SYN3 (synapsin III)

Gene

• Entrez ID: 8224
• Gene name: Synapsin III
• Gene symbol: SYN3
• Synonyms (NCBI Gene): -
• Chromosome: 22
• Chromosome location: 22q12.3
• Summary: This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptog

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519444	GG>AA	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT495092	hsa-miR-186-3p	PAR-CLIP	23708386
MIRT495090	hsa-miR-4792	PAR-CLIP	23708386
MIRT495091	hsa-miR-6807-5p	PAR-CLIP	23708386
MIRT495092	hsa-miR-186-3p	PAR-CLIP	23708386
MIRT495090	hsa-miR-4792	PAR-CLIP	23708386
MIRT495091	hsa-miR-6807-5p	PAR-CLIP	23708386
MIRT1405435	hsa-miR-1207-5p	CLIP-seq
MIRT1405436	hsa-miR-1290	CLIP-seq
MIRT1405437	hsa-miR-3064-5p	CLIP-seq
MIRT1405438	hsa-miR-3126-3p	CLIP-seq
MIRT1405439	hsa-miR-3128	CLIP-seq
MIRT1405440	hsa-miR-331-3p	CLIP-seq
MIRT1405441	hsa-miR-3614-5p	CLIP-seq
MIRT1405442	hsa-miR-3652	CLIP-seq
MIRT1405443	hsa-miR-4430	CLIP-seq
MIRT1405444	hsa-miR-4505	CLIP-seq
MIRT1405445	hsa-miR-4690-5p	CLIP-seq
MIRT1405446	hsa-miR-4720-5p	CLIP-seq
MIRT1405447	hsa-miR-4736	CLIP-seq
MIRT1405448	hsa-miR-4763-3p	CLIP-seq
MIRT1405449	hsa-miR-4799-3p	CLIP-seq
MIRT1405436	hsa-miR-1290	CLIP-seq
MIRT1405450	hsa-miR-3167	CLIP-seq
MIRT1405451	hsa-miR-320a	CLIP-seq
MIRT1405452	hsa-miR-320b	CLIP-seq
MIRT1405453	hsa-miR-320c	CLIP-seq
MIRT1405454	hsa-miR-320d	CLIP-seq
MIRT1405455	hsa-miR-4429	CLIP-seq
MIRT1405456	hsa-miR-495	CLIP-seq
MIRT1405457	hsa-miR-876-5p	CLIP-seq
MIRT2343640	hsa-miR-1343	CLIP-seq
MIRT2343641	hsa-miR-3910	CLIP-seq
MIRT2343642	hsa-miR-548an	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005515	Function	Protein binding	IPI	33961781
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	TAS	15217342
GO:0007268	Process	Chemical synaptic transmission	IEA
GO:0007269	Process	Neurotransmitter secretion	IEA
GO:0007269	Process	Neurotransmitter secretion	TAS	9539796
GO:0008021	Component	Synaptic vesicle	IEA
GO:0008021	Component	Synaptic vesicle	TAS	9539796
GO:0014069	Component	Postsynaptic density	IEA
GO:0016020	Component	Membrane	IEA
GO:0030672	Component	Synaptic vesicle membrane	IBA
GO:0030672	Component	Synaptic vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032228	Process	Regulation of synaptic transmission, GABAergic	TAS	15217342
GO:0045202	Component	Synapse	IEA
GO:0050804	Process	Modulation of chemical synaptic transmission	IEA
GO:0050808	Process	Synapse organization	IBA
GO:0097091	Process	Synaptic vesicle clustering	IBA
GO:0097091	Process	Synaptic vesicle clustering	IEA
GO:0098850	Component	Extrinsic component of synaptic vesicle membrane	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099504	Process	Synaptic vesicle cycle	IEA

Other IDs

• MIM: 602705
• HGNC: 11496
• e!Ensembl: ENSG00000185666

Protein

• UniProt ID: O14994
• Protein name: Synapsin-3 (Synapsin III)
• Protein function: May be involved in the regulation of neurotransmitter release and synaptogenesis.
• PDB: 2P0A
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF10581	Synapsin_N	1 → 31	Synapsin N-terminal	Domain
  PF02078	Synapsin	89 → 191	Synapsin, N-terminal domain	Domain
  PF02750	Synapsin_C	193 → 395	Synapsin, ATP binding domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Neuron specific. Detected predominantly in brain.
• Sequence:

  MNFLRRRLSDSSFMANLPNGYMTDLQRPDSSTSSPASPAMERRHPQPLAASFSSPGSSLF
  SSLSSAMKQAPQATSGLMEPPGPSTPIVQRPRILLVIDDAHTDWSKYFHGKKVNGEIEIR
  VEQAEFSELNLAAYVTGGCMVDMQVVRNGTKVVSRSFKPDFILVRQHAYSMALGEDYRSL
  VIGLQYGGLPAVNSLYSVYNFCSKPWVFSQLIKIFHSLGPEKFPLVEQTFFPNHKPMVTA
  PHFPVVVKLGHAHAGMGKIKVENQLDFQDITSVVAMAKTYATTEAFIDSKYDIRIQKIGS
  NYKAYMRTSISGNWKANTGSAMLEQVAMTERYRLWVDSCSEMFGGLDICAVKAVHSKDGR
  DYIIEVMDSSMPLIGEHVEEDRQLMADLVVSKMSQLPMPGGTAPSPLRPWAPQIKSAKSP
  GQAQLGPQLGQPQPRPPPQGGPRQAQSPQPQRSGSPSQQRLSPQGQQPLSPQSGSPQQQR
  SPGSPQLSRASSGSSPNQASKPGATLASQPRPPVQGRSTSQQGEESKKPAPPHPHLNKSQ
  SLTNSLSTSDTSQRGTPSEDEAKAETIRNLRKSFASLFSD

• Sequence length: 580

Pathways

Reactome:

Serotonin Neurotransmitter Release Cycle
Dopamine Neurotransmitter Release Cycle

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cerebellar vermis atrophy	Pathogenic	rs1057519444	RCV000416436	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Generalized hypotonia	Pathogenic	rs1057519444	RCV000416436	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Pathogenic	rs1057519444	RCV000416436	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Seizure	Pathogenic	rs1057519444	RCV000416436	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Visual impairment	Pathogenic	rs1057519444	RCV000416436	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ARTERIOVENOUS MALFORMATIONS, CEREBRAL	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATROPHIC MACULAR DEGENERATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BENIGN PROSTATIC HYPERPLASIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRAIN ANEURYSM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA AND RELATED DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WET MACULAR DEGENERATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	GWASDB_DG	20385819, 20385826, 21665990		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	GWASCAT_DG	20385819, 20385826, 21665990, 23455636, 26691988		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	23422939		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	BEFREE	29225348		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety disorder	Pubtator	29225348	Associate	★☆☆☆☆ Found in Text Mining only
Anxiety Disorders	Anxiety Disorder	BEFREE	29225348		★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	BEFREE	17413450, 23768104		★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	22543975	Associate	★☆☆☆☆ Found in Text Mining only
Benign Prostatic Hyperplasia	Benign Prostatic Hyperplasia	GWASCAT_DG	30988330		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	BEFREE	16511335		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	LHGDN	16511335		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	16511335		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	GWASCAT_DG	30804561		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	22571925	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy, Partial, with Variable Foci	Epilepsy	BEFREE	16611749		★☆☆☆☆ Found in Text Mining only
Exudative age-related macular degeneration	Exudative Macular Degeneration	GWASCAT_DG	26691988		★☆☆☆☆ Found in Text Mining only
exudative macular degeneration	Exudative macular degeneration	GWASCAT_DG	26691988		★☆☆☆☆ Found in Text Mining only
FUNDUS DYSTROPHY, PSEUDOINFLAMMATORY, OF SORSBY	FUNDUS DYSTROPHY, PSEUDOINFLAMMATORY, OF SORSBY	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Geographic Atrophy	Geographic Atrophy	GWASCAT_DG	26691988		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen Storage Disease Type II	Glycogen storage disease	Pubtator	32979492	Associate	★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	GWASCAT_DG	24487271		★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	21906714, 23422939, 31583032, 33618707	Associate	★☆☆☆☆ Found in Text Mining only
Mitral Valve Stenosis	Mitral Valve Stenosis	BEFREE	16972123		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	BEFREE	14991350, 16972123, 18755822		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	LHGDN	18755822		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15336652, 16082384		★☆☆☆☆ Found in Text Mining only
Osteoarthritis Knee	Osteoarthritis	Pubtator	26068512	Associate	★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	33725949	Associate	★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	30046897		★☆☆☆☆ Found in Text Mining only
Prostatic Hyperplasia	Prostatic hyperplasia	Pubtator	30988330	Associate	★☆☆☆☆ Found in Text Mining only
Pyoderma Gangrenosum	Pyoderma Gangrenosum	GWASCAT_DG	24487271		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	10674637, 10788672, 11340362, 11840510, 14732590, 15900227, 16511335, 17366345, 19102774, 19766700		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	LHGDN	14732590, 15900227, 16511335		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	16511335, 17366345, 19102774, 19766700		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	22571925	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia and related disorders	Schizophrenia	PSYGENET_DG	20050925		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	33253641	Associate	★☆☆☆☆ Found in Text Mining only