Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	6853
Gene name Gene Name - the full gene name approved by the HGNC.	Synapsin I
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SYN1
Synonyms (NCBI Gene) Gene synonyms aliases	EPILX, EPILX1, MRX50, SYN1a, SYN1b, SYNI
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xp11.3-p11.23
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(22)

SNP ID	Visualize variation	Clinical significance	Consequence
rs41298474	G>A	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Coding sequence variant, missense variant
rs137852560	C>T	Pathogenic	Coding sequence variant, stop gained
rs145911562	T>C	Conflicting-interpretations-of-pathogenicity, benign, likely-benign	Synonymous variant, coding sequence variant
rs150248483	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, coding sequence variant
rs200533370	T>C	Conflicting-interpretations-of-pathogenicity, benign, likely-benign	Missense variant, coding sequence variant
rs375440874	A>G	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs397514679	G>A	Pathogenic	Stop gained, coding sequence variant
rs397514680	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs587781185	C>T	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs757027813	G>A,T	Likely-benign, pathogenic	Synonymous variant, coding sequence variant, stop gained
rs886042481	C>A,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs1064797369	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1183386473	C>A,T	Likely-pathogenic	Missense variant, stop gained, coding sequence variant
rs1556857412	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1556857481	->G	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1556860638	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1556860663	T>A	Likely-pathogenic	Splice acceptor variant
rs1569322834	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1603050544	G>A	Pathogenic	Coding sequence variant, stop gained
rs1603051674	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1603078587	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1603078614	G>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all(29)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018882	hsa-miR-335-5p	Microarray	18185580
MIRT733606	hsa-miR-140-5p	Immunofluorescence, qRT-PCR, Western blotting	33987369
MIRT1405388	hsa-miR-1290	CLIP-seq
MIRT1405389	hsa-miR-140-3p	CLIP-seq
MIRT1405390	hsa-miR-1915	CLIP-seq
MIRT1405391	hsa-miR-197	CLIP-seq
MIRT1405392	hsa-miR-296-3p	CLIP-seq
MIRT1405393	hsa-miR-3154	CLIP-seq
MIRT1405394	hsa-miR-3170	CLIP-seq
MIRT1405395	hsa-miR-3937	CLIP-seq
MIRT1405396	hsa-miR-4260	CLIP-seq
MIRT1554366	hsa-miR-1827	CLIP-seq
MIRT1554367	hsa-miR-4257	CLIP-seq
MIRT1554368	hsa-miR-4496	CLIP-seq
MIRT1554369	hsa-miR-4738-3p	CLIP-seq
MIRT1554370	hsa-miR-940	CLIP-seq
MIRT2121599	hsa-miR-4704-3p	CLIP-seq
MIRT2343630	hsa-miR-2110	CLIP-seq
MIRT2343631	hsa-miR-3150a-3p	CLIP-seq
MIRT1405394	hsa-miR-3170	CLIP-seq
MIRT2343632	hsa-miR-4450	CLIP-seq
MIRT2343633	hsa-miR-4667-5p	CLIP-seq
MIRT2343634	hsa-miR-4700-5p	CLIP-seq
MIRT2343635	hsa-miR-4799-5p	CLIP-seq
MIRT2343630	hsa-miR-2110	CLIP-seq
MIRT2343631	hsa-miR-3150a-3p	CLIP-seq
MIRT1405394	hsa-miR-3170	CLIP-seq
MIRT2343632	hsa-miR-4450	CLIP-seq
MIRT2343635	hsa-miR-4799-5p	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
EGR1	Activation	8195167
REST	Unknown	21693630

Show/Hide all(43)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000795	Component	Synaptonemal complex	IEA
GO:0003779	Function	Actin binding	IEA
GO:0005515	Function	Protein binding	IPI	23406870
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	TAS	15217342
GO:0005794	Component	Golgi apparatus	IEA
GO:0005856	Component	Cytoskeleton	IDA	24327345
GO:0007268	Process	Chemical synaptic transmission	IEA
GO:0007268	Process	Chemical synaptic transmission	TAS	2110562
GO:0007269	Process	Neurotransmitter secretion	IEA
GO:0007269	Process	Neurotransmitter secretion	IEA
GO:0008021	Component	Synaptic vesicle	IEA
GO:0008021	Component	Synaptic vesicle	TAS	16141272
GO:0014069	Component	Postsynaptic density	IEA
GO:0019901	Function	Protein kinase binding	IEA
GO:0019901	Function	Protein kinase binding	ISS
GO:0030424	Component	Axon	IEA
GO:0030425	Component	Dendrite	IEA
GO:0030425	Component	Dendrite	IEA
GO:0030672	Component	Synaptic vesicle membrane	IBA
GO:0030672	Component	Synaptic vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0042995	Component	Cell projection	IEA
GO:0044297	Component	Cell body	IEA
GO:0045202	Component	Synapse	IEA
GO:0046928	Process	Regulation of neurotransmitter secretion	TAS	21563316
GO:0048306	Function	Calcium-dependent protein binding	IEA
GO:0048666	Process	Neuron development	IEA
GO:0048786	Component	Presynaptic active zone	IEA
GO:0050804	Process	Modulation of chemical synaptic transmission	IEA
GO:0050808	Process	Synapse organization	IBA
GO:0050808	Process	Synapse organization	IEA
GO:0097091	Process	Synaptic vesicle clustering	IBA
GO:0098685	Component	Schaffer collateral - CA1 synapse	IEA
GO:0098693	Process	Regulation of synaptic vesicle cycle	IEA
GO:0098793	Component	Presynapse	IDA	21441247
GO:0098793	Component	Presynapse	IEA
GO:0098850	Component	Extrinsic component of synaptic vesicle membrane	IEA
GO:0099504	Process	Synaptic vesicle cycle	IEA
GO:0106006	Function	Cytoskeletal protein-membrane anchor activity	TAS	2110562
GO:2000300	Process	Regulation of synaptic vesicle exocytosis	IMP	21441247
GO:2000300	Process	Regulation of synaptic vesicle exocytosis	NAS	10099709

MIM	HGNC	e!Ensembl
313440	11494	ENSG00000008056

Protein

UniProt ID

P17600

Protein name

Synapsin-1 (Brain protein 4.1) (Synapsin I)

Protein function

Neuronal phosphoprotein that coats synaptic vesicles, and binds to the cytoskeleton. Acts as a regulator of synaptic vesicles trafficking, involved in the control of neurotransmitter release at the pre-synaptic terminal (PubMed:21441247, PubMed:

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF10581	Synapsin_N	1 → 32	Synapsin N-terminal	Domain
PF02078	Synapsin	111 → 212	Synapsin, N-terminal domain	Domain
PF02750	Synapsin_C	214 → 416	Synapsin, ATP binding domain	Domain

Sequence

MNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPGAHSPGATPGPGTATAERSSGVAPA
ASPAAPSPGSSGGGGFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAASRVLLVID
EPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKP
DFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSVNSLHSVYNFCDKPWVFAQMVRLHKKLG
TEEFPLIDQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKT
YATAEPFIDAKYDVRVQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTC
SEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMAQALPR
QRQRDASPGRGSHGQTPSPGALPLGRQTSQQPAGPPAQQRPPPQGGPPQPGPGPQRQGPP
LQQRPPPQGQQHLSGLGPPAGSPLPQRLPSPTSAPQQPASQAAPPTQGQGRQSRPVAGGP
GAPPAARPPASPSPQRQAGPPQATRQTSVSGPAPPKASGAPPGGQQRQGPPQKPPGPAGP
TRQASQAGPVPRTGPPTTQQPRPSGPGPAGRPKPQLAQKPSQDVPPPATAAAGGPPHPQL
NKSQSLTNAFNLPEPAPPRPSLSQDEVKAETIRSLRKSFASLFSD

Sequence length

705

Interactions

View interactions

	Reactome
			Serotonin Neurotransmitter Release Cycle Dopamine Neurotransmitter Release Cycle

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Epilepsy, X-Linked, With Variable Learning Disabilities And Behavior Disorders	Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders	rs1556857481, rs1603050544, rs1603078587, rs1603051674, rs137852560, rs397514679, rs757027813, rs1183386473, rs1556860663	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Mental Retardation, X-Linked	Intellectual disability, X-linked 50	N/A	N/A	ClinVar
Neurodevelopmental Disorders	X-linked complex neurodevelopmental disorder	N/A	N/A	GenCC

SYN1 (synapsin I)