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Report for SNP rs2488457

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).

SNP rs2488457 (G -1123>C) is located in the promoter region (Chen et al., 2013).A transcription factor binding site for activator protein 4 (AP-4) at position −1123 is predicted in the presence of the G allele rather than the C allele (Jüliger et al., 2003).

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


Abnormal intestine morphology
Genes 874
ALG13 LETM1 ARID1B UBR1 CPLANE1 ZFPM2 RTEL1 MBTPS2 STX3 EPCAM PORCN CTC1 TGIF1 ANTXR2 SLC18A3 SALL1 RMRP CFTR KIT CFTR XRCC4 SDHD PRKCD RNF43 TGFB1 ASCL1 GDNF ZMPSTE24 DICER1 ECE1 FGF8 WAS AP1S1 PTCH2 PLG FBN2 INPP5E AXIN2 PLA2G4A ASXL1 SALL4 POLG TNFAIP3 COMP PIGV WFS1 IL2RB TRNL1 CYP7B1 EYA1 MPI SPINK5 ALG8 HIRA CEP57 AP1S1 TRNF CD3G CYBA DOK7 EP300 BUB1B DOCK8 SEMA3C GLI2 EDN3 HLA-DPB1 DCC PEX5 MEFV SF3B4 HYLS1 CEP104 KIT IL10 PTEN SLC46A1 BMPR1A NOTCH3 SPIB PIK3C2A ARVCF BACH2 MST1 TMEM237 COG6 PIGV CLCN4 SDHC AMACR CHST14 JMJD1C IL12RB1 F12 CEP41 COL5A1 ND5 MMEL1 HELLS FCGR2A APC MTTP POLG SUFU STAT3 ADAM17 TTC37 TMPRSS6 LONP1 KIT GTF2I CDC45 NRTN BLNK SHPK MID2 CCNQ RPGRIP1L PEX2 GJB2 PMS2 RET ACVRL1 GNAS INPP5E TCTN2 NCF1 RECQL4 ITGB2 PMS1 DLL1 MNX1 LRBA DNMT3B CCR6 GATA6 EFL1 RMRP SIX3 GDNF FANCD2 TMEM237 TRNE NODAL CARMIL2 SDHB MSH2 GATA6 HMBS CHD7 SMAD4 EDNRB BRCA1 CLMP FLNB WHCR GREB1L PEX11B ITGA8 RPS20 FOXP3 AKR1D1 DDX59 GPC4 ACTG2 MPI POLG MED12 FGFR1 KIAA0586 SAA1 ABCC8 RERE L1CAM MSH6 CCBE1 EWSR1 EDN3 EDN3 PGM3 FANCL HLA-DRB1 COX3 FOXF1 RBM10 EFEMP2 SDHD CNKSR2 ALDH18A1 WRAP53 TGFBR2 POLD1 TWNK RAD51C HLA-B FBLN5 COX2 MINPP1 DNAJC21 FAS DCTN4 APC POLR1D ZAP70 SEC23B SOX10 SDHA GLA MYH11 SETD5 TCOF1 KCNJ11 GATA6 COX4I2 KITLG RAD51C DDX59 SLC6A8 ACTG2 IL1RAPL1 CCR1 AK2 PAX3 STRA6 EDNRB APC MKKS GAS1 PALLD RFWD3 RFC2 ARL3 HYMAI TCTN1 PTEN WIPF1 PIK3CA EDN3 NOP10 LIPA RFXANK TYMP CSPP1 NHP2 BMPR1A TRNQ MTTP CD55 IDS MECP2 FANCI MKKS RET KIF7 CCBE1 SOX10 MAD2L2 PEX3 SMAD7 AGTR2 NOD2 ITCH PRKAR1A SBDS RET CFC1 PIGY MYCN GPR35 FANCA STAT1 CYBC1 ABL1 HLA-DPA1 LBR FGFRL1 SLX4 CASP10 RAD21 MTOR TRIP13 MYD88 B3GLCT CLMP SERPING1 PTEN MKS1 FARSB FGF20 ELN DNAJC21 CIITA PLVAP KMT2D PALB2 EDNRB TNFRSF1A SOX10 TP53 ELN RFWD3 HLA-DRB1 MITF B3GALT6 BUB1 INHBA HDAC8 ELN SLC10A2 IL23R RFX5 HCCS MLH3 NOTCH2 MSH2 ND6 SLC39A4 WT1 TJP2 SLC2A2 MYO5B HLA-B MLH3 ZAP70 UFD1 CAVIN1 EIF2AK3 MCM6 TNPO3 DGAT1 ECE1 F5 KAT6A ATP7A AKT1 ATP8B1 NCF1 CXCR4 RBM8A BAAT BUB1 LRP2 CENPF EFL1 APC PEX13 PDGFRA ERAP1 SYP CTC1 SDHB MSH6 APC SRCAP ACTA2 PEX12 DMP1 SPINK1 ZIC2 PLG PIGO PAX3 SOX10 DMD LRRC8A FAS RNF43 DLC1 EXOC6B POLR1C CISD2 NCF2 FTSJ1 CHRM3 KIAA0556 SNAI2 CTLA4 CD79A C1R BRCA1 RPS19 BRCA2 CFTR AIRE TFAP2A NCF2 APC COX7B AKT1 MYC PGAP3 TP53 RELA MVK POLE AKT1 POLG MITF PEX16 ND1 MUTYH PIK3R1 LBR OCRL DIS3L2 TGFBR2 BBS1 AXIN2 TCF4 EDN3 SEMA4A RAC2 PIK3CA UBAC2 FRAS1 TINF2 C4A CTNNB1 RFXAP BMPR1A HBB NPHP1 FANCC CXORF56 MEFV PMS2 PHOX2B RECQL4 RAB39B AMACR CTRC UBE2T PTCH1 RRM2B GATA1 HCFC1 DACT1 SBDS PNLIP NIPBL ERCC2 ARPC1B SPINK5 POU2AF1 TYMP GREM1 ZBTB24 CDON PKD1 NTHL1 PEX12 RASGRP1 CEP290 HYOU1 MUSK DHCR7 PTRH2 MYLK TCTN3 CTNNB1 WNT4 KEAP1 PEX19 USP9X ERCC4 KIFBP CDKN2A FGFR3 GPC1 BMPR1A DISP1 ENG HSD3B7 LMOD1 SNAI2 ERGIC1 FANCF FOXF1 EDN3 ABCB1 OPLAH L1CAM SLC9A3 SMAD4 SLC6A19 PORCN ACOX2 SDHB SLC7A7 SLCO2A1 CLCA4 MLXIPL SI MDM2 CLIP2 BRCA2 DHCR24 CTBP1 ABCB4 LIG4 SH2B1 PAK3 PIGW IQSEC2 NPM1 MSH2 MMP21 SRP54 TMEM216 RET TBL2 PTCHD1 SH3KBP1 NPHP3 TRMT5 IL12A-AS1 FAH MKS1 SEC24C FANCG MYO1H SLC9A7 FLI1 TCF3 SLC29A3 GUCY2C MED12 SEMA3D COMT SAR1B ZNF81 CDKN2A SKI NAA10 APC POLG GPC3 GJB6 SRCAP TDGF1 C12ORF65 NUP88 HMGA2 PEX14 FLCN TRNH PEX10 SERPING1 CD79B PRDM16 PTF1A PHOX2B PACS1 B9D1 TRNL1 CEP120 FANCB KRAS RARB STX1A KMT2A RAD51 ARMC9 GABRD FREM1 GP1BB SKIV2L POLD1 VPS13A BCOR KRAS BCOR SMAD4 EDNRB NOTCH2 SEMA3E CEP41 EDNRB TTC7A SKIV2L JAK3 TBCE RTEL1 NEK1 IL21 TRNS1 JAK3 ASXL1 MLH1 POLA1 PHOX2B XRCC2 SPINT2 FBLN5 F13B SNAI2 RAPSN CYBB CCN2 NIPBL TMEM231 ARX LEMD3 PTPN22 KIT COX1 COL14A1 SAR1B ZEB2 HSD3B7 CEP120 SMAD4 HNRNPU AHI1 KIT TMEM237 SLC5A1 TCF4 LPIN2 TRNW RREB1 TGFB1 STK11 TP63 AHI1 AXIN2 PLAGL1 APC IL12A KLRC4 BTK CCDC22 PDGFRA ALG3 ADAMTS3 PLG DKC1 FRMPD4 SMAD4 STK11 LMNA FGFR2 GDNF TSPAN7 BUB1B FASLG CREBBP RPS6KA3 PRTN3 COL3A1 LTBP4 APC PMPCA MBTPS2 DYNC2H1 PCSK1 SDHC BAZ1B PRSS2 F13A1 ZNF41 SUFU MED12 ND4 WASHC5 RERE DACT1 EDNRB ATRX PHOX2B UBE3B DLG3 ADAMTS3 ASCL1 SERPING1 FAN1 TBX1 ACTG2 MSH3 GTF2IRD1 VANGL1 SALL4 ARX MSH6 SMC3 CC2D2A IRGM BMPR1A FLNA SALL4 MUTYH PARN EP300 ISL1 TNFSF15 TEK CHEK2 USB1 TWNK SETD5 MKS1 TTC7A AGA TRNK IRF5 MYRF ENG MLH1 MNX1 AMER1 RIPK1 POLE HPGD LCT NPHP3 CCDC47 PHOX2B KDM6A COG8 MAP3K7 PGAP2 RPS6KA3 UPF3B NEUROG3 IL10RA TMEM67 WNT2B PTCH1 SIX1 PEX26 BUB3 ZFP57 RET EPHX1 FANCE FANCM IGHM SMO ZNF423 FLNA LIG4 TP53 PIBF1 AAGAB IL12A IL10RB FLCN SETBP1 PIGN MSH2 MLH1 MASP2 FOXH1 ARHGEF6 MBTPS2 USP27X PMS1 FAT4 TMEM138 TEK LRP2 GDF2 SALL4 SLC30A2 CYBB DHODH BDNF CYBA SDHC TTC37 JAK2 MLH1 NSD2 CDCA7 SDHC TERC GDI1 PEX1 SRC NLRC4 PIEZO1 FOXP3 ENPP1 ITGA6 RET PIGL RTTN MYO5B CYP27A1 EP300 CPLX1 PDGFRB SOX10 NSUN2 TGFB1 TRNS2 BMPR1A LIPA PIGO PIK3CA RFX6 RHBDF2 IGLL1 PIK3CA CAV1 HPS1 FOXE1 SIN3A LIMK1 TCF4 MYOD1 ABCB11 FGFR2 KRAS IL6 EPCAM CCDC28B STAT1 GDNF FAS ITGB4 DHCR7 AKR1D1 WAS SHH SMC1A IL2RA TLR4 RET PIGN STAT4 RAD21 HABP2 KLHL7 UBR1 NCF4 NRAS XIAP ZNF711 FLNA B2M EPCAM KLLN SLC6A8 PEX6 SEC23B CBLIF FGFR1 SRP54 SMO PRSS1 PLCG2 GPIHBP1 SALL1 PTEN NCF4 PALB2 BRIP1 NDUFB11 SDHB FERMT1 KCNAB2 CEP57 IRF5 TP53 PTPRJ ARL13B FAT4 ACSL4 TBX1 TERT DNMT3B KIFBP TTC7A
Inflammation of the large intestine
Genes 56
TTC37 RIPK1 OPLAH SLC9A3 CASP10 F13A1 RTEL1 ARPC1B MAP3K7 NCF4 XIAP IL10RA CIITA HLA-DRB1 NLRC4 FOXP3 WIPF1 RASGRP1 LRBA RFXANK TCF4 PRKCD TGFB1 FAS SKIV2L FAS CARMIL2 BACH2 RFX5 RFXAP PLCG2 MST1 IRGM IL10RB WAS GPIHBP1 SKIV2L ZAP70 COG6 HPS1 IL21 FERMT1 FASLG MASP2 IL6 HLA-B POLA1 NOD2 TNFAIP3 ZAP70 RET F13B GPR35 WAS STAT1 ABCB1