ADHDgene Database

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Large-scale studies

Data Summary

Published Variant
- SNP: 1391
- CNV: 398
- Others: 173
Published Gene: 359
Published Region: 128
Pathway by PBA: 8
Study: 361

Detail ...

Gene Report

Basic Info

Approved Symbol	NTF3
Symbol Alias	NGF2
Approved Name	neurotrophin 3
Location	12p13
Position	chr12:5541280-5604465, +
External Links	HGNC: 8023 Entrez Gene: 4908 Ensembl: ENSG00000185652 UCSC: uc001qnk.3
No. of Studies	3 (significant: 1; non-significant: 2; trend: 0)
Source	Literature-origin; Mapped by LD-proxy; Mapped by literature SNP

Gene related studies (count: 3)

Reference	Statistical Values/Author Comments	Result of Statistical Analysis
Ribases M, 2008	a four-marker haplotype (rs4074967-rs6332-rs6489630-rs7956189) global P-value=2.3e-04, Best Haplotype P-value=2.1e-05, adjusted P-value=1.0e-04, OR=1.48 (1.20-1.84) in children; Haplotype-Specific(TACA) P-value=2.1e-05; OR(CI)=1.6 (1.28-2.00), Haplotype-Specific (TGCA) P-value=3.0e-04; OR(CI)=1.48 (1.20-1.84) in children	Significant
Syed Z, 2007	No evidence of association was seen.	Non-significant
Cho SC, 2010(b)	no significant differences in the genotype frequencies and the haplotype analysis; in the case-control and family-based analyses, NTF3 was not significantly associated with ADHD	Non-significant

Gene related SNPs (count: 22)

Literature-origin SNPs (count: 5)

rs_ID	Location	Functional Annotation	No. of Studies (significant/non-significant/trend)
rs6489630	Chr12:5604624(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs7958038	Chr12:5576594(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs7132127	Chr12:5552076(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs6332	Chr12:5603632(Fwd)	intron_variant; nc_transcript_variant; non_coding_exon_variant; synonymous_variant	3(1/2/0)
rs4930767	Chr12:5597381(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)

LD-proxies (count: 17)

rs_ID	Location	Functional Annotation
rs10735050	Chr12:5558306(Fwd)	intron_variant; nc_transcript_variant
rs10492095	Chr12:5561200(Fwd)	intron_variant; nc_transcript_variant
rs17180851	Chr12:5554548(Fwd)	intron_variant; nc_transcript_variant
rs10774330	Chr12:5557893(Fwd)	intron_variant; nc_transcript_variant
rs10849276	Chr12:5594103(Fwd)	intron_variant; nc_transcript_variant
rs11063708	Chr12:5594403(Fwd)	intron_variant; nc_transcript_variant
rs4077470	Chr12:5596812(Fwd)	intron_variant; nc_transcript_variant
rs4930820	Chr12:5597205(Fwd)	intron_variant; nc_transcript_variant
rs3924027	Chr12:5595435(Fwd)	intron_variant; nc_transcript_variant
rs7965477	Chr12:5595747(Fwd)	intron_variant; nc_transcript_variant
rs6489628	Chr12:5596346(Fwd)	intron_variant; nc_transcript_variant
rs7301972	Chr12:5596454(Fwd)	intron_variant; nc_transcript_variant
rs11063703	Chr12:5589409(Fwd)	intron_variant; nc_transcript_variant
rs11063707	Chr12:5594325(Fwd)	intron_variant; nc_transcript_variant
rs7485608	Chr12:5589291(Fwd)	intron_variant; nc_transcript_variant
rs10161033	Chr12:5599646(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs7484401	Chr12:5599902(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variant (count: 0)

Gene related regions (count: 0)

Gene related GO terms (count: 38)

GO terms by PBA (with statistical significance of FDR<0.05) (count: 0)

GO terms by database search (count: 38)

ID	Name	Type	Evidence[PMID]	No. of Genes in ADHDgene
GO:0000187	activation of MAPK activity	Biological Process		21
GO:0002092	positive regulation of receptor internalization	Biological Process		7
GO:0005102	receptor binding	Molecular Function	TAS[2236018]	61
GO:0005165	neurotrophin receptor binding	Molecular Function		1
GO:0005576	extracellular region	Cellular Component		240
GO:0007165	signal transduction	Biological Process	TAS[2236018]	171
GO:0008284	positive regulation of cell proliferation	Biological Process		69
GO:0008083	growth factor activity	Molecular Function		25
GO:0016023	cytoplasmic membrane-bounded vesicle	Cellular Component		16
GO:0008544	epidermis development	Biological Process		12
GO:0030335	positive regulation of cell migration	Biological Process		29
GO:0021675	nerve development	Biological Process		3
GO:0032856	activation of Ras GTPase activity	Biological Process		1
GO:0032148	activation of protein kinase B activity	Biological Process		6
GO:0007267	cell-cell signaling	Biological Process	TAS[2236018]	38
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	Biological Process		16
GO:0007399	nervous system development	Biological Process	TAS[1542658]	54
GO:0007274	neuromuscular synaptic transmission	Biological Process		5
GO:0007411	axon guidance	Biological Process		65
GO:0007403	glial cell fate determination	Biological Process		1
GO:0007422	peripheral nervous system development	Biological Process		7
GO:0007420	brain development	Biological Process		33
GO:0050732	negative regulation of peptidyl-tyrosine phosphorylation	Biological Process		2
GO:0050804	regulation of synaptic transmission	Biological Process		2
GO:0048484	enteric nervous system development	Biological Process		4
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Biological Process		14
GO:0051145	smooth muscle cell differentiation	Biological Process		6
GO:2000251	positive regulation of actin cytoskeleton reorganization	Biological Process		2
GO:0050918	positive chemotaxis	Biological Process		7
GO:0050930	induction of positive chemotaxis	Biological Process		6
GO:0042490	mechanoreceptor differentiation	Biological Process		3
GO:0042552	myelination	Biological Process		7
GO:0033138	positive regulation of peptidyl-serine phosphorylation	Biological Process		10
GO:0042056	chemoattractant activity	Molecular Function		5
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Biological Process		131
GO:0048406	nerve growth factor binding	Molecular Function		3
GO:0043524	negative regulation of neuron apoptotic process	Biological Process		19
GO:0045687	positive regulation of glial cell differentiation	Biological Process		2

Gene related KEGG pathways (count: 2)

ID	Name	No. of Genes in ADHDgene	Brief Description
hsa04722	Neurotrophin signaling pathway	24	Neurotrophins are a family of trophic factors involved in di...... Neurotrophins are a family of trophic factors involved in differentiation and survival of neural cells. The neurotrophin family consists of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT-3), and neurotrophin 4 (NT-4). Neurotrophins exert their functions through engagement of Trk tyrosine kinase receptors or p75 neurotrophin receptor (p75NTR). Neurotrophin/Trk signaling is regulated by connecting a variety of intracellular signaling cascades, which include MAPK pathway, PI-3 kinase pathway, and PLC pathway, transmitting positive signals like enhanced survival and growth. On the other hand, p75NTR transmits both positive and nagative signals. These signals play an important role for neural development and additional higher-order activities such as learning and memory. More...
hsa04010	MAPK signaling pathway	69	The mitogen-activated protein kinase (MAPK) cascade is a hig...... The mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals express at least four distinctly regulated groups of MAPKs, extracellular signal-related kinases (ERK)-1/2, Jun amino-terminal kinases (JNK1/2/3), p38 proteins (p38alpha/beta/gamma/delta) and ERK5, that are activated by specific MAPKKs: MEK1/2 for ERK1/2, MKK3/6 for the p38, MKK4/7 (JNKK1/2) for the JNKs, and MEK5 for ERK5. Each MAPKK, however, can be activated by more than one MAPKKK, increasing the complexity and diversity of MAPK signalling. Presumably each MAPKKK confers responsiveness to distinct stimuli. For example, activation of ERK1/2 by growth factors depends on the MAPKKK c-Raf, but other MAPKKKs may activate ERK1/2 in response to pro-inflammatory stimuli. More...

Genes shared at least 5 GO terms with NTF3 (count: 21)

Gene Symbol	Pathway Count	Pathway List
VEGFA	12	positive regulation of receptor internalization; extracellular region; positive regulation of cell proliferation; growth factor activity; positive regulation of cell migration; nervous system development; positive regulation of peptidyl-tyrosine phosphorylation; positive chemotaxis; induction of positive chemotaxis; positive regulation of peptidyl-serine phosphorylation; chemoattractant activity; positive regulation of transcription from RNA polymerase II promoter;
FGF10	9	activation of MAPK activity; extracellular region; growth factor activity; positive regulation of peptidyl-tyrosine phosphorylation; smooth muscle cell differentiation; positive chemotaxis; induction of positive chemotaxis; chemoattractant activity; positive regulation of transcription from RNA polymerase II promoter;
GDNF	9	receptor binding; extracellular region; signal transduction; growth factor activity; nervous system development; axon guidance; enteric nervous system development; positive regulation of transcription from RNA polymerase II promoter; negative regulation of neuron apoptotic process;
BDNF	7	extracellular region; growth factor activity; nerve development; nervous system development; axon guidance; mechanoreceptor differentiation; negative regulation of neuron apoptotic process;
VEGFB	7	extracellular region; growth factor activity; positive regulation of peptidyl-tyrosine phosphorylation; positive chemotaxis; induction of positive chemotaxis; chemoattractant activity; negative regulation of neuron apoptotic process;
CXCL12	6	receptor binding; extracellular region; signal transduction; growth factor activity; brain development; induction of positive chemotaxis;
INHA	6	receptor binding; extracellular region; signal transduction; growth factor activity; cell-cell signaling; nervous system development;
MIF	6	receptor binding; extracellular region; positive regulation of peptidyl-tyrosine phosphorylation; positive chemotaxis; positive regulation of peptidyl-serine phosphorylation; chemoattractant activity;
FGF4	6	extracellular region; signal transduction; positive regulation of cell proliferation; growth factor activity; cell-cell signaling; positive regulation of transcription from RNA polymerase II promoter;
IL6	6	extracellular region; positive regulation of cell proliferation; growth factor activity; positive regulation of peptidyl-tyrosine phosphorylation; positive regulation of peptidyl-serine phosphorylation; positive regulation of transcription from RNA polymerase II promoter;
INS	6	extracellular region; positive regulation of cell proliferation; positive regulation of cell migration; activation of protein kinase B activity; cell-cell signaling; positive regulation of peptidyl-tyrosine phosphorylation;
ERBB2	6	signal transduction; transmembrane receptor protein tyrosine kinase signaling pathway; nervous system development; axon guidance; peripheral nervous system development; myelination;
MAPK1	5	activation of MAPK activity; signal transduction; positive regulation of cell proliferation; positive regulation of cell migration; axon guidance;
PLA2G1B	5	activation of MAPK activity; receptor binding; extracellular region; signal transduction; positive regulation of transcription from RNA polymerase II promoter;
ARRB2	5	positive regulation of receptor internalization; receptor binding; cytoplasmic membrane-bounded vesicle; brain development; positive regulation of peptidyl-tyrosine phosphorylation;
CLCF1	5	receptor binding; extracellular region; positive regulation of cell proliferation; growth factor activity; negative regulation of neuron apoptotic process;
CNTFR	5	receptor binding; signal transduction; positive regulation of cell proliferation; nervous system development; negative regulation of neuron apoptotic process;
SEMA4D	5	receptor binding; positive regulation of cell migration; axon guidance; negative regulation of peptidyl-tyrosine phosphorylation; positive regulation of peptidyl-tyrosine phosphorylation;
FGF3	5	extracellular region; signal transduction; positive regulation of cell proliferation; growth factor activity; cell-cell signaling;
FGF9	5	extracellular region; signal transduction; positive regulation of cell proliferation; growth factor activity; cell-cell signaling;
NGF	5	extracellular region; growth factor activity; transmembrane receptor protein tyrosine kinase signaling pathway; peripheral nervous system development; negative regulation of neuron apoptotic process;

Genes shared at least 2 KEGG pathways with NTF3 (count: 11)

Gene Symbol	Pathway Count	Pathway List
BDNF	2	Neurotrophin signaling pathway; MAPK signaling pathway;
CRKL	2	Neurotrophin signaling pathway; MAPK signaling pathway;
MAP3K5	2	Neurotrophin signaling pathway; MAPK signaling pathway;
MAPK1	2	Neurotrophin signaling pathway; MAPK signaling pathway;
MAPK3	2	Neurotrophin signaling pathway; MAPK signaling pathway;
MAPK7	2	Neurotrophin signaling pathway; MAPK signaling pathway;
MAPK9	2	Neurotrophin signaling pathway; MAPK signaling pathway;
NGF	2	Neurotrophin signaling pathway; MAPK signaling pathway;
NTRK2	2	Neurotrophin signaling pathway; MAPK signaling pathway;
RELA	2	Neurotrophin signaling pathway; MAPK signaling pathway;
RPS6KA4	2	Neurotrophin signaling pathway; MAPK signaling pathway;

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Region: chr12:5541280..5604465 View in gBrowse