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: CHD3 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 1342576 BREAST c.4729G>A p.E1577K COSMIC PASSENGER/OTHER Benign 2 2334196 LUNG c.4015A>C p.K1339Q COSMIC CANCER Probably Damaging 3 587220 LARGE INTESTINE c.292G>A p.G98R COSMIC PASSENGER/OTHER Benign 4 587224 LARGE INTESTINE c.5701C>T p.R1901C COSMIC PASSENGER/OTHER Probably Damaging 5 587226 LARGE INTESTINE c.5053C>T p.R1685* COSMIC NP NP 6 587302 LARGE INTESTINE c.2363T>C p.F788S COSMIC PASSENGER/OTHER Probably Damaging 7 587332 LARGE INTESTINE c.5861C>A p.P1954H COSMIC PASSENGER/OTHER Probably Damaging 8 587342 LARGE INTESTINE c.1356G>T p.E452D COSMIC CANCER Benign 9 587342 LARGE INTESTINE c.3421C>A p.L1141M COSMIC CANCER Probably Damaging 10 587376 LARGE INTESTINE c.3010T>G p.F1004V COSMIC PASSENGER/OTHER Probably Damaging 11 AMO1 HAEMATOPOIETIC AND LYMPHOID TISSUE c.2593A>G p.I865V COSMIC PASSENGER/OTHER Benign 12 CHC155T LIVER c.5323C>G p.P1775A COSMIC PASSENGER/OTHER Probably Damaging 13 DLBCL705 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1432T>C p.Y478H COSMIC PASSENGER/OTHER Possibly Damaging 14 DLBCL785 HAEMATOPOIETIC AND LYMPHOID TISSUE c.2678C>T p.S893F COSMIC PASSENGER/OTHER Probably Damaging 15 DLBCL793 HAEMATOPOIETIC AND LYMPHOID TISSUE c.861G>T p.K287N COSMIC PASSENGER/OTHER Probably Damaging 16 DLBCL799 HAEMATOPOIETIC AND LYMPHOID TISSUE c.861G>T p.K287N COSMIC PASSENGER/OTHER Probably Damaging 17 ESO-0292 OESOPHAGUS c.613T>C p.S205P COSMIC PASSENGER/OTHER Possibly Damaging 18 ESO-1133 OESOPHAGUS c.911A>T p.K304M COSMIC PASSENGER/OTHER Probably Damaging 19 ESO-717 OESOPHAGUS c.1664T>C p.V555A COSMIC PASSENGER/OTHER Benign 20 H1155 LUNG c.5630C>T p.A1877V COSMIC PASSENGER/OTHER Probably Damaging 21 H1299 LUNG c.5735C>T p.T1912M COSMIC PASSENGER/OTHER Possibly Damaging 22 HCT-15 LARGE INTESTINE c.521C>A p.A174D COSMIC PASSENGER/OTHER Probably Damaging 23 ID46 HAEMATOPOIETIC AND LYMPHOID TISSUE c.929T>C p.V310A COSMIC PASSENGER/OTHER Benign 24 IPMN11 PANCREAS c.3002C>G p.T1001S COSMIC PASSENGER/OTHER Probably Damaging 25 LAU149 SKIN c.3128C>T p.P1043L COSMIC PASSENGER/OTHER Possibly Damaging 26 LC_C6 LUNG c.435G>C p.E145D COSMIC PASSENGER/OTHER Benign 27 LUAD-B02594 LUNG c.1246G>T p.G416C COSMIC PASSENGER/OTHER Probably Damaging 28 LUAD-NYU201 LUNG c.700A>C p.I234L COSMIC PASSENGER/OTHER Benign 29 LUAD-RT-S01777 LUNG c.4876G>T p.G1626* COSMIC NP NP 30 LUAD-RT-S01831 LUNG c.725T>C p.L242P COSMIC PASSENGER/OTHER Probably Damaging 31 LUAD-S01356 LUNG c.4243C>A p.R1415S COSMIC PASSENGER/OTHER Probably Damaging 32 LUAD-S01405 LUNG c.188G>A p.G63E COSMIC PASSENGER/OTHER Possibly Damaging 33 LUAD-S01478 LUNG c.5471A>C p.H1824P COSMIC PASSENGER/OTHER Probably Damaging 34 MD-220 CENTRAL NERVOUS SYSTEM c.721G>C p.A241P COSMIC PASSENGER/OTHER Benign 35 MOLT-4 HAEMATOPOIETIC AND LYMPHOID TISSUE c.4531C>T p.R1511C COSMIC PASSENGER/OTHER Probably Damaging 36 OV207 OVARY c.1379G>A p.R460H COSMIC CANCER Probably Damaging 37 PA285 PANCREAS c.4778T>C p.M1593T COSMIC PASSENGER/OTHER Benign 38 PR-00-1165 PROSTATE c.5793C>T p.Y1931Y COSMIC NP NP 39 PR-09-2517 PROSTATE c.4034A>C p.K1345T COSMIC CANCER Probably Damaging 40 RK064_C01 LIVER c.561C>T p.T187T COSMIC NP NP 41 S00501 LUNG c.3097T>C p.Y1033H COSMIC PASSENGER/OTHER Probably Damaging 42 SWE-22 PROSTATE c.3004C>T p.R1002* COSMIC NP NP 43 SWE-2B PROSTATE c.1200C>A p.A400A COSMIC NP NP 44 T97 PROSTATE c.1730delT p.M577fs*33 COSMIC NP NP 45 TCGA-05-4410-01 LUNG c.719C>T p.P240L COSMIC PASSENGER/OTHER Possibly Damaging 46 TCGA-05-5420-01 LUNG c.4385A>G p.H1462R COSMIC PASSENGER/OTHER Probably Damaging 47 TCGA-21-5787-01 LUNG c.2243G>T p.R748L COSMIC PASSENGER/OTHER Probably Damaging 48 TCGA-24-1843-01 OVARY c.1381G>C p.V461L COSMIC PASSENGER/OTHER Probably Damaging 49 TCGA-29-1763-01 OVARY c.5706C>T p.S1902S COSMIC NP NP 50 TCGA-34-5231-01 LUNG c.1602A>T p.P534P COSMIC NP NP 51 TCGA-39-5021-01 LUNG c.284A>G p.Y95C COSMIC PASSENGER/OTHER Probably Damaging 52 TCGA-44-8119-01 LUNG c.2140C>G p.P714A COSMIC PASSENGER/OTHER Probably Damaging 53 TCGA-60-2724-01 LUNG c.1933G>T p.G645W COSMIC PASSENGER/OTHER Probably Damaging 54 TCGA-61-1895-01 OVARY c.510G>T p.R170S COSMIC PASSENGER/OTHER Probably Damaging 55 TCGA-61-1900-01 OVARY c.5475C>G p.P1825P COSMIC NP NP 56 TCGA-66-2734-01 LUNG c.3357C>A p.I1119I COSMIC NP NP 57 TCGA-69-7979-01 LUNG c.2348A>C p.H783P COSMIC PASSENGER/OTHER Probably Damaging 58 TCGA-75-5126-01 LUNG c.1018G>T p.G340C COSMIC PASSENGER/OTHER Benign 59 TCGA-78-7539-01 LUNG c.418C>G p.L140V COSMIC PASSENGER/OTHER Benign 60 TCGA-A2-A0YM-01 BREAST c.1868G>A p.R623H COSMIC PASSENGER/OTHER Probably Damaging 61 TCGA-A3-3363-01 KIDNEY c.3303C>A p.Y1101* COSMIC NP NP 62 TCGA-A3-3363-01 KIDNEY c.5117G>A p.R1706Q COSMIC PASSENGER/OTHER Possibly Damaging 63 TCGA-A5-A0GB-01 ENDOMETRIUM c.107A>G p.D36G COSMIC PASSENGER/OTHER Benign 64 TCGA-A5-A0GB-01 ENDOMETRIUM c.5574C>T p.N1858N COSMIC NP NP 65 TCGA-A5-A0GP-01 ENDOMETRIUM c.5676C>T p.I1892I COSMIC NP NP 66 TCGA-A5-A0VP-01 ENDOMETRIUM c.1027C>T p.R343C COSMIC PASSENGER/OTHER Probably Damaging 67 TCGA-A5-A0VP-01 ENDOMETRIUM c.2242C>T p.R748C COSMIC PASSENGER/OTHER Probably Damaging 68 TCGA-A6-2676-01 LARGE INTESTINE c.5910_5912delGAA p.K1972delK COSMIC NP NP 69 TCGA-A6-5661-01 LARGE INTESTINE c.1612delC p.R540fs*16 COSMIC NP NP 70 TCGA-A6-6653-01 LARGE INTESTINE c.1550delG p.E519fs*4 COSMIC NP NP 71 TCGA-A6-6653-01 LARGE INTESTINE c.1612delC p.R540fs*16 COSMIC NP NP 72 TCGA-A6-6781-01 LARGE INTESTINE c.196C>T p.R66* COSMIC NP NP 73 TCGA-A8-A0AB-01 BREAST c.664G>C p.E222Q COSMIC PASSENGER/OTHER Probably Damaging 74 TCGA-AA-3492-01 LARGE INTESTINE c.1099delG p.E368fs*116 COSMIC NP NP 75 TCGA-AA-3710-01 LARGE INTESTINE c.4544C>T p.P1515L COSMIC PASSENGER/OTHER Probably Damaging 76 TCGA-AA-3713-01 LARGE INTESTINE c.1549_1550insG p.E519fs*68 COSMIC NP NP 77 TCGA-AA-3713-01 LARGE INTESTINE c.3563C>T p.A1188V COSMIC PASSENGER/OTHER Probably Damaging 78 TCGA-AA-3715-01 LARGE INTESTINE c.1207C>A p.L403I COSMIC PASSENGER/OTHER Probably Damaging 79 TCGA-AA-3715-01 LARGE INTESTINE c.639G>A p.A213A COSMIC NP NP 80 TCGA-AA-3845-01 LARGE INTESTINE c.3738G>T p.K1246N COSMIC CANCER Probably Damaging 81 TCGA-AA-3864-01 LARGE INTESTINE c.2377C>A p.P793T COSMIC CANCER Probably Damaging 82 TCGA-AA-A00J-01 LARGE INTESTINE c.4789G>A p.A1597T COSMIC PASSENGER/OTHER Benign 83 TCGA-AA-A00N-01 LARGE INTESTINE c.2031G>T p.K677N COSMIC PASSENGER/OTHER Probably Damaging 84 TCGA-AA-A00N-01 LARGE INTESTINE c.2896C>T p.R966W COSMIC CANCER Probably Damaging 85 TCGA-AA-A010-01 LARGE INTESTINE c.470A>C p.H157P COSMIC PASSENGER/OTHER Possibly Damaging 86 TCGA-AA-A01Q-01 LARGE INTESTINE c.2110G>A p.E704K COSMIC PASSENGER/OTHER Benign 87 TCGA-AD-6895-01 LARGE INTESTINE c.5786C>T p.P1929L COSMIC PASSENGER/OTHER Benign 88 TCGA-AG-A002-01 LARGE INTESTINE c.3029G>A p.R1010Q COSMIC PASSENGER/OTHER Possibly Damaging 89 TCGA-AG-A002-01 LARGE INTESTINE c.5198C>T p.S1733L COSMIC PASSENGER/OTHER Possibly Damaging 90 TCGA-AK-3451-01 KIDNEY c.3303C>A p.Y1101* COSMIC NP NP 91 TCGA-AP-A051-01 ENDOMETRIUM c.4104G>T p.E1368D COSMIC PASSENGER/OTHER Probably Damaging 92 TCGA-AP-A051-01 ENDOMETRIUM c.984T>C p.S328S COSMIC NP NP 93 TCGA-AP-A059-01 ENDOMETRIUM c.3563C>T p.A1188V COSMIC PASSENGER/OTHER Probably Damaging 94 TCGA-AP-A0LG-01 ENDOMETRIUM c.252C>T p.Y84Y COSMIC NP NP 95 TCGA-AP-A0LQ-01 ENDOMETRIUM c.5684G>A p.R1895H COSMIC PASSENGER/OTHER Probably Damaging 96 TCGA-AR-A1AI-01 BREAST c.632C>T p.A211V COSMIC PASSENGER/OTHER Probably Damaging 97 TCGA-AX-A060-01 ENDOMETRIUM c.5183G>T p.R1728L COSMIC PASSENGER/OTHER Probably Damaging 98 TCGA-AX-A0J0-01 ENDOMETRIUM c.3918C>A p.I1306I COSMIC NP NP 99 TCGA-AX-A0J0-01 ENDOMETRIUM c.5014T>G p.L1672V COSMIC PASSENGER/OTHER Benign 100 TCGA-AX-A0J1-01 ENDOMETRIUM c.1161delG p.G388fs*96 COSMIC NP NP 101 TCGA-AY-6197-01 LARGE INTESTINE c.1612delC p.R540fs*16 COSMIC NP NP 102 TCGA-AZ-4315-01 LARGE INTESTINE c.197G>A p.R66Q COSMIC PASSENGER/OTHER Probably Damaging 103 TCGA-AZ-6600-01 LARGE INTESTINE c.4731A>G p.E1577E COSMIC NP NP 104 TCGA-AZ-6601-01 LARGE INTESTINE c.4183C>A p.P1395T COSMIC PASSENGER/OTHER Probably Damaging 105 TCGA-AZ-6601-01 LARGE INTESTINE c.5591T>C p.V1864A COSMIC PASSENGER/OTHER Probably Damaging 106 TCGA-B0-4712-01 KIDNEY c.1099G>A p.G367R COSMIC PASSENGER/OTHER Probably Damaging 107 TCGA-B0-5400-01 KIDNEY c.2056C>A p.L686I COSMIC PASSENGER/OTHER Benign 108 TCGA-B5-A0JY-01 ENDOMETRIUM c.5919G>A p.E1973E COSMIC NP NP 109 TCGA-B5-A0K6-01 ENDOMETRIUM c.3233G>A p.R1078Q COSMIC PASSENGER/OTHER Probably Damaging 110 TCGA-B5-A11E-01 ENDOMETRIUM c.2550G>T p.E850D COSMIC PASSENGER/OTHER Benign 111 TCGA-B5-A11E-01 ENDOMETRIUM c.800G>A p.G267D COSMIC PASSENGER/OTHER Probably Damaging 112 TCGA-B5-A11J-01 ENDOMETRIUM c.307C>T p.R103* COSMIC NP NP 113 TCGA-B5-A11N-01 ENDOMETRIUM c.5159A>G p.H1720R COSMIC PASSENGER/OTHER Possibly Damaging 114 TCGA-B5-A11X-01 ENDOMETRIUM c.4024C>T p.R1342W COSMIC CANCER Probably Damaging 115 TCGA-B5-A11Y-01 ENDOMETRIUM c.5089C>T p.R1697* COSMIC NP NP 116 TCGA-BG-A0LX-01 ENDOMETRIUM c.4425C>T p.A1475A COSMIC NP NP 117 TCGA-BH-A0BP-01 BREAST c.1627C>T p.Q543* COSMIC NP NP 118 TCGA-BH-A1FC-01 BREAST c.1219G>C p.D407H COSMIC PASSENGER/OTHER Probably Damaging 119 TCGA-BP-4961-01 KIDNEY c.3420C>T p.G1140G COSMIC NP NP 120 TCGA-BS-A0UA-01 ENDOMETRIUM c.3628C>T p.R1210W COSMIC PASSENGER/OTHER Probably Damaging 121 TCGA-BS-A0UF-01 ENDOMETRIUM c.1713A>C p.E571D COSMIC PASSENGER/OTHER Probably Damaging 122 TCGA-BS-A0UF-01 ENDOMETRIUM c.2916C>A p.V972V COSMIC NP NP 123 TCGA-BS-A0UJ-01 ENDOMETRIUM c.2924A>G p.N975S COSMIC PASSENGER/OTHER Probably Damaging 124 TCGA-BS-A0UJ-01 ENDOMETRIUM c.3367A>G p.N1123D COSMIC PASSENGER/OTHER Probably Damaging 125 TCGA-BS-A0UL-01 ENDOMETRIUM c.4381C>T p.R1461C COSMIC PASSENGER/OTHER Probably Damaging 126 TCGA-BS-A0UM-01 ENDOMETRIUM c.4531C>T p.R1511C COSMIC PASSENGER/OTHER Probably Damaging 127 TCGA-BS-A0UV-01 ENDOMETRIUM c.1835C>T p.P612L COSMIC PASSENGER/OTHER Probably Damaging 128 TCGA-BS-A0UV-01 ENDOMETRIUM c.2773C>T p.L925F COSMIC PASSENGER/OTHER Probably Damaging 129 TCGA-C8-A12U-01 BREAST c.2095_2097delAAG p.K703delK COSMIC NP NP 130 TCGA-CF-A1HS-01 URINARY TRACT c.3563C>T p.A1188V COSMIC PASSENGER/OTHER Probably Damaging 131 TCGA-CJ-5677-01 KIDNEY c.3126C>T p.S1042S COSMIC NP NP 132 TCGA-CK-6746-01 LARGE INTESTINE c.326delA p.K111fs*30 COSMIC NP NP 133 TCGA-D1-A0ZO-01 ENDOMETRIUM c.3781G>A p.A1261T COSMIC CANCER Benign 134 TCGA-D1-A103-01 ENDOMETRIUM c.632C>T p.A211V COSMIC PASSENGER/OTHER Probably Damaging 135 TCGA-D1-A15X-01 ENDOMETRIUM c.3083G>A p.C1028Y COSMIC PASSENGER/OTHER Probably Damaging 136 TCGA-D1-A15X-01 ENDOMETRIUM c.5735C>T p.T1912M COSMIC PASSENGER/OTHER Possibly Damaging 137 TCGA-D1-A16X-01 ENDOMETRIUM c.2582C>T p.S861L COSMIC PASSENGER/OTHER Probably Damaging 138 TCGA-D1-A177-01 ENDOMETRIUM c.359A>G p.K120R COSMIC PASSENGER/OTHER Benign 139 TCGA-D1-A17C-01 ENDOMETRIUM c.2053G>T p.E685* COSMIC NP NP 140 TCGA-D1-A17Q-01 ENDOMETRIUM c.3318C>T p.I1106I COSMIC NP NP 141 TCGA-D1-A17Q-01 ENDOMETRIUM c.3723C>T p.N1241N COSMIC NP NP 142 TCGA-D5-6927-01 LARGE INTESTINE c.2289delG p.L765fs*1 COSMIC NP NP 143 TCGA-DK-A1AC-01 URINARY TRACT c.19G>A p.V7M COSMIC PASSENGER/OTHER Benign 144 TCGA-DK-A3IL-01 URINARY TRACT c.2328C>T p.Y776Y COSMIC NP NP 145 TCGA-DK-A3IS-01 URINARY TRACT c.1026C>T p.V342V COSMIC NP NP 146 TCGA-DS-A0VM-01 CERVIX c.3004C>T p.R1002* COSMIC NP NP 147 TCGA-DY-A1H8-01 LARGE INTESTINE c.4731A>G p.E1577E COSMIC NP NP 148 TCGA-E2-A1IN-01 BREAST c.532C>G p.P178A COSMIC PASSENGER/OTHER Probably Damaging 149 TCGA-F4-6854-01 LARGE INTESTINE c.5760C>A p.Y1920* COSMIC NP NP 150 TCGA-FU-A23L-01 CERVIX c.721G>C p.A241P COSMIC PASSENGER/OTHER Benign 151 TCGA-G4-6309-01 LARGE INTESTINE c.1612delC p.R540fs*16 COSMIC NP NP 152 TCGA-G4-6588-01 LARGE INTESTINE c.1612delC p.R540fs*16 COSMIC NP NP 153 TCGA-G4-6628-01 LARGE INTESTINE c.3636G>A p.G1212G COSMIC NP NP 154 TCGA-GV-A3QI-01 URINARY TRACT c.1716C>G p.I572M COSMIC PASSENGER/OTHER Probably Damaging 155 WA19 PROSTATE c.2366T>G p.L789R COSMIC CANCER Probably Damaging 156 WA23 PROSTATE c.841C>T p.R281C COSMIC PASSENGER/OTHER Possibly Damaging 157 WA55 PROSTATE c.1494C>T p.P498P COSMIC NP NP 158 YUDEXA SKIN c.2467C>T p.R823W COSMIC PASSENGER/OTHER Probably Damaging 159 YUKIL SKIN c.5198C>T p.S1733L COSMIC PASSENGER/OTHER Possibly Damaging 160 cSCCP4 SKIN c.1168G>T p.E390* COSMIC NP NP 161 cSCCP8 SKIN c.4243C>T p.R1415C COSMIC PASSENGER/OTHER Probably Damaging 162 pfg008T STOMACH c.2690G>T p.R897M COSMIC PASSENGER/OTHER Probably Damaging 163 pfg025T STOMACH c.811C>T p.R271W COSMIC PASSENGER/OTHER Probably Damaging
*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 (+)
Users must enabled the Java in their browser to see structure.
Users can also download Java from here.Modelled Structure Structures available in PDB Structure is not available in PDB -
Structure Domains (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PF08073 CHDNT 147 201 1.6e-31 PB007563 Pfam-B_7563 346 420 2.1e-05 PF00628 PHD 381 425 3.2e-11 PB005262 Pfam-B_5262 428 497 0.00035 PF00628 PHD 458 502 1.2e-09 PB011224 Pfam-B_11224 469 507 0.00056 PF00385 Chromo 547 570 0.00016 PF00385 Chromo 632 681 6.6e-13 PF00176 SNF2_N 739 1035 2e-68 PB014180 Pfam-B_14180 1057 1092 2.3e-05 PB015666 Pfam-B_15666 1057 1169 0.00017 PB018422 Pfam-B_18422 1059 1085 4.7e-06 PF00271 Helicase_C 1095 1174 1.1e-15 PB008129 Pfam-B_8129 1103 1267 1.4e-23 PF06465 DUF1087 1295 1357 3.3e-25 PF06461 DUF1086 1378 1517 4.8e-65 PF08074 CHDCT2 1735 1907 9.7e-101 -
Sequence Alignment (+)
Users must enabled the Java in their browser to see sequence alignments.
Users can also download Java from here.1. Variants are not present in 1000 Genomes!!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 CHD3 CHD3 CHD3 ENSP00000332628 Q12873 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q12873 CHD3 ENSP00000332628 CHD3 Q12873 Expression Atlas Protein Atlas OMIM IntAct PharmGKB CHD3 ENSP00000332628 602120 Q12873 PA26454
