Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

ADD to My Gene Set

Comment on Gene

View All Comments on Gene

Basic Info

Approved Symbol	SYNGR1
Approved Name	synaptogyrin 1
Location	22q13
Position	chr22:39349925-39385588, 1
External Links	HGNC: 11498 Entrez Gene: 9145 Ensembl: ENSG00000100321
No. of Studies	3 (Positive: 2; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 3)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Wang, Y.,2009	SNP: rs715505	The frequencies of the alleles or genotypes did not differ significantly between the case group and the control group.No association was found in this study.	Negative	Comment on Study
Yosifova, A.,2009	SNP: rs715505, rs909685	Significant association of SNP in this gene with BD in our population was observed.	Positive	Comment on Study
Verma, R.,2005(a)	SNP: rs2010904, rs2012906, rs4821888, rs6001566, rs715505, rs739363, rs760741, rs760742, rs909685 Other variant: SYNGR1_exon6_Asn(ins/del), SYNGR1_exon3_Ser97Ser	Our results support SYNGR1 as a probable susceptibility gene for SCZ and BPAD. Also, the observed association of SYNGR1 with both SCZ and BPAD suggests the likely involvement of a common pathway in the etiology of these disorders.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 9)

GO terms by PBA (count: 1)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016021	integral component of membrane	cellular component	IEA; NAS[9760194]	219

GO terms by database search (count: 8)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0048169	regulation of long-term neuronal synaptic plasticity	biological process	ISS	8
GO:0006605	protein targeting	biological process	IEA	5
GO:0031594	neuromuscular junction	cellular component	IBA	9
GO:0030672	synaptic vesicle membrane	cellular component	IBA	7
GO:0042470	melanosome	cellular component	IEA	15
GO:0005515	protein binding	molecular function	IPI[25416956]	563
GO:0048172	regulation of short-term neuronal synaptic plasticity	biological process	ISS	4
GO:0030054	cell junction	cellular component	IEA	88

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 0)

Related other genetic factors

Gene related SNPs (count: 23)

Literature-origin SNPs (count: 9)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs760742	chr22:39359185 - 39359185(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs760741	chr22:39357261 - 39357261(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs2010904	chr22:39356986 - 39356986(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)
rs6001566	chr22:39378443 - 39378443(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	1(0/1/0)
rs909685	chr22:39351666 - 39351666(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	2(1/1/0)
rs4821888	chr22:39374592 - 39374592(1)	intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2012906	chr22:39365240 - 39365240(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs715505	chr22:39355246 - 39355246(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	3(1/2/0)
rs739363	chr22:39364878 - 39364878(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 14)

rs_ID	Location	Functional Annotation
rs2049986	chr22:39360849 - 39360849(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs715503	chr22:39362248 - 39362248(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs2069235	chr22:39351775 - 39351775(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3788551	chr22:39356522 - 39356522(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9607634	chr22:39349236 - 39349236(1)	upstream_gene_variant
rs5757642	chr22:39368819 - 39368819(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs5750806	chr22:39371006 - 39371006(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs17001013	chr22:39369374 - 39369374(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs16985831	chr22:39369288 - 39369288(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs5757644	chr22:39370435 - 39370435(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7286714	chr22:39369599 - 39369599(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs2012907	chr22:39365250 - 39365250(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs16985827	chr22:39369220 - 39369220(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs16985820	chr22:39368549 - 39368549(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 2)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
SYNGR1_exon3_Ser97Ser	point mutation	exon3	1 (1/0/0)
SYNGR1_exon6_Asn(ins/del)	insertion/deletion	exon6	1 (0/1/0)

Gene related regions (count: 5)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
22q12.3-13.32	chr22:31800000-49100000	1 (0/1/0)
Chr 22	chr22:0-50818468	2 (0/1/1)
22q12.3-q13.33	chr22:31800000-50818468	1 (1/0/0)
22q13	chr22:37200000-50818468	1 (1/0/0)
22q13.1	chr22:37200000-40600000	1 (0/0/1)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Description	Result Category
16215643	Our results support SYNGR1 as a probable susceptibility gene for SCZ and BPAD. Also, the observed association of SYNGR1 with both SCZ and BPAD suggests the likely involvement of a common pathway in the etiology of these disorders.	Positive

Overlap with SZ from candidate gene intersection analysis (count: 4)

Reference	ID in SZGene	Result Category
19158809	466	Negative
19641478	466	Positive
17049558	466	Negative
16215643	466	Positive

Gene relationship with MDD

View in gBrowse

Region: chr22:39349925..39385588 View in gBrowse