Gene Report

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Basic Info

Approved Symbol	NFIX
Symbol Alias	NF1A
Approved Name	nuclear factor I/X (CCAAT-binding transcription factor)
Location	19p13.3
Position	chr19:12995608-13098796, 1
External Links	HGNC: 7788 Entrez Gene: 4784 Ensembl: ENSG00000008441 UCSC: uc010xmx.2
No. of Studies	4 (Positive: 0; Negative: 3; trend: 1)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 4)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Kondo, K.,2013	SNP: rs472913	No significant association was observed.	Negative	Comment on Study
Sklar, P.,2011	SNP: rs11085829	No significant association was observed.	Negative	Comment on Study
Lee, H. J., 2013	SNP: rs41350144, rs2024789, rs7556462, rs4915737, rs7553582, rs1125777	These data suggest that genetic variants in the NF1A gene region may predispose to seasonal patterned of mania in bipolar disorder.	Trend	Comment on Study
Green, E. K.,2012	SNP: rs11085829	BD ImmunoChip:P-value = 0.98,OR = 1.001;ImmunoChip, PGC-BD combined data:P-balue = 0.000249,OR = 0.931 No significant association was observed.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 12)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005634	nucleus	cellular component	IBA	283
GO:0003677	DNA binding	molecular function	IEA	83
GO:0003700	sequence-specific DNA binding transcription factor activity	molecular function	TAS[7590749]	66

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0048708	astrocyte differentiation	biological process	IEA	2
GO:0003705	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity	molecular function	TAS[7937100]	7
GO:0005515	protein binding	molecular function	IPI[25416956]	563
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	IDA[19706729]	62
GO:0021707	cerebellar granule cell differentiation	biological process	IEA	2
GO:0006366	transcription from RNA polymerase II promoter	biological process	TAS[7937100]	31
GO:0006260	DNA replication	biological process	IEA	7
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[19706729]	91
GO:0021680	cerebellar Purkinje cell layer development	biological process	IEA	3

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 4)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
NFIX	NFIB	NO	in vitro	9099724
NFIX	PIR	NO	in vivo;yeast 2-hybrid	9079676
NFIX	RFX1	NO	in vitro;in vivo	12624117
NFIX	SKI	YES	in vitro	9380514

Related other genetic factors

Gene related SNPs (count: 14)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs11085829	chr19:13063498 - 13063498(1)	intron_variant; NMD_transcript_variant	2(0/2/0)
rs2024789	chr1:61351329 - 61351329(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/0/1)
rs472913	chr1:60629886 - 60629886(1)	intron_variant; non_coding_transcript_variant	2(0/1/1)
rs4915737	chr1:61356611 - 61356611(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs7553582	chr1:61358703 - 61358703(1)	intron_variant; non_coding_transcript_variant	1(0/0/1)
rs41350144	chr1:61350127 - 61350127(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/0/1)
rs7556462	chr1:61356147 - 61356147(1)	intron_variant; non_coding_transcript_variant	1(0/0/1)
rs1125777	chr1:61366218 - 61366218(1)	intron_variant; non_coding_transcript_variant	1(0/0/1)

rs_ID	Location	Functional Annotation
rs1077151	chr19:13040294 - 13040294(1)	intron_variant; NMD_transcript_variant
rs1017180	chr19:13083958 - 13083958(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs4926298	chr19:13042221 - 13042221(1)	intron_variant; NMD_transcript_variant
rs931068	chr19:13047864 - 13047864(1)	intron_variant; NMD_transcript_variant
rs931067	chr19:13047969 - 13047969(1)	intron_variant; NMD_transcript_variant
rs10423745	chr19:13066001 - 13066001(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
19p13-q13	chr19:0-58617616	1 (0/1/0)
Chr 19	chr19:0-58617616	2 (0/2/0)
19p13	chr19:0-19900000	2 (0/1/1)

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

Gene relationship with SZ

Reference	Description	Result Category
23967141	Significant association was observed.	Positive

Gene relationship with MDD

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Region: chr19:12995608..13098796 View in gBrowse