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Report for SNP rs2476601

Developed by Shray Alag, 2020.
SNP Clinical Trial Gene

There is one clinical trial.

Clinical Trials

1 Lymphoid Tyrosine Phosphatase Gene Polymorphisms in Inflammatory Bowel Disease

This study aims: 1. To investigate the association between single nucleotide polymorphisms of PTPN22 gene (rs2476601, rs33996649 and rs2488457) and inflammatory bowel disease. 2. To correlate the relation between the studied SNPs and disease activity /response to therapy.

NCT04284878 Inflammatory Bowel Diseases Genetic: PCR-RFLP
MeSH:Intestinal Diseases Inflammatory Bowel Diseases
HPO:Abnormal intestine morphology Inflammation of the large intestine

To investigate the association between single nucleotide polymorphisms of PTPN22 gene (rs2476601, rs33996649 and rs2488457) and inflammatory bowel disease.

Association between single nucleotide polymorphisms of Lymphoid Tyrosine Phosphatase gene (rs2476601, rs33996649 and rs2488457) and inflammatory bowel disease.

There are 24 exons in the gene (NCBI website).About 21 SNPs were found in PTPN22 gene (rs1310182, rs3789604, rs33996649, rs1217414, rs2476601, rs12760457, rs2488457,,,,etc).SNP rs2476601 (C1858>T) in exon 14 results in the substitution of arginine 620 with a tryptophan residue in the protein product (referred to as 620W variant) (Spalinger et al., 2016).

Primary Outcomes

Description: Three single nucleotide polymorphisms in the lymphoid tyrosine phosphatase gene(SNP (G788>A) in exon10, SNP (C1858>T) in exon 14 and SNP (G -1123>C) in the promoter region ) will be assessed in 100 patients diagnosed as inflammatory bowel disease and 100 healthy subjects by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) to detect association between these polymorphisms and inflammatory bowel disease

Measure: Association between single nucleotide polymorphisms of Lymphoid Tyrosine Phosphatase gene (rs2476601, rs33996649 and rs2488457) and inflammatory bowel disease

Time: baseline

Secondary Outcomes

Description: Serum Erythrocyte Sedimentation Rate ,C-Reactive Protien ,Anti Nuclear Antibody ,Antineutrophil Cytoplasmic Antibody (ANCA) and Anti Saccharomyces Cerevisiae (ASCA) and fecal calprotectin will be done to all patients.The three investigated polymorphisms in LYP will be correlated with the markers of disease activity and IBD patients response to therapy.

Measure: To correlate the relation between the studied SNPs and disease activity /response to therapy.

Time: baseline

HPO Nodes

HP:0002242: Abnormal intestine morphology
Genes 879
MID2 WHCR CTC1 PORCN MYO5B MYO5B COL5A1 ADAMTS3 CXORF56 GATA1 TCF4 TCTN3 SMAD7 SKIV2L TTC37 C12ORF65 CFC1 RNF43 HSD3B7 EFL1 CTRC TRNL1 SDHC SETD5 TGFB1 ANTXR2 SMO OCRL TP53 TINF2 FOXP3 PACS1 PMS2 PHOX2B RET ABCB11 DSE SETBP1 ZMPSTE24 LMOD1 ASXL1 USP9X KIF7 AGA PTCH2 ERAP1 RPS20 BMPR1A BMPR1A CHST14 TP53 TSPAN7 TBX1 PEX11B PIEZO1 EPCAM B2M CLMP ND1 COX2 EYA1 EIF2AK3 EFEMP2 GLI2 PAX3 HABP2 MYH11 TP63 NCF2 KIAA0556 XRCC2 COG8 ACTG2 EDNRB DCC SPINK5 LCT SNAI2 ACTG2 SOX10 COX7B MLH1 CEP41 MEFV PIGN CCBE1 TMEM216 ACSL4 HMGA2 F13B FBLN5 TRNS1 AP1S1 FREM1 F5 TEK CENPF MNX1 SEC24C MLH3 FLNA SDHC ADAMTS3 HLA-DRB1 ZIC2 SLCO2A1 MMP21 DNMT3B APC SDHB UPF3B PAK3 HLA-DPA1 ACVRL1 GATA6 SDHB ARL13B RET MSH2 AKR1D1 MKKS APC LTBP4 FGFR1 BAAT ERCC4 LRP2 CLMP ARX FOXF1 BRCA2 STAT1 SBDS VPS13A SEMA3D MSH6 AMACR APC CCDC22 DISP1 PEX5 BRCA1 ZBTB24 RFWD3 HPS1 MTTP ASXL1 ELN JAK2 MPI HMBS AGTR2 PTEN DCTN4 F12 DKC1 ND5 PEX3 FBLN5 GPC3 PEX10 RIPK1 ERCC2 AXIN2 MUSK RPGRIP1L MYC DMD CEP57 FGF20 KIAA0586 NTHL1 RREB1 ACOX2 TWNK CCR6 MTOR FANCC PGM3 MYLK SMO KLLN LEMD3 SPINK5 HLA-DRB1 DLL1 EPHX1 F13A1 SBDS GP1BB EFL1 COX4I2 RARB KIFBP DIS3L2 RAD51C NRTN NSUN2 FRMPD4 POLA1 CYBC1 STAT3 HYLS1 UBR1 PEX1 C1R PRTN3 MSH2 RECQL4 SALL4 IL2RB MKKS RAC2 EDN3 ITGA6 RET PNLIP ZFP57 AXIN2 GDNF AKT1 MUTYH ARMC9 IRGM ZNF81 TERT TRNF SALL4 PAX3 PTEN MITF SDHC PRDM16 FLI1 STK11 SLC2A2 ITCH LPIN2 SMC3 TBCE CD3G SKI DHODH RBM10 SRCAP KIFBP ATRX CHRM3 UBE2T SLC29A3 SLC9A3 SMAD4 SH3KBP1 CD79B SRP54 PIGO LMNA AKR1D1 KITLG RERE BACH2 MSH3 SLC9A7 ABCB1 FBN2 ASCL1 GREB1L FAH KIT GDNF GATA6 ALG13 FANCL DHCR24 PEX14 KEAP1 CHD7 POLE PIGW EDNRB MYCN PMS1 SERPING1 MITF NSD2 PIK3C2A SH2B1 MNX1 FGFR1 POU2AF1 SERPING1 CLIP2 SEC23B SETD5 CAVIN1 RFXAP TCF3 HLA-B GNAS NOTCH2 DACT1 BUB1B GAS1 MBTPS2 SOX10 PLG PARN SHH SRC GDNF FOXH1 SNAI2 RFXANK CAV1 BMPR1A UBAC2 DHCR7 POLG NOTCH2 USB1 IL23R MTTP EDN3 PMS1 UBE3B HSD3B7 RMRP HLA-B FLNA FANCA MSH6 TMPRSS6 BCOR NCF1 SLC6A8 APC PIK3CA FANCM RET PIGV RBM8A HELLS ITGB2 EPCAM B9D1 KRAS POLG TRIP13 ZAP70 UBR1 APC AKT1 PIGN SDHA APC XIAP RASGRP1 SMAD4 BRCA2 SDHB RMRP SDHC IL10RA LRP2 GTF2I SLC39A4 DLC1 TRNW IL2RA ARID1B SLX4 TRNH CYBA VANGL1 AXIN2 ARPC1B TCOF1 RPS19 GPR35 TBX1 TFAP2A HCCS PRKCD PCSK1 SRCAP PLG PTCHD1 USP27X RAPSN PGAP2 FANCI TP53 MUTYH SEMA3C AKT1 CCDC47 KAT6A PTCH1 AP1B1 BMPR1A FAN1 IRF5 FAS FERMT1 CYP7B1 CIITA SI ADAM17 PEX16 APC PALLD PLCG2 GATA6 ZNF711 TRNE CTC1 TTC7A FARSB NPHP3 CFTR ARL3 XRCC4 MED12 PLA2G4A BDNF MLH3 TMEM231 RPS6KA3 IGLL1 AHI1 CBLIF MYOD1 POLG RERE ENG PRSS1 PTCH1 MEFV NCF4 RELA ATP7A SRP54 PEX13 CLCA4 JAK3 ABCB4 TNFSF15 CEP104 PEX6 PHOX2B SDHD DDX59 IL6 SOX10 MAP3K7 IL12A GABRD WT1 FASLG FOXF1 CTBP1 ATP8B1 PHOX2B BUB1 PEX12 ENG SDHD CTNNB1 MKS1 EDN3 HCFC1 MST1 TRNL1 GPIHBP1 FGFR3 EXOC6B IL12A-AS1 WFS1 TCTN1 GPC4 SMAD4 SUFU MKS1 IL10RB AMER1 HDAC8 DOK7 PEX2 TCF4 APC DNAJC21 KMT2A MASP2 ASCL1 RECQL4 EDN3 MVK POLD1 C12ORF65 TYMP KRAS PTEN PALB2 SEMA4A MED12 TMEM67 TEK UFD1 NHP2 MCM6 FGF8 SMAD4 IL1RAPL1 LRBA TDGF1 FLNB B3GLCT FGFRL1 FGFR2 CDCA7 DNAJC21 RET SOX10 EDN3 PGAP3 TRNQ LONP1 SIN3A NDUFB11 JMJD1C FGFR2 PALB2 FAT4 CC2D2A MDM2 TTC7A WAS SLC18A3 CFTR KDM6A FANCE RAD21 RFX6 IL12A LIG4 RTTN NCF1 MKS1 RAD51 EWSR1 INHBA DMP1 PEX19 PORCN SEMA3E SMC1A HYMAI MLH1 NPHP3 RET FANCD2 LBR TNPO3 DYNC2H1 NEK1 DDX59 GLA MLH1 FOXE1 FLCN IQSEC2 ABL1 TCF4 RFWD3 GDNF NEUROG3 STAT4 CTNNB1 FRAS1 STK11 CSPP1 EP300 AMACR SYP COMT NAA10 WAS AK2 TRMT5 SOX10 TGFBR2 L1CAM MYO1H FAT4 ZNF41 POLG PIGY TNFRSF1A POLD1 CHEK2 COX1 LIPA ISL1 MSH2 NUP88 AHI1 SLC6A19 ABCC8 BMPR1A ACTG2 SIX3 ND4 SEC23B SALL4 ZNF423 OPLAH PTPN22 KIT HYOU1 HPGD ELN CYP27A1 TGFB1 BMPR1A RPS6KA3 USF3 CYBB BUB3 RNF43 CCN2 ACTA2 CCR1 MAD2L2 TMEM237 ITGA8 MSH6 FOXP3 WASHC5 KIT WRAP53 CEP57 RFC2 PDGFRA KIT WNT4 WIPF1 CEP41 SPINT2 PEX12 TERC CFTR TGFB1 CDKN2A GJB2 IDS BUB1 ND6 CTLA4 INPP5E EP300 GPC1 BRCA1 SF3B4 FLCN TNFAIP3 NODAL JAK3 DOCK8 MBTPS2 PHOX2B ZFPM2 SPINK1 LIPA SUFU KLRC4 TMEM237 L1CAM ARHGEF6 POLE PEX26 PLAGL1 POLR1D KCNAB2 CARMIL2 POLG CISD2 LRRC8A KIT LIMK1 WNT2B SERPING1 TBL2 PMPCA TGIF1 CEP290 CDC45 ENPP1 ALDH18A1 DGAT1 SHPK CPLANE1 STRA6 EP300 FCGR2A PIBF1 GREM1 TCTN2 ALG3 TP53 COL14A1 SLC6A8 RHBDF2 TWNK HIRA NCF2 LIG4 CCBE1 RAD21 GDI1 BBS1 KMT2D NPHP1 CD79A EDN3 BRIP1 SLC5A1 PIGO NIPBL FANCF PDGFRA BLNK ALG8 DACT1 PLVAP FAS SIX1 DHCR7 BUB1B RET HLA-DPB1 CNKSR2 SLC10A2 PTRH2 ELN TMEM138 NCF4 SMAD4 STAT1 TTC37 IL12RB1 IRF5 ITGB4 C4A EDNRB INPP5E MINPP1 POLR1C TRNK KCNJ11 CLCN4 DNMT3B PIK3CA NLRC4 STX1A HNRNPU BTK EPCAM TMEM237 PKD1 FLNA ERGIC1 SKIV2L CXCR4 PIK3R1 SAR1B RTEL1 COL3A1 CHST14 SLC46A1 DLG3 CD55 CCDC28B ECE1 TJP2 TLR4 PIK3CA GUCY2C SDHB SAA1 CEP120 CCND1 IL10 GJB6 EDNRB NOTCH3 SAR1B RTEL1 GDF2 PMS2 HBB PIGV CASP10 SALL4 LETM1 COMP RAD51C ARVCF FTSJ1 IL21 COX3 PIGL ZAP70 PIK3CA PDGFRB CEP120 CCNQ PHOX2B BCOR TYMP SLC30A2 MYD88 PTF1A NPM1 COG6 DICER1 SLC7A7 CYBA NOD2 RFX5 ZEB2 AIRE B3GALT6 TRNS2 MLXIPL FANCG KLHL7 AP1S1 TGFBR2 EDNRB ARX NRAS RRM2B AAGAB BAZ1B MLH1 FANCB CPLX1 KRAS MYRF CYBB STX3 PTEN TTC7A NOP10 MSH2 ECE1 APC PRSS2 MMEL1 MBTPS2 SALL1 IGHM MPI EDNRB FAS RAB39B SALL1 LBR SPIB CDON MECP2 NIPBL PTPRJ GTF2IRD1 SNAI2 CREBBP MED12 CDKN2A PRKAR1A
Protein Mutations 1
C10D
SNP 8
rs1217414 rs12760457 rs1310182 rs2097432 rs2476601 rs2488457 rs33996649 rs3789604
HP:0002037: Inflammation of the large intestine
Genes 56
TNFAIP3 SKIV2L NCF4 TCF4 LRBA SKIV2L TTC37 RFXAP ZAP70 RET IL6 MAP3K7 FAS FERMT1 RTEL1 FASLG CIITA CARMIL2 XIAP RASGRP1 CASP10 HLA-DRB1 PLCG2 FOXP3 F13A1 STAT1 IL10RA WAS WAS IL21 SLC9A3 MST1 RFXANK ZAP70 WIPF1 GPIHBP1 TGFB1 F13B POLA1 FAS IL10RB BACH2 ABCB1 HPS1 COG6 NLRC4 NOD2 HLA-B ARPC1B RFX5 GPR35 MASP2 IRGM PRKCD RIPK1 OPLAH
Protein Mutations 1
R139C
SNP 9
rs1217414 rs12760457 rs1310182 rs2097432 rs2476601 rs2488457 rs33996649 rs3789604 rs9557195