SYN2 synapsin II [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYN2provided by HGNC
Official Full Name: synapsin IIprovided by HGNC
Primary source: HGNC:HGNC:11495
See related: Ensembl:ENSG00000157152 MIM:600755; AllianceGenome:HGNC:11495
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: SYNII
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 encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014]
Expression: Biased expression in brain (RPKM 41.0) and fat (RPKM 5.3) See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.2

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (12004388..12192032)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (12002345..12190266)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (12045862..12233532)

Chromosome 3 - NC_000003.12 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?

Our findings support that ASB16-AS1 and SYN2 may represent two novel functional genes underlying bone mineral density variation
Title: Integration of summary data from GWAS and eQTL studies identified novel causal BMD genes with functional predictions.
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.
Both GABRA6 and Synapsin II polymorphisms are important risk factors for the development of idiopathic generalized epilepsy in a South Indian population.
Title: Association of GABRA6 1519 T>C (rs3219151) and Synapsin II (rs37733634) gene polymorphisms with the development of idiopathic generalized epilepsy.
Results identify SYN2 as a novel predisposing gene for autism spectrum disorders (ASD) and strengthen the hypothesis that a disturbance of synaptic homeostasis underlies ASD.
Title: SYN2 is an autism predisposing gene: loss-of-function mutations alter synaptic vesicle cycling and axon outgrowth.
Synapsin II is involved in the molecular pathway of lithium treatment in bipolar disorder
Title: Synapsin II is involved in the molecular pathway of lithium treatment in bipolar disorder.
SYN2 rs3773364 A>G polymorphism is not a risk factor for susceptibility to epilepsy in this case-control study and meta-analysis.
Title: Lack of association between synapsin II (SYN2) gene polymorphism and susceptibility epilepsy: a case-control study and meta-analysis.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Results from our study indicate the involvement of SYN2 gene polymorphism in conferring risk to epilepsy; however, the genetic variant does not seem to modulate drug-response in epilepsy pharmacotherapy.
Title: Association of intronic polymorphism rs3773364 A>G in synapsin-2 gene with idiopathic epilepsy.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
A case-control study with synapsin II was conducted in 506 bipolar disorder patients and 507 healthy individuals from the Han Chinese population. No association was found in this study.
Title: No association between bipolar disorder and syngr1 or synapsin II polymorphisms in the Han Chinese population.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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
Schizophrenia MedGen: C0036341 OMIM: 181500 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
New gene functions in megakaryopoiesis and platelet formation. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-76712 (e-PCR)
- UniSTS:78110

SHGC-14394 (e-PCR)
- UniSTS:10785

G16552 (e-PCR)
- UniSTS:69156

SHGC-76710 (e-PCR)
- UniSTS:45353

SHGC-84455 (e-PCR)
- UniSTS:104750

RH66385 (e-PCR)
- UniSTS:54

TIMP4_1491 (e-PCR)
- UniSTS:277817

AF096867 (e-PCR)
- UniSTS:163397

SHGC-76716 (e-PCR)
- UniSTS:18792

SHGC-53473 (e-PCR)
- UniSTS:44164

D3S732 (e-PCR)
- UniSTS:147599

SHGC-79283 (e-PCR)
- UniSTS:102799

RH80633 (e-PCR)
- UniSTS:91557

RH99325 (e-PCR)
- UniSTS:84157

D3S1259 (e-PCR)
- UniSTS:50365

WI-19747 (e-PCR)
- UniSTS:38098

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	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

Process	Evidence Code	Pubs
involved_in calcium-ion regulated exocytosis	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in neurotransmitter secretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle clustering	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle clustering	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of SNARE complex	IEA Inferred from Electronic Annotation more info
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: synapsin-2

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_011728.3 RefSeqGene

Range

5002..192646

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003178.6 → NP_003169.2 synapsin-2 isoform IIb

See identical proteins and their annotated locations for NP_003169.2

Status: REVIEWED

Description

Transcript Variant: This variant (IIb) is alternatively spliced at its 3' end, compared to variant IIa. It encodes isoform IIb, which contains a shorter C-terminus with a distinct domain I, compared to isoform IIa.

Source sequence(s)

ABBA01025208, AC022234, AC026166, AC091492

Consensus CDS

CCDS74901.1

UniProtKB/TrEMBL

Q59GM1

Related

ENSP00000484916.1, ENST00000620175.4

Conserved Domains (3) summary

pfam02078
Location:115 → 212

Synapsin; Synapsin, N-terminal domain

pfam02750
Location:214 → 416

Synapsin_C; Synapsin, ATP binding domain

pfam10581
Location:2 → 30

Synapsin_N; Synapsin N-terminal
NM_133625.6 → NP_598328.1 synapsin-2 isoform IIa

See identical proteins and their annotated locations for NP_598328.1

Status: REVIEWED

Description

Transcript Variant: This variant (IIa) represents the shorter transcript but encodes the longer isoform (IIa), which has an alternate C-terminus with distinct H and E domains, compared to isoform IIb.

Source sequence(s)

ABBA01025208, AC022234, AC026166, AC091492

Consensus CDS

CCDS74900.1

UniProtKB/Swiss-Prot

A0A087WW96, A0A087X2E3, A8MY98, Q92777

UniProtKB/TrEMBL

Q86VA8

Related

ENSP00000480050.1, ENST00000621198.5

Conserved Domains (3) summary

pfam02078
Location:115 → 212

Synapsin; Synapsin, N-terminal domain

pfam02750
Location:214 → 416

Synapsin_C; Synapsin, ATP binding domain

pfam10581
Location:2 → 30

Synapsin_N; Synapsin N-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

12004388..12192032

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006713311.4 → XP_006713374.1 synapsin-2 isoform X1

UniProtKB/TrEMBL

Q59GM1

Conserved Domains (3) summary

pfam02078
Location:115 → 212

Synapsin; Synapsin, N-terminal domain

pfam02750
Location:214 → 416

Synapsin_C; Synapsin, ATP binding domain

pfam10581
Location:2 → 30

Synapsin_N; Synapsin N-terminal
XM_006713312.5 → XP_006713375.1 synapsin-2 isoform X2

Conserved Domains (1) summary

pfam02750
Location:53 → 255

Synapsin_C; Synapsin, ATP binding domain
XM_006713313.3 → XP_006713376.1 synapsin-2 isoform X4

Conserved Domains (1) summary

cl17255
Location:1 → 159

ATP-grasp_4; ATP-grasp domain
XM_017007087.2 → XP_016862576.1 synapsin-2 isoform X3