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SYNGR1 synaptogyrin 1 [ Homo sapiens (human) ]

Gene ID: 9145, updated on 7-Apr-2024

Summary

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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
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Genomic context

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See SYNGR1 in Genome Data Viewer
Location:
22q13.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39349991..39385575)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39820668..39856199)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39745996..39781580)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39712838-39713726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39715507-39716396 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39716397-39717285 Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene Sharpr-MPRA regulatory region 3662 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene ribosomal protein L3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39753396-39753924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39755840-39756638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39757867-39758453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39758454-39759039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39769919-39770434 Neighboring gene Sharpr-MPRA regulatory region 1576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811177-39811678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811679-39812178 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39824885-39825527 Neighboring gene uncharacterized LOC100506472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39829518-39830236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39830237-39830954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19048 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39843664-39843855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39844165-39845073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19050 Neighboring gene CRISPRi-validated cis-regulatory element chr22.2018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39866163-39867092 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39869361-39869718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39869884-39870813 Neighboring gene beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase Neighboring gene MGAT3 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1. Löw C, et al. PLoS One, 2012. PMID 22675529, Free PMC Article
  2. Association study and mutational screening of SYNGR1 as a candidate susceptibility gene for schizophrenia. Iatropoulos P, et al. Psychiatr Genet, 2009 Oct. PMID 19641478
  3. Identification of rare mutations of synaptogyrin 1 gene in patients with schizophrenia. Cheng MC, et al. J Psychiatr Res, 2007 Dec. PMID 17049558
  4. SYNGR1 is associated with schizophrenia and bipolar disorder in southern India. Verma R, et al. J Hum Genet, 2005. PMID 16215643
  5. A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia. Verma R, et al. Biol Psychiatry, 2004 Jan 15. PMID 14732601

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: TAB1

Homology

Clone Names

  • MGC1939

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 azurophil granule membrane TAS
Traceable Author Statement
more info
  
located_in melanosome IEA
Inferred from Electronic Annotation
more info
  
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

  1. NG_047102.1 RefSeqGene

    Range
    5043..40627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39349991..39385575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39820668..39856199
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43759.2 GenPept UniProtKB/Swiss-Prot:O43759

Gene LinkOut

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