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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6853
Gene name	Synapsin I
Gene symbol	SYN1
Synonyms (NCBI Gene)	EPILXEPILX1MRX50SYN1aSYN1bSYNI
Chromosome	X
Chromosome location	Xp11.3-p11.23
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

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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

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miRTarBase ID	miRNA	Experiments	Reference
MIRT018882	hsa-miR-335-5p	Microarray	18185580
MIRT733606	hsa-miR-140-5p	ImmunofluorescenceqRT-PCRWestern 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

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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

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

489

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Epilepsy	Pathogenic	rs2147912740	RCV004798924
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders	Pathogenic; Likely pathogenic	rs2147912005, rs2147912333, rs2147927599, rs2147928664, rs2147912740, rs941190653, rs2147933505, rs2147913419, rs2147912165, rs2147912678, rs2147912440, rs923033810, rs2519712575, rs2519685866, rs2519686907 View all (31 more)	RCV001379126 RCV001378193 RCV001380293 RCV001388304 RCV001733750 RCV003772104 RCV001786325 RCV002468644 RCV002007256 RCV001972459 RCV002001459 RCV002508162 RCV002508164 RCV002508166 RCV002508169 RCV002508170 RCV002508171 RCV002508172 RCV002291324 RCV002291326 RCV002291327 RCV002291328 RCV002291273 RCV002837594 RCV003064162 RCV003040987 RCV000010542 RCV003509886 RCV003510848 RCV003510299 RCV003622768 RCV003622677 RCV003622963 RCV003623202 RCV005091219 RCV000555972 RCV000590941 RCV000034815 RCV003313114 RCV000805246 RCV001002794 RCV001027689 RCV002508156 RCV001204925 RCV001227508 RCV002508159
Intellectual disability	Likely pathogenic; Pathogenic	rs2057891984	RCV001260825
Intellectual disability, X-linked 50	Pathogenic; Likely pathogenic	rs2147927599, rs941190653, rs2519686818, rs753517348, rs1556860638, rs2057891984, rs2057941303	RCV002246361 RCV001762014 RCV002508167 RCV004515771 RCV003313114 RCV002508157 RCV001291935
Seizure	Pathogenic	rs2057771219	RCV001201164
SYN1-related disorder	Likely pathogenic; Pathogenic	rs2147913419, rs397514679	RCV003401758 RCV003407398

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Autism spectrum disorder	Uncertain significance	rs2519687670	RCV003127352
Cholangiocarcinoma	Benign	rs12394306, rs377385507	RCV005889313 RCV005868052
History of neurodevelopmental disorder	Benign; Likely benign; Conflicting classifications of pathogenicity	rs1142636, rs62636605, rs187134574, rs145911562, rs373928763, rs200533370, rs772106134	RCV000715263 RCV000716489 RCV000716736 RCV000715821 RCV000717595 RCV000715955 RCV000721050
Neurodevelopmental disorder	Uncertain significance	rs2057770933	RCV001844411
See cases	Uncertain significance	rs745743511	RCV002287442
SYN1-related neurodevelopmental disorder	Uncertain significance	rs2147912337	RCV005626561
X-linked complex neurodevelopmental disorder	Conflicting classifications of pathogenicity	rs372445055	RCV002225495

SYN1 (synapsin I)