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mutLBSgeneDB |
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| Gene summary for PTPN6 |
 Gene summary |
| Basic gene Info. | Gene symbol | PTPN6 |
| Gene name | protein tyrosine phosphatase, non-receptor type 6 | |
| Synonyms | HCP|HCPH|HPTP1C|PTP-1C|SH-PTP1|SHP-1|SHP-1L|SHP1 | |
| Cytomap | UCSC genome browser: 12p13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002831.5, NM_080548.4,NM_080549.3, | |
| Description | hematopoietic cell phosphatasehematopoietic cell protein-tyrosine phosphataseprotein-tyrosine phosphatase 1Cprotein-tyrosine phosphatase SHP-1tyrosine-protein phosphatase non-receptor type 6 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 176883 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000111679 | ||
| HPRD : 01475 | ||
| Vega : OTTHUMG00000168518 | ||
| Protein | UniProt: P29350 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PTPN6 | |
| BioGPS: 5777 | ||
| Pathway | NCI Pathway Interaction Database: PTPN6 | |
| KEGG: PTPN6 | ||
| REACTOME: PTPN6 | ||
| Pathway Commons: PTPN6 | ||
| Context | iHOP: PTPN6 | |
| ligand binding site mutation search in PubMed: PTPN6 | ||
| UCL Cancer Institute: PTPN6 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0006470 | protein dephosphorylation | 11266449 | GO:0008283 | cell proliferation | 11266449 | GO:0018108 | peptidyl-tyrosine phosphorylation | 18802077 | GO:0030154 | cell differentiation | 11266449 | GO:0035335 | peptidyl-tyrosine dephosphorylation | 11266449 | GO:0070372 | regulation of ERK1 and ERK2 cascade | 11266449 |
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| Ligand binding site mutations for PTPN6 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | R459 | R459H | GBM | 1 | S496 | R495C | HNSC | 1 | R275 | R275C | LUAD | 1 | V146 | S148F | SKCM | 1 | R275 | N274S | STAD | 1 | T106 | D104N | UCEC | 1 | R492 | R492Q | UCEC | 1 | R492 | A493V | UCEC | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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| Protein structure related information for PTPN6 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | R492 | A493V | 0.18983916 | R275 | R275C | -1.4277523 | R459 | R459H | -1.2941971 | R492 | R492Q | -1.0341539 | T106 | D104N | -0.80723337 | S496 | R495C | -0.7287429 | R275 | N274S | -0.27666158 | V146 | S148F | -0.010462186 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for PTPN6 from PDB |
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| Differential gene expression and gene-gene network for PTPN6 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for PTPN6 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0006663 | Calcinosis | 1 | Biomarker |
| umls:C0018824 | Heart Valve Diseases | 1 | Biomarker |
| umls:C0035228 | Respiratory Hypersensitivity | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PTPN6 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PTPN6 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (UNK,UNK,TYR,UNK) | 4gs0 | B | R275 R459 | SO4 | SULFATE | 3ps5 | A | R459 | SO4 | SULFATE | 4gry | A | R459 | PO4 | PHOSPHATE ION | 4grz | A | R459 | PO4 | PHOSPHATE ION | 4hjq | A | R459 | PO4 | PHOSPHATE ION | 4hjq | B | R459 | SO4 | SULFATE | 3ps5 | A | T106 |
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| Conservation information for LBS of PTPN6 |
| Multiple alignments for P29350 in multiple species |
| LBS | AA sequence | # species | Species | A202 | TGIEEASGAFV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A455 | IVHCSAGIGRT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C453 | PIIVHCSAGIG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D419 | YLSWPDHGVPS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E108 | SDPTSERWYHG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E121 | SGGQAESLLQA | 2 | Mus musculus, Rattus norvegicus | E121 | SGGQAETLLQA | 1 | Homo sapiens | E200 | KKTGIEEASGA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E201 | KTGIEEASGAF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F282 | KNILPFDHSRV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G117 | HGHMSGGQAET | 1 | Homo sapiens | G117 | HGHISGGQAES | 1 | Mus musculus | G117 | HGHMSGGQAES | 1 | Rattus norvegicus | G118 | GHMSGGQAETL | 1 | Homo sapiens | G118 | GHISGGQAESL | 1 | Mus musculus | G118 | GHMSGGQAESL | 1 | Rattus norvegicus | G179 | GRYTVGGSETF | 2 | Mus musculus, Rattus norvegicus | G179 | GRYTVGGLETF | 1 | Homo sapiens | G180 | RYTVGGSETFD | 2 | Mus musculus, Rattus norvegicus | G180 | RYTVGGLETFD | 1 | Homo sapiens | G421 | SWPDHGVPSEP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G456 | VHCSAGIGRTG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G458 | CSAGIGRTGTI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G497 | RAQRSGMVQTE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H166 | PLRVTHIKVMC | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H420 | LSWPDHGVPSE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I167 | LRVTHIKVMCE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I199 | FKKTGIEEASG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I279 | NRYKNILPFDH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I457 | HCSAGIGRTGT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K168 | RVTHIKVMCEG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K257 | QKQEVKNLHQR | 2 | Homo sapiens, Mus musculus | K257 | QKQEAKNLHQR | 1 | Rattus norvegicus | K277 | SKNRYKNILPF | 2 | Mus musculus, Rattus norvegicus | K277 | GKNRYKNILPF | 1 | Homo sapiens | K34 | ARPSRKNQGDF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K360 | EKGRNKCVPYW | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L139 | LVRESLSQPGD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N278 | KNRYKNILPFD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P418 | QYLSWPDHGVP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q254 | ESLQKQEVKNL | 2 | Homo sapiens, Mus musculus | Q254 | ESLQKQEAKNL | 1 | Rattus norvegicus | Q500 | RSGMVQTEAQY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R136 | WTFLVRESLSQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R275 | NKSKNRYKNIL | 2 | Mus musculus, Rattus norvegicus | R275 | NKGKNRYKNIL | 1 | Homo sapiens | R30 | GSFLARPSRKN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R33 | LARPSRKNQGD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R358 | EVEKGRNKCVP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R459 | SAGIGRTGTII | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R492 | TIQMVRAQRSG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S107 | CSDPTSERWYH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S138 | FLVRESLSQPG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S140 | VRESLSQPGDF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S32 | FLARPSRKNQG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S40 | NQGDFSLSVRV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S454 | IIVHCSAGIGR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S496 | VRAQRSGMVQT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T106 | NCSDPTSERWY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T165 | SPLRVTHIKVM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T188 | TFDSLTDLVEH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T460 | AGIGRTGTIIV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V146 | QPGDFVLSVLN | 2 | Mus musculus, Rattus norvegicus | V146 | QPGDFVLSVLS | 1 | Homo sapiens | V178 | GGRYTVGGSET | 2 | Mus musculus, Rattus norvegicus | V178 | GGRYTVGGLET | 1 | Homo sapiens | Y276 | KSKNRYKNILP | 2 | Mus musculus, Rattus norvegicus | Y276 | KGKNRYKNILP | 1 | Homo sapiens |
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