-485-5p	CLIP-seq
MIRT1315700	hsa-miR-542-3p	CLIP-seq
MIRT1315701	hsa-miR-548an	CLIP-seq
MIRT1315702	hsa-miR-942	CLIP-seq
MIRT1315703	hsa-miR-1587	CLIP-seq
MIRT1315704	hsa-miR-3122	CLIP-seq
MIRT1315705	hsa-miR-3126-5p	CLIP-seq
MIRT1315706	hsa-miR-3689d	CLIP-seq
MIRT1315707	hsa-miR-3913-5p	CLIP-seq
MIRT1315708	hsa-miR-4318	CLIP-seq
MIRT1315709	hsa-miR-4417	CLIP-seq
MIRT1315710	hsa-miR-4492	CLIP-seq
MIRT1315711	hsa-miR-4498	CLIP-seq
MIRT1315712	hsa-miR-450b-3p	CLIP-seq
MIRT1315713	hsa-miR-4656	CLIP-seq
MIRT1315714	hsa-miR-4675	CLIP-seq
MIRT1315715	hsa-miR-4710	CLIP-seq
MIRT1315716	hsa-miR-4741	CLIP-seq
MIRT1315717	hsa-miR-4792	CLIP-seq
MIRT1315718	hsa-miR-541	CLIP-seq
MIRT1315719	hsa-miR-654-5p	CLIP-seq
MIRT1315720	hsa-miR-762	CLIP-seq
MIRT1315721	hsa-miR-769-3p	CLIP-seq
MIRT2093909	hsa-miR-4727-5p	CLIP-seq
MIRT2093910	hsa-miR-4769-3p	CLIP-seq
MIRT1315705	hsa-miR-3126-5p	CLIP-seq
MIRT2318403	hsa-miR-4310	CLIP-seq
MIRT2318404	hsa-miR-433	CLIP-seq
MIRT2318405	hsa-miR-4527	CLIP-seq
MIRT2318406	hsa-miR-4666-5p	CLIP-seq
MIRT2318407	hsa-miR-4698	CLIP-seq
MIRT2318408	hsa-miR-488	CLIP-seq
MIRT2318409	hsa-miR-549	CLIP-seq
MIRT2318410	hsa-miR-628-5p	CLIP-seq
MIRT2318411	hsa-miR-7	CLIP-seq
MIRT2458544	hsa-miR-1271	CLIP-seq
MIRT2458545	hsa-miR-182	CLIP-seq
MIRT2458546	hsa-miR-1972	CLIP-seq
MIRT2458547	hsa-miR-4642	CLIP-seq
MIRT2458548	hsa-miR-4650-5p	CLIP-seq
MIRT2458549	hsa-miR-4711-5p	CLIP-seq
MIRT2458550	hsa-miR-96	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005509	Function	Calcium ion binding	ISS
GO:0005515	Function	Protein binding	IPI	11377421, 15207266, 32296183
GO:0005544	Function	Calcium-dependent phospholipid binding	ISS
GO:0005546	Function	Phosphatidylinositol-4,5-bisphosphate binding	ISS
GO:0005886	Component	Plasma membrane	IEA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0008021	Component	Synaptic vesicle	TAS	10099709
GO:0008270	Function	Zinc ion binding	IEA
GO:0008270	Function	Zinc ion binding	ISS
GO:0008289	Function	Lipid binding	IEA
GO:0008430	Function	Selenium binding	ISS
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016082	Process	Synaptic vesicle priming	IEA
GO:0019898	Component	Extrinsic component of membrane	ISS
GO:0030141	Component	Secretory granule	ISS
GO:0030672	Component	Synaptic vesicle membrane	IEA
GO:0030672	Component	Synaptic vesicle membrane	ISS
GO:0031267	Function	Small GTPase binding	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032991	Component	Protein-containing complex	ISS
GO:0042301	Function	Phosphate ion binding	ISS
GO:0042995	Component	Cell projection	IEA
GO:0043005	Component	Neuron projection	IBA
GO:0043005	Component	Neuron projection	ISS
GO:0043197	Component	Dendritic spine	IEA
GO:0044877	Function	Protein-containing complex binding	ISS
GO:0045202	Component	Synapse	IBA
GO:0045202	Component	Synapse	IEA
GO:0045202	Component	Synapse	ISS
GO:0045211	Component	Postsynaptic membrane	IBA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0045956	Process	Positive regulation of calcium ion-dependent exocytosis	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0061669	Process	Spontaneous neurotransmitter secretion	IEA
GO:0070679	Function	Inositol 1,4,5 trisphosphate binding	ISS
GO:0098850	Component	Extrinsic component of synaptic vesicle membrane	IBA
GO:0099502	Process	Calcium-dependent activation of synaptic vesicle fusion	IBA
GO:1901981	Function	Phosphatidylinositol phosphate binding	TAS	10099709

Other IDs

• MIM: 612159
• HGNC: 17056
• e!Ensembl: ENSG00000089169

Protein

• UniProt ID: Q9Y2J0
• Protein name: Rabphilin-3A (Exophilin-1)
• Protein function: Plays an essential role in docking and fusion steps of regulated exocytosis (By similarity). At the presynaptic level, RPH3A is recruited by RAB3A to the synaptic vesicle membrane in a GTP-dependent manner where it modulates synaptic vesicle tra
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02318	FYVE_2	48 → 161	FYVE-type zinc finger	Family
  PF00168	C2	407 → 516	C2 domain	Domain
  PF00168	C2	565 → 671	C2 domain	Domain

• Sequence:

  MTDTVFSNSSNRWMYPSDRPLQSNDKEQLQAGWSVHPGGQPDRQRKQEELTDEEKEIINR
  VIARAEKMEEMEQERIGRLVDRLENMRKNVAGDGVNRCILCGEQLGMLGSACVVCEDCKK
  NVCTKCGVETNNRLHSVWLCKICIEQREVWKRSGAWFFKGFPKQVLPQPMPIKKTKPQQP
  VSEPAAPEQPAPEPKHPARAPARGDSEDRRGPGQKTGPDPASAPGRGNYGPPVRRASEAR
  MSSSSRDSESWDHSGGAGDSSRSPAGLRRANSVQASRPAPGSVQSPAPPQPGQPGTPGGS
  RPGPGPAGRFPDQKPEVAPSDPGTTAPPREERTGGVGGYPAVGAREDRMSHPSGPYSQAS
  AAAPQPAAARQPPPPEEEEEEANSYDSDEATTLGALEFSLLYDQDNSSLQCTIIKAKGLK
  PMDSNGLADPYVKLHLLPGASKSNKLRTKTLRNTRNPIWNETLVYHGITDEDMQRKTLRI
  SVCDEDKFGHNEFIGETRFSLKKLKPNQRKNFNICLERVIPMKRAGTTGSARGMALYEEE
  QVERVGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGK
  KAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISA
  KGERLKHWYECLKNKDKKIERWHQLQNENHVSSD

• Sequence length: 694

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL MYASTHENIC SYNDROME	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESOPHAGEAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESOPHAGEAL CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GENERALISED EPILEPSY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYASTHENIC SYNDROMES, CONGENITAL	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARTIAL EPILEPSY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RPH3A-related condition	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UPPER AERODIGESTIVE TRACT NEOPLASM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	LHGDN	17981610		★☆☆☆☆ Found in Text Mining only
Central Diabetes Insipidus	Diabetes Insipidus	BEFREE	28420857, 29367474		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	21536019		★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	GWASDB_DG	23202125		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Coronary heart disease	Coronary Heart Disease	GWASDB_DG	21971053		★☆☆☆☆ Found in Text Mining only
Dyskinetic syndrome	Dyskinetic Syndrome	BEFREE	28823933		★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington Disease	BEFREE	17877635		★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington Disease	LHGDN	17877635		★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington disease	Pubtator	17877635	Associate	★☆☆☆☆ Found in Text Mining only
Learning Disabilities	Learning disorders	Pubtator	29441694	Associate	★☆☆☆☆ Found in Text Mining only
Lewy Body Disease	Lewy Body Disease	LHGDN	15207266		★☆☆☆☆ Found in Text Mining only
Myasthenic Syndromes Congenital	Myasthenic syndrome	Pubtator	29441694	Associate	★☆☆☆☆ Found in Text Mining only
Myasthenic Syndromes, Congenital	Myasthenic Syndrome	BEFREE	29441694		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nervous System Diseases	Nervous system disease	Pubtator	29441694	Associate	★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	29441694		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	28823933		★☆☆☆☆ Found in Text Mining only
Pituitary Diseases	Pituitary Diseases	BEFREE	29367474		★☆☆☆☆ Found in Text Mining only
Tetralogy of Fallot	Tetralogy of Fallot	GWASDB_DG	23297363		★☆☆☆☆ Found in Text Mining only