Gene Report

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Basic Info

Approved Symbol	PTPRT
Symbol Alias	RPTPrho, KIAA0283
Approved Name	protein tyrosine phosphatase, receptor type, T
Location	20q12-q13
Position	chr20:42072752-43189970, -1
External Links	HGNC: 9682 Entrez Gene: 11122 Ensembl: ENSG00000196090 UCSC: uc010ggj.3
No. of Studies	2 (Positive: 0; Negative: 1; trend: 1)
Overlap with SZ?	NO
Overlap with MDD?	YES

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Sklar, P.,2011	SNP: rs6102917	No significant association was observed.	Negative	Comment on Study
Green, E. K.,2012	SNP: rs6102947	BD ImmunoChip:P-value = 0.2562,OR = 1.189;ImmunoChip, PGC-BD combined data:P-balue = 0.0000513,OR = 1.289 Suggestive association was found.	Trend	Comment on Study

Gene functional annotation

Gene related GO terms (count: 16)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045296	cadherin binding	molecular function	IPI[16973135]	7
GO:0016021	integral component of membrane	cellular component	NAS[9602027]	219
GO:0007155	cell adhesion	biological process	NAS[16973135]	42
GO:0005886	plasma membrane	cellular component	IDA[18644975]	360

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0008013	beta-catenin binding	molecular function	IPI[16973135]	14
GO:0004725	protein tyrosine phosphatase activity	molecular function	IMP[16973135]	6
GO:0005515	protein binding	molecular function	IPI[16273344]	563
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	biological process	IMP[16973135]	16
GO:0007165	signal transduction	biological process	NAS[16973135]	136
GO:0045295	gamma-catenin binding	molecular function	IDA[16973135]	2
GO:0009986	cell surface	cellular component	IDA[18644975]	40
GO:0045294	alpha-catenin binding	molecular function	IDA[16973135]	3
GO:0035335	peptidyl-tyrosine dephosphorylation	biological process	IEA; IMP[16973135]	9
GO:0006470	protein dephosphorylation	biological process	IDA[16973135]	10
GO:0070097	delta-catenin binding	molecular function	IPI[16973135]	1
GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	biological process	IDA[18644975]	7

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 1)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
PTPRT	PTPRN	NO	in vitro;yeast 2-hybrid	16273344

Related other genetic factors

Gene related SNPs (count: 15)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs6102947	chr20:42612212 - 42612212(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant	1(0/0/1)
rs6102917	chr20:42590779 - 42590779(1)	intron_variant; NMD_transcript_variant	1(0/1/0)

rs_ID	Location	Functional Annotation
rs6030378	chr20:42627137 - 42627137(1)	intron_variant; NMD_transcript_variant
rs6102944	chr20:42612022 - 42612022(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102945	chr20:42612060 - 42612060(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102946	chr20:42612178 - 42612178(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102948	chr20:42612265 - 42612265(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102940	chr20:42610986 - 42610986(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102941	chr20:42611075 - 42611075(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102942	chr20:42611088 - 42611088(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102943	chr20:42611205 - 42611205(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs2057071	chr20:42603397 - 42603397(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant
rs2057072	chr20:42603572 - 42603572(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant
rs877440	chr20:42610278 - 42610278(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6102939	chr20:42610918 - 42610918(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 20	chr20:0-64444167	4 (0/3/1)
20p11-q13	chr20:17900000-64444167	1 (1/0/0)

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

Gene relationship with SZ

Gene relationship with MDD

Reference	Description	Category in MDD	Link in MK4MDD
15303102	Genes altered in major depressive disorder	Pos	PTPRT

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Region: chr20:42072752..43189970 View in gBrowse