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Report for SNP rs3789604

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

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 901
EPCAM KMT2D CTBP1 SLC6A8 PRSS1 EDN3 CLCN4 INSR KRAS BLNK KCNAB2 BACH2 ARID1B STK11 STAT3 SPINK1 TCF4 ABCB1 EPCAM POLG MEFV CASP10 CTLA4 BRIP1 ATRX GPR35 MYLK TMEM138 TYMP TTC37 SALL4 SMO CHD7 ARHGEF6 HCCS PEX1 GLA CCR1 ND4 CCR6 TTC7A MLH3 PTCH1 PTF1A MSH2 MSH3 ATP7A STX3 B9D1 PIK3CA TCF4 ARX AP1B1 RUNX1 TRNK SETBP1 TFAP2A CEP57 PTCH1 SEMA3E CHST14 INPP5E MUTYH BCOR KIT TCTN2 SLX4 PALB2 PEX10 MITF BCOR CD3G IL10RB RAD21 F12 C4A BUB3 DHODH MNX1 LIPA GREB1L RPS6KA3 ARL3 CTNNB1 FCGR2A FANCA KLHL7 MST1 PEX12 DSE NCF4 SLC2A2 TCTN1 FOXF1 EDNRB F5 TEK AP1S1 SI XRCC2 TTC7A ASCL1 DICER1 MDM2 FGF8 MTTP OCRL ARL13B ERCC2 SRP54 TINF2 HSD3B7 LTBP4 ACTA2 CEP104 GTF2IRD1 UFD1 LETM1 FANCB TDGF1 FAS KIAA0586 CTC1 GPIHBP1 RFXANK CEP57 LPIN2 FANCM IRF5 PTPRJ GPC1 KITLG POLG WIPF1 GPC4 XRCC4 EP300 DIS3L2 TGFB1 VANGL1 ARMC9 NCF1 CLIP2 COG6 COMT INAVA HLA-DRB1 ACTG2 WAS DOK7 ZFP57 IL23R LBR ERAP1 TRMT5 SMAD4 APC DNMT3B ENPP1 DMPK HIRA BRCA1 CEP41 IQSEC2 MSH6 CPLX1 MSH6 WFS1 PMS1 CREBBP APC PLG SEC23B STK11 TJP2 HBB ZNF41 TEK IGLL1 CHRM3 PCSK1 STX1A ND6 AKT1 PLA2G2A RNF43 TERT HLA-B RMRP MKS1 BRCA2 IL2RB TRNL1 BMPR1A MAD2L2 ZMPSTE24 GREM1 MED12 ACOX2 MEFV SYP FOXP3 RTEL1 APC IL12RB1 SDHB PACS1 PLAGL1 NODAL MSH6 SEMA3C PEX13 SLC9A7 NEK1 SOX10 MED12 RPS20 FGFR2 KMT2A AGA PTEN RFWD3 PIGN ACTG2 PIBF1 ABL1 NCF1 IL2RA MYC SLC7A7 CAVIN1 CDC45 TCF4 APC DLL1 ALG8 CTC1 SRC RET TRNL1 MED12 HDAC8 PALB2 FGFR1 SDHC SDHD CHEK2 PIK3CA DHCR7 KIT MNX1 RTTN AMACR KEAP1 APC RECQL4 PEX16 PMS2 POLG MITF SNAI2 SALL4 SDHB TRNF EPHX1 CCDC28B SLCO2A1 PHOX2B PDGFRA APC AURKA AMER1 SALL1 HCFC1 PRDM16 AXIN2 ADAMTS3 TP53 NEUROG3 HYOU1 ITGB4 SDHC CBLIF ND1 MSH2 MBTPS2 RREB1 PLA2G4A SDHC TRNE UBE3B NPHP3 CFTR SLC5A1 AKR1D1 PHOX2B MKKS EDN3 FAT4 RET IL21 PEX19 HLA-DRB1 FOXE1 BDNF LMOD1 TBCE SOX10 FBLN5 GJB2 ANTXR2 HELLS PHOX2B TGFBR2 KCNJ11 KRAS RECQL4 GDNF DGAT1 FAS PKD1 FANCD2 CNKSR2 MBTPS2 MMP21 DISP1 PDGFRL SOX10 LRP2 SLC39A4 AXIN2 ABCB4 PLCG2 SEMA4A TWNK NRAS BAZ1B EDN3 CYP7B1 TRNS2 ASCL1 POLE TLR2 PIK3CA CENPF CCBE1 EDN3 SIN3A ASXL1 MKS1 FREM1 PIGO UBR1 SMAD4 CFTR GP1BB CFC1 TGFB1 PIK3CA EFL1 SBDS RAD51 PTCHD1 ACSL4 KIT SLC6A8 SOX10 PEX11B FAH LIG4 CEP41 CDK8 SAR1B RNF43 STAT1 ALG3 BMPR1A FGFR2 TET2 PAX3 FGFR3 SLC10A2 PTEN APC XIAP RAC2 ERGIC1 NTHL1 RELA AIRE STAT4 SF3B4 CDCA7 L1CAM PIGV PIGO TCOF1 POLE ALG13 RFX5 AKT1 ADAMTS3 APC PMS1 PIGL RAD51C PAK3 CDKN2A ENG GUCY2C L1CAM PGM3 TMEM67 TBX1 IL12A PAX3 CTRC MLH1 PTPN12 MLH3 SETD5 FRMPD4 MAP3K7 CCDC22 COL14A1 MYOD1 IL10RA BBS1 AXIN2 EP300 ECE1 PARN EDNRB SMAD4 HMBS FOXF1 PRKAR1A PIGW DMD CXCR4 MASP2 IRGM GATA6 GABRD RET NRTN ITGA8 MUSK RET MPI MSH2 AHI1 C12ORF65 KIF7 SPINK5 IL6 NDUFB11 C12ORF65 TNFSF15 HYLS1 PRKCD FLNA RPS19 CCN2 FAT4 KDM6A RPS6KA3 SUFU EFL1 ZNF81 LIPA DOCK8 PIGY CCDC47 TMEM231 LIMK1 MINPP1 FANCL FGF20 KIFBP CD79A DDX59 LIG4 ARL6 ELN IL12A-AS1 KIT SLC6A19 FOXH1 LCT PORCN PRSS2 WRAP53 RAB39B MYRF DLC1 CTNNB1 FGFRL1 WNT2B CLCA4 GDNF HABP2 SALL4 SAA1 SERPING1 BMPR1A ITGA6 AKT1 LRBA BAAT DDX59 KLRC4 PLG PEX6 HMGA2 NCF4 POLG EP300 PALLD TRNQ CDKN2A POLR1D RET CTLA4 IL1RAPL1 B3GALT6 CYBC1 MTOR SRCAP HSD3B7 MYD88 B2M TP53 LRP2 FLI1 SIX3 RAD21 PMS2 EDN3 GAS1 FASLG COX3 SDHD SMAD4 ARVCF MID2 C1R RERE OPLAH INPP5E TGIF1 SPINK5 TGFB1 SKI SLC9A3 SDHC SLC18A3 MKKS UBR1 CISD2 B3GLCT TSPAN7 TNFAIP3 SEMA3D LEMD3 HLA-DPB1 ZAP70 RFXAP UBE2T AHI1 TMEM216 F13A1 TRNS1 ATP8B1 COMP SMC1A LMNA ARX TWNK GDNF TRNH PIGV TMEM237 EFEMP2 PEX14 PORCN FLCN RBM10 IL12A SPIB RFC2 ERCC4 NLRC4 POLD1 DCC CAV1 CCNQ NCF2 CC2D2A SRP54 DHCR24 ABCC8 SPINT2 NSD2 PMPCA MYCN SKIV2L JMJD1C ARPC1B PDGFRB CEP120 SIX1 BRCA2 ZBTB24 COX1 NSUN2 JAK3 NAA10 IDS POLR1C TYMP ZFPM2 SBDS RPGRIP1L RAD51C ND5 ITCH MYO5B BRCA1 BUB1B PRTN3 ZEB2 CYBB POLD1 SNAI2 ZNF711 ELN MUTYH PLVAP RET COL5A1 KIT GATA6 EDNRB RMRP GDI1 TCTN3 PIK3C2A STRA6 SETD5 PIEZO1 PTCH2 TBX1 CCBE1 MMEL1 BUB1 JAK2 COX2 WNT4 IRF5 GNAS SEC24C DYNC2H1 FAS CCND1 CPLANE1 ODC1 SAR1B PEX2 ISL1 STAT1 GPC3 PGAP2 NUP88 FANCE CYBA CBL SDHB NPHP3 TMEM237 SLC46A1 CHST14 NOP10 SMO MPI RFWD3 PDGFRA FTSJ1 UPF3B SRCAP RIPK1 COX7B IGHM CLMP MYH11 TTC7A CDON NIPBL PTEN SLC29A3 SERPING1 COG8 ADAM17 KIFBP FBLN5 PNLIP NPHP1 CSPP1 PEX5 ACVRL1 CXORF56 RRM2B DCTN4 FLCN ECE1 ABCB11 FRAS1 EDNRB FANCF EXOC6B LONP1 MYO1H PEX26 AKR1D1 TRIP13 CFTR SEC23B SALL4 JAK3 SMC3 GDNF ZIC2 MYO5B SNAI2 SH3KBP1 KAT6A RHBDF2 TTC37 FARSB FANCG NIPBL RERE ASXL1 KATNIP PTRH2 MLXIPL ALDH18A1 SALL1 PEX12 FANCI TNFRSF1A MLH1 PIGN UBAC2 EYA1 POLG ZAP70 TP63 BUB1 CARMIL2 DNMT3B RTEL1 EWSR1 CEP120 GJB6 AK2 ASXL1 SERPING1 TNPO3 TGFBR2 MECP2 HLA-DPA1 LRRC8A SHPK BAX TLR4 DMP1 FAN1 ZNF423 RAPSN BMPR1A LBR NOTCH2 MLH1 FOXP3 DACT1 MLH1 EDNRB KLLN GATA1 BMPR1A GTF2I MVK EDNRB GDF2 WAS FLNA PTEN MCC USP27X EPCAM DHCR7 FBN2 IL10 RASGRP1 FLNA SHH CIITA NPM1 SH2B1 INHBA TMEM237 BMPR1A POU2AF1 DNAJC21 COX4I2 SKIV2L SOX10 MLH3 VPS13A NOTCH3 AGTR2 DACT1 HLA-B WT1 TP53 PTPN22 RARB CEP290 CYBA TRNW SRP54 GLI2 EDN3 CD79B TERC HPS1 WASHC5 AAGAB TP53 SRSF2 CYP27A1 KRAS HNRNPU BUB1B NCF2 RET DLG3 FANCC WHCR RAD54B TBL2 SDHB NOD2 MSH2 TMPRSS6 RBM8A CLMP AP1S1 NOTCH2 RFX6 FERMT1 ITGB2 TCF3 MCM6 CYBB PIK3R1 USF3 DNAJC21 MTTP SDHA ACTG2 NHP2 PEX3 SUFU HPGD EIF2AK3 BTK ELN ENG CD55 HYMAI PHOX2B GATA6 USB1 USP9X FLNB MBTPS2 PHOX2B SMAD4 PGAP3 APC AMACR SMAD7 DKC1 MKS1 POLA1 F13B SLC30A2 FGFR1 COL3A1
Protein Mutations 1
C10D
SNP 8
rs1217414 rs12760457 rs1310182 rs2097432 rs2476601 rs2488457 rs33996649 rs3789604
HP:0002037: Inflammation of the large intestine
Genes 57
RFXANK MAP3K7 NLRC4 IL10RA WIPF1 BACH2 STAT1 FOXP3 RTEL1 FASLG ABCB1 WAS NOD2 TGFB1 IL10RB CASP10 XIAP FAS MASP2 RIPK1 IRGM ZAP70 COG6 RASGRP1 FERMT1 CIITA INAVA OPLAH GPR35 MST1 HLA-DRB1 CARMIL2 WAS TTC37 SKIV2L SLC9A3 PLCG2 ARPC1B SKIV2L LRBA RFX5 HLA-B TNFAIP3 FAS IL6 ZAP70 RFXAP NCF4 F13A1 PRKCD TCF4 RET POLA1 F13B IL21 HPS1 GPIHBP1
Protein Mutations 1
R139C
SNP 9
rs1217414 rs12760457 rs1310182 rs2097432 rs2476601 rs2488457 rs33996649 rs3789604 rs9557195