Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	HLA-A
Approved Name	major histocompatibility complex, class I, A
Location	6p21.3
Position	chr6:29941260-29945884, 1
External Links	HGNC: 4931 Entrez Gene: 3105 Ensembl: ENSG00000206503 UCSC: uc003nol.3
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Jun, T. Y.,2002	Other variant: HLA-A_polymorphism	The results of the present study suggest that HLA alleles may not confer susceptibility to bipolar disorder in the Korean population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 42)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005102	receptor binding	molecular function	IBA; IPI[19124746]	37
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0005887	integral component of plasma membrane	cellular component	NAS[6609814]	158
GO:0016020	membrane	cellular component	IDA[19946888]	137

GO terms by database search (count: 38)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0070971	endoplasmic reticulum exit site	cellular component	IDA[20946353]	3
GO:2000568	positive regulation of memory T cell activation	biological process	IDA[22031944]	1
GO:0050776	regulation of immune response	biological process	TAS	4
GO:0042270	protection from natural killer cell mediated cytotoxicity	biological process	IDA[18502829]; IDA[18502829]	2
GO:0032729	positive regulation of interferon-gamma production	biological process	IDA[22031944]	7
GO:0044822	poly(A) RNA binding	molecular function	IDA[22658674]	44
GO:0009986	cell surface	cellular component	IDA[22031944]; ISS	40
GO:0000139	Golgi membrane	cellular component	TAS	36
GO:0005797	Golgi medial cisterna	cellular component	IDA[8805302]	1
GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	biological process	TAS	7
GO:0019221	cytokine-mediated signaling pathway	biological process	TAS	23
GO:0002480	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent	biological process	TAS	3
GO:2000566	positive regulation of CD8-positive, alpha-beta T cell proliferation	biological process	IDA[25631937]	1
GO:0005794	Golgi apparatus	cellular component	IDA[20946353]; ISS	60
GO:0050690	regulation of defense response to virus by virus	biological process	TAS	4
GO:0016032	viral process	biological process	IEA; TAS	26
GO:0042612	MHC class I protein complex	cellular component	IDA[22031944]; ISS	3
GO:0016045	detection of bacterium	biological process	IMP[22321387]	2
GO:0030670	phagocytic vesicle membrane	cellular component	TAS	6
GO:0046977	TAP binding	molecular function	IDA[8617941]	2
GO:0060337	type I interferon signaling pathway	biological process	TAS	7
GO:0001916	positive regulation of T cell mediated cytotoxicity	biological process	IDA[22031944]; IEA	4
GO:0005515	protein binding	molecular function	IPI[23401559]	563
GO:0042605	peptide antigen binding	molecular function	IBA; IDA[22031944]; IMP[23566939]; ISS	3
GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	cellular component	TAS	3
GO:0006955	immune response	biological process	IMP[22321387]; NAS[6609814]	19
GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	biological process	TAS	5
GO:0042608	T cell receptor binding	molecular function	IDA[8955188]	2
GO:0002486	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	biological process	IDA[22031944]	2
GO:0042590	antigen processing and presentation of exogenous peptide antigen via MHC class I	biological process	TAS	5
GO:0012507	ER to Golgi transport vesicle membrane	cellular component	TAS	3
GO:0005783	endoplasmic reticulum	cellular component	IDA[20946353]; ISS	49
GO:0019731	antibacterial humoral response	biological process	IDA[25631937]	2
GO:0031901	early endosome membrane	cellular component	TAS	8
GO:0050830	defense response to Gram-positive bacterium	biological process	IDA[25631937]	7
GO:0060333	interferon-gamma-mediated signaling pathway	biological process	TAS	10
GO:0030881	beta-2-microglobulin binding	molecular function	IC[25631937]; IDA[3309677]; IMP[23566939]; ISS	1
GO:0070062	extracellular vesicular exosome	cellular component	IDA[11487543]	176

Gene related KEGG pathways (count: 7)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04514	Cell adhesion molecules (CAMs)	14

KEGG pathways by database search (count: 6)

ID	Name	No. of Genes in BDgene
hsa05320	Autoimmune thyroid disease	6
hsa05330	Allograft rejection	6
hsa05332	Graft-versus-host disease	7
hsa04650	Natural killer cell mediated cytotoxicity	13
hsa04940	Type I diabetes mellitus	10
hsa04612	Antigen processing and presentation	7

Gene related BioCarta pathways (count: 3)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 3)

ID	Name	No. of Genes in BDgene
mhcPathway	Antigen Processing and Presentation	1
nkcellsPathway	Ras-Independent pathway in NK cell-mediated cytotoxicity	3
ctlPathway	CTL mediated immune response against target cells	1

Gene related interactors from protein-protein interactions data in HPRD (count: 20)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
HLA-A	B2M	NO	in vitro;in vivo	93026 , 11502003 , 1448153
HLA-A	CD8A	NO	in vitro	10809759 , 9177355
HLA-A	TRB@	NO	in vitro	10435578 , 14563323 , 8906788 , 8955188 , 9586631
HLA-A	CANX	NO	in vivo	17467700
HLA-A	ERBB2	YES	in vitro	10593938
HLA-A	BCAP31	NO	in vivo	11163199
HLA-A	TRA@	NO	in vitro	9586631
HLA-A	MAGEA4	NO	in vitro	11502003
HLA-A	UBB	NO	in vivo	14722266
HLA-A	MAGEA1	NO	in vitro	8647853
HLA-A	APLP2	NO	in vivo	19184004
HLA-A	KIR3DL2	NO	in vitro;in vivo	8617928 , 8760804
HLA-A	LILRB2	NO	in vitro	12853576 , 9531263
HLA-A	DEK	NO	in vitro;in vivo	9684994
HLA-A	PRKCA	NO	in vitro;in vivo	2941417
HLA-A	LILRB1	NO	in vitro	12897781
HLA-A	TAPBP	NO	in vitro;in vivo	8769474
HLA-A	DERL1	NO	in vitro	15215855
HLA-A	SRC	NO	in vitro	6304688 , 6333425
HLA-A	PDIA3	NO	in vitro;in vivo	9545232 , 17467700

Related other genetic factors

Gene related SNPs (count: 2)

Literature-origin SNPs (count: 0)

LD-proxies (count: 2)

rs_ID	Literature-origin SNPs with LD	Location	Functional Annotation
rs439935		chrCHR_HSCHR6_MHC_SSTO_CTG1:29929461 - 29929461(1)	downstream_gene_variant; upstream_gene_variant
rs1655900		chrCHR_HSCHR6_MHC_SSTO_CTG1:29938126 - 29938126(1)	downstream_gene_variant; 3_prime_UTR_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 1)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
HLA-A_polymorphism	others		1 (0/1/0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 6	chr6:0-170805979	3 (0/3/0)
6p22	chr6:15200000-30500000	1 (0/1/0)
6p23-p21.1	chr6:13400000-46200000	1 (1/0/0)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr6:29941260..29945884 View in gBrowse