SYN1 synapsin I [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYN1provided by HGNC
Official Full Name: synapsin Iprovided by HGNC
Primary source: HGNC:HGNC:11494
See related: Ensembl:ENSG00000008056 MIM:313440; AllianceGenome:HGNC:11494
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SYNI; EPILX; MRX50; SYN1a; SYN1b; EPILX1
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 synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein encoded serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations in this gene may be associated with X-linked disorders with primary neuronal degeneration such as Rett syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 99.5) and adrenal (RPKM 5.6) See more
Orthologs: mouse all
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Genomic context

Location:: Xp11.3-p11.23

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (47571901..47619857, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (46981791..47029757, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (47431300..47479256, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Familial SYN1 variants related neurodevelopmental disorders in Asian pediatric patients.
Title: Familial SYN1 variants related neurodevelopmental disorders in Asian pediatric patients.
Novel SYN1 Variant in Two Brothers with Focal Epilepsy and Their Prompt Response to Valproate.
Title: Novel SYN1 Variant in Two Brothers with Focal Epilepsy and Their Prompt Response to Valproate.
An interaction between synapsin and C9orf72 regulates excitatory synapses and is impaired in ALS/FTD.
Title: An interaction between synapsin and C9orf72 regulates excitatory synapses and is impaired in ALS/FTD.
Synapsin Condensates Recruit alpha-Synuclein.
Title: Synapsin Condensates Recruit alpha-Synuclein.
Cooperative function of synaptophysin and synapsin in the generation of synaptic vesicle-like clusters in non-neuronal cells.
Title: Cooperative function of synaptophysin and synapsin in the generation of synaptic vesicle-like clusters in non-neuronal cells.
Semaphorin 3A controls enteric neuron connectivity and is inversely associated with synapsin 1 expression in Hirschsprung disease.
Title: Semaphorin 3A controls enteric neuron connectivity and is inversely associated with synapsin 1 expression in Hirschsprung disease.
Autoantibodies to synapsin I sequestrate synapsin I and alter synaptic function.
Title: Autoantibodies to synapsin I sequestrate synapsin I and alter synaptic function.
A surface-based group study using novel diffusion and quantitative multiparametric imaging on 13 SYN1Q555X mutation carriers and 13 age- and sex-matched controls. Results showed significant microstructural alterations in several regions usually involved in oral and written language as well as dyslexia. The most significant changes in these regions were lowered mean diffusivity and increased fractional anisotropy.
Title: Effects of SYN1(Q555X) mutation on cortical gray matter microstructure.
Authors identified the c.236 C > G/p.S79W mutation in SYN1 as causative for the non-syndromic ID of the MRX50 family. Accordingly, the in vitro characterization of S79W SynI clearly indicates that the mutation does not interfere with neurodevelopmental aspects, but perturbs spontaneous SV exocytosis, SV clustering and SV lateral mobility along axons.
Title: A novel SYN1 missense mutation in non-syndromic X-linked intellectual disability affects synaptic vesicle life cycle, clustering and mobility.
These findings contribute to previous work showing dysregulation of Synapsins, particularly SYN2, in mood disorders and improve our understanding of the regulatory mechanisms that precipitate these changes likely leading to the BD or MDD phenotype.
Title: DNA hypomethylation of Synapsin II CpG islands associates with increased gene expression in bipolar disorder and major depression.

Submit: New GeneRIF Correction See all GeneRIFs (28)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders MedGen: C5774177 OMIM: 300491 GeneReviews: Not available	not available
Intellectual disability, X-linked 50 MedGen: C1848087 OMIM: 300115 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2022-07-12) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2022-07-12) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Treatment of microglia cells with HIV-1 Tat shows TAU5 and synapsin-1 positive inclusions in cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-L24038 (e-PCR)
- UniSTS:48135

AL023622 (e-PCR)
- UniSTS:68642

STS-M58378 (e-PCR)
- UniSTS:11300

STS-AA001911 (e-PCR)
- UniSTS:74040

RH93525 (e-PCR)
- UniSTS:85565

STS-M13829 (e-PCR)
- UniSTS:72051

GDB:192509 (e-PCR)
- UniSTS:98973

WI-6972 (e-PCR)
- UniSTS:18142

RH79877 (e-PCR)
- UniSTS:89581

SGC30176 (e-PCR)
- UniSTS:47359

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	TAS Traceable Author Statement more info	PubMed
enables actin binding	IEA Inferred from Electronic Annotation more info
enables calcium-dependent protein binding	IEA Inferred from Electronic Annotation more info
enables cytoskeletal protein-membrane anchor activity	TAS Traceable Author Statement more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in neuron development	IEA Inferred from Electronic Annotation more info
involved_in regulation of neurotransmitter secretion	TAS Traceable Author Statement more info	PubMed
involved_in regulation of synaptic vesicle cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synaptic vesicle exocytosis	NAS Non-traceable Author Statement more info	PubMed
involved_in synapse organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse organization	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle clustering	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle cycle	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cell body	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in extrinsic component of synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in presynapse	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic active zone	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle	TAS Traceable Author Statement more info	PubMed
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptonemal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: synapsin-1

Names: brain protein 4.1; synapsin Ib

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008437.1 RefSeqGene

Range

5001..52957

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006950.3 → NP_008881.2 synapsin-1 isoform Ia

See identical proteins and their annotated locations for NP_008881.2

Status: REVIEWED

Description

Transcript Variant: This variant (Ia) represents the longer transcript, and encodes the longer isoform (Ia). This isoform (Ia) contains a distinct domain E, as compared to isoform Ib.

Source sequence(s)

AI929645, BC036711, BC048799, Z84466

Consensus CDS

CCDS14280.1

UniProtKB/Swiss-Prot

B1AJQ1, O75825, P17600, Q5H9A9

Related

ENSP00000295987.7, ENST00000295987.13

Conserved Domains (4) summary

PRK07764
Location:494 → 686

PRK07764; DNA polymerase III subunits gamma and tau; Validated

pfam02078
Location:115 → 212

Synapsin; N-terminal domain

pfam10581
Location:1 → 27

Synapsin_N; Synapsin N-terminal

cl17255
Location:214 → 416

CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
NM_133499.2 → NP_598006.1 synapsin-1 isoform Ib

See identical proteins and their annotated locations for NP_598006.1

Status: REVIEWED

Description

Transcript Variant: This variant (Ib) utilizes an alternative splice acceptor site in terminal exon compared to variant Ia, resulting in the lack of an internal segment and a frameshift. This variant encodes isoform Ib, which contains a shorter carboxyl terminus and a distinct domain F, as compared to isoform Ia.

Source sequence(s)

AI929645, BC036711, BC048799

Consensus CDS

CCDS35233.1

UniProtKB/Swiss-Prot

P17600

Related

ENSP00000343206.4, ENST00000340666.5

Conserved Domains (4) summary

PHA03247
Location:498 → 669

PHA03247; large tegument protein UL36; Provisional

pfam02078
Location:115 → 212

Synapsin; N-terminal domain

pfam10581
Location:1 → 27

Synapsin_N; Synapsin N-terminal

cl17255
Location:214 → 416

CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain