SYNGR1 synaptogyrin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYNGR1provided by HGNC
Official Full Name: synaptogyrin 1provided by HGNC
Primary source: HGNC:HGNC:11498
See related: Ensembl:ENSG00000100321 MIM:603925; AllianceGenome:HGNC:11498
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
Summary: This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 53.1), ovary (RPKM 17.1) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (39349991..39385575)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (39820668..39856199)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (39745996..39781580)

Chromosome 22 - NC_000022.11 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?

SYNGR1 was soluble and stable in a variety of mild detergents and multiple biophysical methods confirmed the folded state of the protein.
Title: Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1.
The results of association study support a contribution of SYNGR1 to schizophrenia susceptibility.
Title: Association study and mutational screening of SYNGR1 as a candidate susceptibility gene for schizophrenia.
A case-control study with synaptogyrin 1 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.
Observational study of gene-disease association. (HuGE Navigator)
Title: No association between bipolar disorder and syngr1 or synapsin II polymorphisms in the Han Chinese population.
These mutations were not found in 507 control subjects, suggesting further functional assays are warranted to verify their relevance to the pathogenesis of schizophrenia.
Title: Identification of rare mutations of synaptogyrin 1 gene in patients with schizophrenia.
Our results support SYNGR1 as a probable susceptibility gene for schizophrenia and bipolar disorder.
Title: SYNGR1 is associated with schizophrenia and bipolar disorder in southern India.
This research found a novel nonsense mutation (Trp27Ter) in exon 2 of the SYNGR1 gene in a family multiply affected with schizophrenia. And expressed in the brain.
Title: A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia.

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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

EBI GWAS Catalog

Description
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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

D22S1047 (e-PCR)
- UniSTS:7454

RH121595 (e-PCR)
- UniSTS:134367

SHGC-84542 (e-PCR)
- UniSTS:102883

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in protein targeting	IEA Inferred from Electronic Annotation more info
involved_in regulated exocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of long-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of short-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic vesicle membrane organization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in azurophil granule membrane	TAS Traceable Author Statement more info
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in neuromuscular junction	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: synaptogyrin-1

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_047102.1 RefSeqGene

Range

5043..40627

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_004711.5 → NP_004702.2 synaptogyrin-1 isoform 1a

See identical proteins and their annotated locations for NP_004702.2

Status: REVIEWED

Description

Transcript Variant: This variant (1a) represents the longest transcript and encodes the longest predominantly expressed isoform.

Source sequence(s)

AA412350, AJ002305, BC000731, BI667990, BX501388, DA337769

Consensus CDS

CCDS13989.1

UniProtKB/Swiss-Prot

A6NP69, A8K0E2, O43757, O43758, O43759, Q53Y02, Q96J56, Q9UGZ4

Related

ENSP00000332287.5, ENST00000328933.10

Conserved Domains (1) summary

pfam01284
Location:21 → 167

MARVEL; Membrane-associating domain
NM_145731.4 → NP_663783.1 synaptogyrin-1 isoform 1b

See identical proteins and their annotated locations for NP_663783.1

Status: REVIEWED

Description

Transcript Variant: This variant (1b) has a distinct 3' UTR and contains an alternate 3' coding exon, as compared to variant 1a. The encoded isoform (1b) has a distinct C-terminus, compared to isoform 1a.

Source sequence(s)

AJ002304, AW304782, BC000731, BI667990

Consensus CDS

CCDS13990.1

UniProtKB/TrEMBL

B5MCD7

Related

ENSP00000318845.4, ENST00000318801.8

Conserved Domains (1) summary

pfam01284
Location:21 → 167

MARVEL; Membrane-associating domain
NM_145738.3 → NP_663791.1 synaptogyrin-1 isoform 1c

See identical proteins and their annotated locations for NP_663791.1

Status: REVIEWED

Description

Transcript Variant: This variant (1c) encodes the shortest isoform. It contains a distinct 5' UTR and 5' coding region resulting in a frameshift and downstream translation initiation site, when compared to isoform 1a.

Source sequence(s)

AJ002303, AJ002304, AL022326, AW304782

Consensus CDS

CCDS13991.1

UniProtKB/Swiss-Prot

O43759

Related

ENSP00000370946.4, ENST00000381535.4

Conserved Domains (1) summary

pfam01284
Location:35 → 168

MARVEL; Membrane-associating domain