dbEM
A Database of Epigenetic Modifiers
Cite: Nanda JS, Kumar R, Raghava GP. (2016) dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. Sci Rep. 6:19340.
Protein: PRDM2 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 585208 LUNG c.4975G>T p.A1659S COSMIC PASSENGER/OTHER Benign 2 587238 LARGE INTESTINE c.127G>A p.G43S COSMIC PASSENGER/OTHER Probably Damaging 3 587256 LARGE INTESTINE c.4459delA p.V1490fs*74 COSMIC NP NP 4 587316 LARGE INTESTINE c.831T>A p.D277E COSMIC PASSENGER/OTHER Benign 5 587338 LARGE INTESTINE c.846A>T p.E282D COSMIC PASSENGER/OTHER Benign 6 587342 LARGE INTESTINE c.4094C>T p.T1365M COSMIC PASSENGER/OTHER Probably Damaging 7 587350 LARGE INTESTINE c.846A>T p.E282D COSMIC PASSENGER/OTHER Benign 8 587374 LARGE INTESTINE c.1220G>A p.R407Q COSMIC PASSENGER/OTHER Probably Damaging 9 587376 LARGE INTESTINE c.4567A>C p.K1523Q COSMIC PASSENGER/OTHER Possibly Damaging 10 761 HAEMATOPOIETIC AND LYMPHOID TISSUE c.3502G>A p.V1168M COSMIC PASSENGER/OTHER Probably Damaging 11 761-01-1TD HAEMATOPOIETIC AND LYMPHOID TISSUE c.3502G>A p.V1168M COSMIC PASSENGER/OTHER Probably Damaging 12 8015299 PANCREAS c.5010C>T p.S1670S COSMIC NP NP 13 BN43T LIVER c.1794A>G p.I598M COSMIC PASSENGER/OTHER Probably Damaging 14 E7 EYE c.4798T>C p.S1600P COSMIC PASSENGER/OTHER Benign 15 ESO-1130 OESOPHAGUS c.3615T>G p.N1205K COSMIC PASSENGER/OTHER Probably Damaging 16 ESO-161 OESOPHAGUS c.1221A>C p.R407R COSMIC NP NP 17 ESO-721 OESOPHAGUS c.1225G>T p.E409* COSMIC NP NP 18 ESO-859 OESOPHAGUS c.4910T>C p.F1637S COSMIC PASSENGER/OTHER Possibly Damaging 19 HCC2998 LARGE INTESTINE c.1409C>A p.S470Y COSMIC PASSENGER/OTHER Probably Damaging 20 HCC69T LIVER c.4324C>T p.Q1442* COSMIC NP NP 21 ID51 HAEMATOPOIETIC AND LYMPHOID TISSUE c.849_850delTG p.D283fs*2 COSMIC NP NP 22 LC_S11 LUNG c.2338G>T p.D780Y COSMIC PASSENGER/OTHER Probably Damaging 23 LUAD-F00162 LUNG c.2392C>T p.P798S COSMIC PASSENGER/OTHER Benign 24 LUAD-F00162 LUNG c.2445_2452delTAGCAGTG p.S816fs*17 COSMIC NP NP 25 LUAD-LIP77 LUNG c.2362G>A p.G788R COSMIC PASSENGER/OTHER Probably Damaging 26 LUAD-NYU1027 LUNG c.3989C>T p.T1330I COSMIC PASSENGER/OTHER Possibly Damaging 27 LUAD-YINHD LUNG c.5082G>T p.P1694P COSMIC NP NP 28 MDA-N HAEMATOPOIETIC AND LYMPHOID TISSUE c.2108_2109insACC p.P703_A704insP COSMIC NP NP 29 ME009T SKIN c.4421C>T p.A1474V COSMIC PASSENGER/OTHER Benign 30 OV207 OVARY c.1519G>A p.E507K COSMIC PASSENGER/OTHER Probably Damaging 31 RK003_C01 LIVER c.3564G>T p.G1188G COSMIC NP NP 32 RK064_C01 LIVER c.4458_4459insA p.V1490fs*6 COSMIC NP NP 33 S00501 LUNG c.3772G>A p.E1258K COSMIC PASSENGER/OTHER Possibly Damaging 34 SNB75 CENTRAL NERVOUS SYSTEM c.3376_3378delGTT p.V1126delV COSMIC NP NP 35 TARGET-30-PAPTLA AUTONOMIC GANGLIA c.980C>A p.S327* COSMIC NP NP 36 TCGA-05-4432-01 LUNG c.3123G>A p.M1041I COSMIC PASSENGER/OTHER Benign 37 TCGA-13-0720-01 OVARY c.2694C>T p.G898G COSMIC NP NP 38 TCGA-21-5782-01 LUNG c.4239G>A p.S1413S COSMIC NP NP 39 TCGA-21-5786-01 LUNG c.4584G>T p.Q1528H COSMIC PASSENGER/OTHER Benign 40 TCGA-22-4591-01 LUNG c.1042G>C p.E348Q COSMIC PASSENGER/OTHER Probably Damaging 41 TCGA-25-1623-01 OVARY c.2104_2105insCTC p.P703_A704insP COSMIC NP NP 42 TCGA-29-1761-01 OVARY c.2772T>A p.D924E COSMIC PASSENGER/OTHER Benign 43 TCGA-35-4122-01 LUNG c.4507G>T p.A1503S COSMIC PASSENGER/OTHER Benign 44 TCGA-37-4133-01 LUNG c.2020A>G p.T674A COSMIC PASSENGER/OTHER Benign 45 TCGA-44-2659-01 LUNG c.2387G>T p.S796I COSMIC PASSENGER/OTHER Probably Damaging 46 TCGA-44-3398-01 LUNG c.722C>A p.T241N COSMIC PASSENGER/OTHER Benign 47 TCGA-44-6779-01 LUNG c.5060G>A p.R1687Q COSMIC PASSENGER/OTHER Probably Damaging 48 TCGA-49-4490-01 LUNG c.3021C>T p.C1007C COSMIC NP NP 49 TCGA-49-6742-01 LUNG c.4639C>T p.P1547S COSMIC PASSENGER/OTHER Probably Damaging 50 TCGA-56-5897-01 LUNG c.4983G>C p.L1661F COSMIC PASSENGER/OTHER Benign 51 TCGA-60-2698-01 LUNG c.3595G>C p.E1199Q COSMIC PASSENGER/OTHER Probably Damaging 52 TCGA-66-2768-01 LUNG c.5048G>A p.R1683H COSMIC PASSENGER/OTHER Probably Damaging 53 TCGA-70-6723-01 LUNG c.1221A>C p.R407R COSMIC NP NP 54 TCGA-78-7145-01 LUNG c.1999C>G p.L667V COSMIC PASSENGER/OTHER Possibly Damaging 55 TCGA-78-7147-01 LUNG c.4842G>C p.R1614S COSMIC PASSENGER/OTHER Possibly Damaging 56 TCGA-91-6836-01 LUNG c.2506G>T p.G836C COSMIC PASSENGER/OTHER Probably Damaging 57 TCGA-97-7554-01 LUNG c.2827G>T p.D943Y COSMIC PASSENGER/OTHER Possibly Damaging 58 TCGA-A5-A0G5-01 ENDOMETRIUM c.1415T>G p.V472G COSMIC PASSENGER/OTHER Probably Damaging 59 TCGA-A5-A0GH-01 ENDOMETRIUM c.2809A>G p.T937A COSMIC PASSENGER/OTHER Benign 60 TCGA-A5-A0VP-01 ENDOMETRIUM c.1227G>A p.E409E COSMIC NP NP 61 TCGA-A6-2672-01 LARGE INTESTINE c.2900C>A p.P967H COSMIC PASSENGER/OTHER Probably Damaging 62 TCGA-A6-2676-01 LARGE INTESTINE c.2001T>C p.L667L COSMIC NP NP 63 TCGA-A6-2678-01 LARGE INTESTINE c.4047C>G p.H1349Q COSMIC PASSENGER/OTHER Probably Damaging 64 TCGA-A6-3809-01 LARGE INTESTINE c.2675T>C p.L892P COSMIC PASSENGER/OTHER Probably Damaging 65 TCGA-A6-6781-01 LARGE INTESTINE c.4768A>G p.K1590E COSMIC PASSENGER/OTHER Benign 66 TCGA-A7-A0CJ-01 BREAST c.1887G>A p.L629L COSMIC NP NP 67 TCGA-A8-A06X-01 BREAST c.3889A>T p.S1297C COSMIC PASSENGER/OTHER Probably Damaging 68 TCGA-AA-3492-01 LARGE INTESTINE c.2883G>A p.L961L COSMIC NP NP 69 TCGA-AA-3492-01 LARGE INTESTINE c.4270delA p.N1426fs*3 COSMIC NP NP 70 TCGA-AA-3492-01 LARGE INTESTINE c.81G>A p.P27P COSMIC NP NP 71 TCGA-AA-3510-01 LARGE INTESTINE c.4333G>A p.D1445N COSMIC PASSENGER/OTHER Possibly Damaging 72 TCGA-AA-3514-01 LARGE INTESTINE c.1184G>A p.C395Y COSMIC CANCER Probably Damaging 73 TCGA-AA-3516-01 LARGE INTESTINE c.5055G>A p.A1685A COSMIC NP NP 74 TCGA-AA-3554-01 LARGE INTESTINE c.846A>T p.E282D COSMIC PASSENGER/OTHER Benign 75 TCGA-AA-3663-01 LARGE INTESTINE c.3481C>T p.P1161S COSMIC PASSENGER/OTHER Benign 76 TCGA-AA-3672-01 LARGE INTESTINE c.2726G>T p.G909V COSMIC PASSENGER/OTHER Benign 77 TCGA-AA-3697-01 LARGE INTESTINE c.847_849delGAT p.D287delD COSMIC NP NP 78 TCGA-AA-3845-01 LARGE INTESTINE c.5038T>C p.Y1680H COSMIC PASSENGER/OTHER Probably Damaging 79 TCGA-AA-3966-01 LARGE INTESTINE c.4459delA p.V1490fs*74 COSMIC NP NP 80 TCGA-AA-3984-01 LARGE INTESTINE c.164A>C p.K55T COSMIC PASSENGER/OTHER Probably Damaging 81 TCGA-AA-3989-01 LARGE INTESTINE c.3244T>A p.S1082T COSMIC PASSENGER/OTHER Probably Damaging 82 TCGA-AA-A00J-01 LARGE INTESTINE c.1082C>A p.P361Q COSMIC PASSENGER/OTHER Probably Damaging 83 TCGA-AA-A00K-01 LARGE INTESTINE c.4241C>A p.S1414* COSMIC NP NP 84 TCGA-AA-A01R-01 LARGE INTESTINE c.5048G>A p.R1683H COSMIC PASSENGER/OTHER Probably Damaging 85 TCGA-AD-5900-01 LARGE INTESTINE c.4423G>A p.A1475T COSMIC PASSENGER/OTHER Probably Damaging 86 TCGA-AD-5900-01 LARGE INTESTINE c.4936delG p.P1648fs*14 COSMIC NP NP 87 TCGA-AD-6964-01 LARGE INTESTINE c.832_834delGAA p.E282delE COSMIC NP NP 88 TCGA-AD-6964-01 LARGE INTESTINE c.834A>T p.E278D COSMIC PASSENGER/OTHER Benign 89 TCGA-AG-3892-01 LARGE INTESTINE c.3312A>C p.E1104D COSMIC PASSENGER/OTHER Benign 90 TCGA-AG-A002-01 LARGE INTESTINE c.3838A>G p.I1280V COSMIC PASSENGER/OTHER Benign 91 TCGA-AP-A051-01 ENDOMETRIUM c.2390C>A p.P797H COSMIC PASSENGER/OTHER Probably Damaging 92 TCGA-AP-A051-01 ENDOMETRIUM c.4183C>T p.R1395* COSMIC NP NP 93 TCGA-AP-A059-01 ENDOMETRIUM c.2240G>T p.S747I COSMIC PASSENGER/OTHER Probably Damaging 94 TCGA-AP-A059-01 ENDOMETRIUM c.4686G>A p.S1562S COSMIC NP NP 95 TCGA-AP-A059-01 ENDOMETRIUM c.773C>T p.A258V COSMIC PASSENGER/OTHER Possibly Damaging 96 TCGA-AP-A0LE-01 ENDOMETRIUM c.4420G>A p.A1474T COSMIC PASSENGER/OTHER Benign 97 TCGA-AP-A0LM-01 ENDOMETRIUM c.1229G>A p.R410Q COSMIC PASSENGER/OTHER Probably Damaging 98 TCGA-AP-A0LM-01 ENDOMETRIUM c.3173C>A p.S1058Y COSMIC PASSENGER/OTHER Probably Damaging 99 TCGA-AP-A0LT-01 ENDOMETRIUM c.1497A>G p.R499R COSMIC NP NP 100 TCGA-AX-A05Z-01 ENDOMETRIUM c.4919A>C p.K1640T COSMIC PASSENGER/OTHER Possibly Damaging 101 TCGA-AX-A0J0-01 ENDOMETRIUM c.1655A>C p.D552A COSMIC PASSENGER/OTHER Probably Damaging 102 TCGA-AX-A0J0-01 ENDOMETRIUM c.3632G>A p.R1211Q COSMIC PASSENGER/OTHER Possibly Damaging 103 TCGA-AX-A0J1-01 ENDOMETRIUM c.2337C>T p.S779S COSMIC NP NP 104 TCGA-AY-6386-01 LARGE INTESTINE c.2694C>T p.G898G COSMIC NP NP 105 TCGA-AZ-4315-01 LARGE INTESTINE c.4423G>A p.A1475T COSMIC PASSENGER/OTHER Probably Damaging 106 TCGA-AZ-4315-01 LARGE INTESTINE c.4665G>A p.Q1555Q COSMIC NP NP 107 TCGA-AZ-4315-01 LARGE INTESTINE c.5145C>A p.F1715L COSMIC PASSENGER/OTHER Benign 108 TCGA-AZ-6601-01 LARGE INTESTINE c.4942C>T p.P1648S COSMIC PASSENGER/OTHER Probably Damaging 109 TCGA-AZ-6601-01 LARGE INTESTINE c.672G>A p.P224P COSMIC NP NP 110 TCGA-B5-A0JY-01 ENDOMETRIUM c.2533G>A p.E845K COSMIC PASSENGER/OTHER Probably Damaging 111 TCGA-B5-A0JY-01 ENDOMETRIUM c.3850G>T p.D1284Y COSMIC PASSENGER/OTHER Probably Damaging 112 TCGA-B5-A0JY-01 ENDOMETRIUM c.4241C>T p.S1414L COSMIC PASSENGER/OTHER Possibly Damaging 113 TCGA-B5-A0K6-01 ENDOMETRIUM c.1627G>T p.E543* COSMIC NP NP 114 TCGA-B5-A0K9-01 ENDOMETRIUM c.3108C>T p.P1036P COSMIC NP NP 115 TCGA-B5-A11E-01 ENDOMETRIUM c.1925C>T p.A642V COSMIC PASSENGER/OTHER Probably Damaging 116 TCGA-B5-A11E-01 ENDOMETRIUM c.3238G>A p.A1080T COSMIC PASSENGER/OTHER Probably Damaging 117 TCGA-BG-A0VZ-01 ENDOMETRIUM c.121C>T p.R41W COSMIC PASSENGER/OTHER Probably Damaging 118 TCGA-BS-A0TJ-01 ENDOMETRIUM c.348G>A p.L116L COSMIC NP NP 119 TCGA-BS-A0UF-01 ENDOMETRIUM c.2337C>T p.S779S COSMIC NP NP 120 TCGA-BS-A0UV-01 ENDOMETRIUM c.4241C>T p.S1414L COSMIC PASSENGER/OTHER Possibly Damaging 121 TCGA-C4-A0F7-01 URINARY TRACT c.2996C>A p.S999Y COSMIC PASSENGER/OTHER Possibly Damaging 122 TCGA-C8-A275-01 BREAST c.831_832insGAA p.E282_D283insE COSMIC NP NP 123 TCGA-CH-5769-01 PROSTATE c.1387G>A p.A463T COSMIC PASSENGER/OTHER Benign 124 TCGA-CM-4743-01 LARGE INTESTINE c.2248C>A p.L750I COSMIC PASSENGER/OTHER Possibly Damaging 125 TCGA-CM-5861-01 LARGE INTESTINE c.2862C>A p.P954P COSMIC NP NP 126 TCGA-D1-A103-01 ENDOMETRIUM c.4702C>T p.P1568S COSMIC PASSENGER/OTHER Benign 127 TCGA-D1-A160-01 ENDOMETRIUM c.3045C>A p.T1015T COSMIC NP NP 128 TCGA-D5-6532-01 LARGE INTESTINE c.2535A>G p.E845E COSMIC NP NP 129 TCGA-DI-A0WH-01 ENDOMETRIUM c.338T>C p.L113S COSMIC PASSENGER/OTHER Probably Damaging 130 TCGA-DK-A1AC-01 URINARY TRACT c.904G>A p.E302K COSMIC PASSENGER/OTHER Benign 131 TCGA-DK-A2I6-01 URINARY TRACT c.1913A>G p.K638R COSMIC PASSENGER/OTHER Possibly Damaging 132 TCGA-E2-A15P-01 BREAST c.3369_3371delTGT p.V1126delV COSMIC NP NP 133 TCGA-G4-6299-01 LARGE INTESTINE c.4168_4169delGG p.G1390fs*14 COSMIC NP NP 134 TCGA-G4-6304-01 LARGE INTESTINE c.852T>A p.D284E COSMIC PASSENGER/OTHER Benign 135 TCGA-G4-6321-01 LARGE INTESTINE c.2692G>A p.G898S COSMIC PASSENGER/OTHER Probably Damaging 136 TCGA-G4-6628-01 LARGE INTESTINE c.3993C>T p.T1331T COSMIC NP NP 137 TCGA-G4-6628-01 LARGE INTESTINE c.834A>T p.E278D COSMIC PASSENGER/OTHER Benign 138 TCGA-GV-A3JX-01 URINARY TRACT c.403G>A p.E135K COSMIC PASSENGER/OTHER Probably Damaging 139 TK10 KIDNEY c.5000_5001delAG p.E1667fs*34 COSMIC NP NP 140 WA22 PROSTATE c.3832T>A p.S1278T COSMIC PASSENGER/OTHER Probably Damaging 141 WA56 PROSTATE c.4444C>T p.P1482S COSMIC PASSENGER/OTHER Probably Damaging 142 YUZINO SKIN c.4598A>G p.K1533R COSMIC PASSENGER/OTHER Probably Damaging 143 ccRCC-27 KIDNEY c.4618delG p.G1540fs*24 COSMIC NP NP 144 pfg008T STOMACH c.4459delA p.V1490fs*74 COSMIC NP NP
*NP: Not Predicted -
Copy number variation and expression profile (+)
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Gene Essentiality Data (+)
Note: Lower the GARP score (more negative), higher the essentiality of the gene. P-value tells about the significane of GARP score.test -
Tertiary structure (+)
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Structure Domains (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PB002602 Pfam-B_2602 4 209 2.7e-90 PB013260 Pfam-B_13260 75 113 0.00091 PF00856 SET 93 141 1.2e-05 PF13894 zf-C2H2_4 360 382 0.0058 PF00096 zf-C2H2 390 412 0.0037 PF13894 zf-C2H2_4 483 506 0.0031 PF13894 zf-C2H2_4 1134 1156 0.92 PF13894 zf-C2H2_4 1191 1214 1.1 PF13894 zf-C2H2_4 1455 1473 0.07 -
Sequence Alignment (+)
Users must enabled the Java in their browser to see sequence alignments.
Users can also download Java from here.1. Sequence alignment with 1000 genome variations:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 2. Mutants are not present in CCLE!!3. Sequence alignment with COSMIC mutants:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 4. Sequence alignment with homologus proteins:
Click on button to get Sequence alignment with Coverage, Consensus and Quality -
Sequence Profiles (+)
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Post Translational Modifications (+)
$x "); for($d=2;$d<$l777;$d++) { fwrite($FP6,$row6[$d]); fwrite($FP7,"$row6[$d] "); fwrite($FP6,"\t"); } fwrite($FP6,"\n"); fwrite($FP7,""); } fclose($FP6); echo""; } else{echo"
"; ##### table ##### $ptm_tr=file_get_contents("$dir/ptm"); if($ptm_tr != '') { echo"S. No. Position Amino acid Type Post translational modifications are not found!!";} ?> -
Other Databases Link (+)
Proteomics DB COSMIC Gene Atlas STRING PIR PRDM2 PRDM2 PRDM2 ENSP00000235372 Q13029 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q13029 PRDM2 ENSP00000235372 PRDM2 Q13029 Expression Atlas Protein Atlas OMIM IntAct PharmGKB PRDM2 ENSP00000235372 601196 Q13029 PA33715
