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: KDM5C |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 001 KIDNEY c.4213G>C p.E1405Q COSMIC PASSENGER/OTHER Probably Damaging 2 001 KIDNEY c.4219delG p.D1407fs*5 COSMIC NP NP 3 2334196 LUNG c.3460G>T p.E1154* COSMIC NP NP 4 587222 LARGE INTESTINE c.472G>A p.E158K COSMIC PASSENGER/OTHER Probably Damaging 5 587270 LARGE INTESTINE c.1772G>A p.G591E COSMIC CANCER Probably Damaging 6 587278 LARGE INTESTINE c.1810G>A p.G604S COSMIC PASSENGER/OTHER Benign 7 587284 LARGE INTESTINE c.1853G>A p.C618Y COSMIC PASSENGER/OTHER Possibly Damaging 8 587316 LARGE INTESTINE c.3563G>C p.C1188S COSMIC CANCER Probably Damaging 9 587332 LARGE INTESTINE c.2437C>T p.Q813* COSMIC NP NP 10 587336 LARGE INTESTINE c.1133G>T p.R378L COSMIC PASSENGER/OTHER Possibly Damaging 11 CLL115 HAEMATOPOIETIC AND LYMPHOID TISSUE c.3176G>T p.R1059L COSMIC PASSENGER/OTHER Probably Damaging 12 ESO-717 OESOPHAGUS c.4247A>G p.N1416S COSMIC PASSENGER/OTHER Benign 13 H1155 LUNG c.938G>A p.R313Q COSMIC PASSENGER/OTHER Probably Damaging 14 HCC107T LIVER c.3160C>A p.L1054I COSMIC PASSENGER/OTHER Possibly Damaging 15 HCC111T LIVER c.1861G>T p.D621Y COSMIC PASSENGER/OTHER Possibly Damaging 16 HN_62426 UPPER AERODIGESTIVE TRACT c.2559C>T p.L853L COSMIC NP NP 17 HN_63080 UPPER AERODIGESTIVE TRACT c.1006G>C p.D336H COSMIC PASSENGER/OTHER Probably Damaging 18 K101 KIDNEY c.2206delG p.D736fs*28 COSMIC NP NP 19 K126 KIDNEY c.4008_4009insA p.R1337fs*10 COSMIC NP NP 20 K127 KIDNEY c.840_841insGATG p.V281fs*10 COSMIC NP NP 21 K180 KIDNEY c.2041C>T p.R681* COSMIC NP NP 22 K185 KIDNEY c.1553A>G p.H518R COSMIC PASSENGER/OTHER Probably Damaging 23 K20 KIDNEY c.4270C>T p.Q1424* COSMIC NP NP 24 K218 KIDNEY c.179_180delTG p.V60fs*14 COSMIC NP NP 25 K29 KIDNEY c.142C>T p.P48S COSMIC PASSENGER/OTHER Probably Damaging 26 K295 KIDNEY c.388A>T p.K130* COSMIC NP NP 27 LUAD-B02594 LUNG c.1494G>T p.K498N COSMIC PASSENGER/OTHER Probably Damaging 28 LUAD-NYU160 LUNG c.3635G>T p.R1212L COSMIC PASSENGER/OTHER Benign 29 LUAD-NYU184 LUNG c.272A>T p.K91I COSMIC PASSENGER/OTHER Probably Damaging 30 LUAD-RT-S01721 LUNG c.3820G>A p.E1274K COSMIC PASSENGER/OTHER Probably Damaging 31 LUAD-S01478 LUNG c.1546G>C p.E516Q COSMIC PASSENGER/OTHER Probably Damaging 32 MD-324 CENTRAL NERVOUS SYSTEM c.2764delC p.Q922fs*13 COSMIC NP NP 33 MN-1047 MENINGES c.1726C>G p.L576V COSMIC PASSENGER/OTHER Probably Damaging 34 PD2140a KIDNEY c.3664T>C p.S1222P COSMIC PASSENGER/OTHER Benign 35 PD2207a KIDNEY c.1933G>T p.E645* COSMIC NP NP 36 PD3289a KIDNEY c.3385_3386insT p.D1129fs*75 COSMIC NP NP 37 PD3293a KIDNEY c.807delC p.T270fs*2 COSMIC NP NP 38 PD3302a KIDNEY c.661G>T p.E221* COSMIC NP NP 39 PD3339a KIDNEY c.3148delG p.D1050fs*5 COSMIC NP NP 40 PD3357a KIDNEY c.1935_1936GG>CT p.E645_E646>D* COSMIC NP NP 41 PD4085a BREAST c.2150C>T p.S717L COSMIC PASSENGER/OTHER Probably Damaging 42 PR-04-3113 PROSTATE c.1973T>C p.L658P COSMIC PASSENGER/OTHER Probably Damaging 43 S01728 LUNG c.1074G>C p.L358L COSMIC NP NP 44 SWE-3B PROSTATE c.3534G>T p.S1178S COSMIC NP NP 45 T47D BREAST c.2758C>T p.Q920* COSMIC NP NP 46 T47D BREAST c.2761C>G p.L921V COSMIC PASSENGER/OTHER Possibly Damaging 47 TCGA-04-1331-01 OVARY c.2735G>A p.G912E COSMIC PASSENGER/OTHER Benign 48 TCGA-05-4244-01 LUNG c.2023C>T p.Q675* COSMIC NP NP 49 TCGA-05-4396-01 LUNG c.2350G>T p.E784* COSMIC NP NP 50 TCGA-05-4417-01 LUNG c.753G>C p.M251I COSMIC PASSENGER/OTHER Benign 51 TCGA-05-4420-01 LUNG c.1518G>T p.M506I COSMIC PASSENGER/OTHER Probably Damaging 52 TCGA-09-2056-01 OVARY c.4286C>T p.P1429L COSMIC PASSENGER/OTHER Probably Damaging 53 TCGA-22-5485-01 LUNG c.2266C>A p.L756I COSMIC PASSENGER/OTHER Probably Damaging 54 TCGA-24-1434-01 OVARY c.1688_1689insT p.L564fs*58 COSMIC NP NP 55 TCGA-24-1549-01 OVARY c.1928C>T p.S643F COSMIC PASSENGER/OTHER Probably Damaging 56 TCGA-24-1604-01 OVARY c.67G>C p.E23Q COSMIC PASSENGER/OTHER Probably Damaging 57 TCGA-24-1844-01 OVARY c.1524_1532delCTCAGCCTT p.S509_F511delSAF COSMIC NP NP 58 TCGA-34-2608-01 LUNG c.1156G>C p.E386Q COSMIC PASSENGER/OTHER Probably Damaging 59 TCGA-36-1575-01 OVARY c.536G>A p.R179H COSMIC PASSENGER/OTHER Benign 60 TCGA-49-6742-01 LUNG c.3660C>G p.L1220L COSMIC NP NP 61 TCGA-55-7570-01 LUNG c.769C>G p.L257V COSMIC PASSENGER/OTHER Benign 62 TCGA-55-7914-01 LUNG c.2289G>T p.L763L COSMIC NP NP 63 TCGA-60-2724-01 LUNG c.1937A>T p.E646V COSMIC PASSENGER/OTHER Possibly Damaging 64 TCGA-64-1677-01 LUNG c.898C>G p.H300D COSMIC PASSENGER/OTHER Benign 65 TCGA-66-2755-01 LUNG c.503A>T p.Q168L COSMIC PASSENGER/OTHER Benign 66 TCGA-66-2791-01 LUNG c.1840G>T p.A614S COSMIC PASSENGER/OTHER Benign 67 TCGA-69-7979-01 LUNG c.2100C>A p.L700L COSMIC NP NP 68 TCGA-A2-A0CX-01 BREAST c.2941G>A p.E981K COSMIC PASSENGER/OTHER Probably Damaging 69 TCGA-A2-A0YK-01 BREAST c.2955G>A p.E985E COSMIC NP NP 70 TCGA-A5-A0GW-01 ENDOMETRIUM c.3642_3643delGT p.V1216fs*83 COSMIC NP NP 71 TCGA-A6-2672-01 LARGE INTESTINE c.1661C>A p.P554H COSMIC PASSENGER/OTHER Probably Damaging 72 TCGA-A6-2676-01 LARGE INTESTINE c.2798A>C p.E933A COSMIC PASSENGER/OTHER Possibly Damaging 73 TCGA-A6-5660-01 LARGE INTESTINE c.3666T>C p.S1222S COSMIC NP NP 74 TCGA-A7-A26E-01 BREAST c.3226_3227insCGACAGG p.L1076fs*56 COSMIC NP NP 75 TCGA-A7-A26E-01 BREAST c.3227_3228insACC p.L1076_T1077insP COSMIC NP NP 76 TCGA-A8-A094-01 BREAST c.1377A>C p.K459N COSMIC PASSENGER/OTHER Possibly Damaging 77 TCGA-A8-A0A7-01 BREAST c.3820G>A p.E1274K COSMIC PASSENGER/OTHER Probably Damaging 78 TCGA-AA-3516-01 LARGE INTESTINE c.3563G>C p.C1188S COSMIC CANCER Probably Damaging 79 TCGA-AA-3555-01 LARGE INTESTINE c.3497G>A p.R1166H COSMIC PASSENGER/OTHER Benign 80 TCGA-AA-3555-01 LARGE INTESTINE c.4579G>A p.E1527K COSMIC PASSENGER/OTHER Benign 81 TCGA-AA-3697-01 LARGE INTESTINE c.1927T>C p.S643P COSMIC PASSENGER/OTHER Probably Damaging 82 TCGA-AA-3710-01 LARGE INTESTINE c.3757C>A p.P1253T COSMIC PASSENGER/OTHER Probably Damaging 83 TCGA-AA-3947-01 LARGE INTESTINE c.2041C>T p.R681* COSMIC NP NP 84 TCGA-AA-3977-01 LARGE INTESTINE c.760G>T p.D254Y COSMIC PASSENGER/OTHER Benign 85 TCGA-AA-3979-01 LARGE INTESTINE c.2662_2663insCC p.R888fs*48 COSMIC NP NP 86 TCGA-AF-2693-01 LARGE INTESTINE c.3664T>C p.S1222P COSMIC PASSENGER/OTHER Benign 87 TCGA-AP-A051-01 ENDOMETRIUM c.2138C>T p.T713M COSMIC PASSENGER/OTHER Probably Damaging 88 TCGA-AP-A051-01 ENDOMETRIUM c.230C>T p.A77V COSMIC PASSENGER/OTHER Probably Damaging 89 TCGA-AP-A051-01 ENDOMETRIUM c.3316G>A p.A1106T COSMIC PASSENGER/OTHER Benign 90 TCGA-AP-A059-01 ENDOMETRIUM c.3546C>A p.S1182S COSMIC NP NP 91 TCGA-AP-A059-01 ENDOMETRIUM c.4255A>G p.I1419V COSMIC PASSENGER/OTHER Probably Damaging 92 TCGA-AP-A059-01 ENDOMETRIUM c.999G>A p.G333G COSMIC NP NP 93 TCGA-AP-A0LM-01 ENDOMETRIUM c.3640G>A p.V1214M COSMIC PASSENGER/OTHER Probably Damaging 94 TCGA-AX-A0J1-01 ENDOMETRIUM c.3874G>A p.A1292T COSMIC PASSENGER/OTHER Probably Damaging 95 TCGA-AX-A0J1-01 ENDOMETRIUM c.4304G>A p.R1435H COSMIC PASSENGER/OTHER Benign 96 TCGA-B0-4816-01 KIDNEY c.1606G>T p.G536W COSMIC PASSENGER/OTHER Probably Damaging 97 TCGA-B0-5077-01 KIDNEY c.1775A>T p.E592V COSMIC PASSENGER/OTHER Benign 98 TCGA-B0-5094-01 KIDNEY c.2392G>T p.E798* COSMIC NP NP 99 TCGA-B0-5106-01 KIDNEY c.1536C>G p.C512W COSMIC PASSENGER/OTHER Probably Damaging 100 TCGA-B0-5698-01 KIDNEY c.3329C>G p.S1110* COSMIC NP NP 101 TCGA-B5-A0JY-01 ENDOMETRIUM c.2296C>T p.R766W COSMIC PASSENGER/OTHER Probably Damaging 102 TCGA-B5-A0K6-01 ENDOMETRIUM c.1737T>C p.H579H COSMIC NP NP 103 TCGA-B5-A11E-01 ENDOMETRIUM c.2516G>T p.G839V COSMIC PASSENGER/OTHER Possibly Damaging 104 TCGA-B5-A11E-01 ENDOMETRIUM c.3076C>T p.L1026F COSMIC PASSENGER/OTHER Probably Damaging 105 TCGA-B5-A11E-01 ENDOMETRIUM c.3691C>A p.P1231T COSMIC PASSENGER/OTHER Benign 106 TCGA-B5-A11E-01 ENDOMETRIUM c.4451G>A p.S1484N COSMIC PASSENGER/OTHER Benign 107 TCGA-B5-A11E-01 ENDOMETRIUM c.690T>C p.N230N COSMIC NP NP 108 TCGA-B5-A11R-01 ENDOMETRIUM c.3869_3874delGCCGCG p.G1290_R1291delGR COSMIC NP NP 109 TCGA-B5-A11Y-01 ENDOMETRIUM c.1104C>T p.C368C COSMIC NP NP 110 TCGA-BG-A0LX-01 ENDOMETRIUM c.1493A>G p.K498R COSMIC PASSENGER/OTHER Probably Damaging 111 TCGA-BG-A0MQ-01 ENDOMETRIUM c.471C>T p.Y157Y COSMIC NP NP 112 TCGA-BH-A0BM-01 BREAST c.483T>G p.V161V COSMIC NP NP 113 TCGA-BK-A0C9-01 ENDOMETRIUM c.1497G>A p.V499V COSMIC NP NP 114 TCGA-BK-A0C9-01 ENDOMETRIUM c.248T>C p.L83P COSMIC PASSENGER/OTHER Probably Damaging 115 TCGA-BP-5000-01 KIDNEY c.2437C>T p.Q813* COSMIC NP NP 116 TCGA-BP-5169-01 KIDNEY c.2189G>T p.C730F COSMIC CANCER Probably Damaging 117 TCGA-BP-5190-01 KIDNEY c.2198A>C p.H733P COSMIC PASSENGER/OTHER Probably Damaging 118 TCGA-BP-5195-01 KIDNEY c.865A>T p.K289* COSMIC NP NP 119 TCGA-BS-A0UF-01 ENDOMETRIUM c.2806C>T p.R936C COSMIC PASSENGER/OTHER Benign 120 TCGA-BS-A0UJ-01 ENDOMETRIUM c.2109T>C p.D703D COSMIC NP NP 121 TCGA-BS-A0UL-01 ENDOMETRIUM c.3158G>A p.G1053D COSMIC PASSENGER/OTHER Probably Damaging 122 TCGA-CI-6622-01 LARGE INTESTINE c.1933G>T p.E645* COSMIC NP NP 123 TCGA-CK-6746-01 LARGE INTESTINE c.1741G>A p.V581M COSMIC PASSENGER/OTHER Probably Damaging 124 TCGA-CM-4752-01 LARGE INTESTINE c.536G>A p.R179H COSMIC PASSENGER/OTHER Benign 125 TCGA-CM-5344-01 LARGE INTESTINE c.663A>G p.E221E COSMIC NP NP 126 TCGA-CM-5348-01 LARGE INTESTINE c.3664T>C p.S1222P COSMIC PASSENGER/OTHER Benign 127 TCGA-CM-5861-01 LARGE INTESTINE c.4260G>A p.W1420* COSMIC NP NP 128 TCGA-CM-5863-01 LARGE INTESTINE c.2949G>A p.W983* COSMIC NP NP 129 TCGA-CM-5868-01 LARGE INTESTINE c.2777A>G p.E926G COSMIC PASSENGER/OTHER Benign 130 TCGA-CM-6171-01 LARGE INTESTINE c.1719C>A p.P573P COSMIC NP NP 131 TCGA-CZ-5464-01 KIDNEY c.1586G>A p.G529D COSMIC CANCER Probably Damaging 132 TCGA-CZ-5467-01 KIDNEY c.643A>T p.R215* COSMIC NP NP 133 TCGA-D1-A103-01 ENDOMETRIUM c.276C>A p.F92L COSMIC PASSENGER/OTHER Probably Damaging 134 TCGA-D1-A103-01 ENDOMETRIUM c.64G>A p.A22T COSMIC PASSENGER/OTHER Benign 135 TCGA-D1-A17A-01 ENDOMETRIUM c.2266C>A p.L756I COSMIC PASSENGER/OTHER Probably Damaging 136 TCGA-D1-A17Q-01 ENDOMETRIUM c.1720A>G p.N574D COSMIC PASSENGER/OTHER Probably Damaging 137 TCGA-D1-A17R-01 ENDOMETRIUM c.1771G>A p.G591R COSMIC CANCER Probably Damaging 138 TCGA-D5-7000-01 LARGE INTESTINE c.1600T>C p.W534R COSMIC PASSENGER/OTHER Probably Damaging 139 TCGA-DM-A1D0-01 LARGE INTESTINE c.1927T>C p.S643P COSMIC PASSENGER/OTHER Probably Damaging 140 TCGA-DM-A1D4-01 LARGE INTESTINE c.535C>T p.R179C COSMIC PASSENGER/OTHER Probably Damaging 141 TCGA-EY-A1GS-01 ENDOMETRIUM c.1156G>C p.E386Q COSMIC PASSENGER/OTHER Probably Damaging 142 TCGA-F4-6459-01 LARGE INTESTINE c.663A>G p.E221E COSMIC NP NP 143 TCGA-F4-6809-01 LARGE INTESTINE c.3664T>C p.S1222P COSMIC PASSENGER/OTHER Benign 144 TCGA-G4-6293-01 LARGE INTESTINE c.1395A>T p.E465D COSMIC PASSENGER/OTHER Benign 145 TCGA-G4-6293-01 LARGE INTESTINE c.2005_2007delGAG p.E669delE COSMIC NP NP 146 TCGA-G4-6293-01 LARGE INTESTINE c.3666T>C p.S1222S COSMIC NP NP 147 TCGA-G4-6304-01 LARGE INTESTINE c.535C>T p.R179C COSMIC PASSENGER/OTHER Probably Damaging 148 TCGA-G4-6588-01 LARGE INTESTINE c.3177G>T p.R1059R COSMIC NP NP 149 cSCCP8 SKIN c.4468G>T p.E1490* COSMIC NP NP 150 ccRCC-14 KIDNEY c.693_696delAGAG p.E232fs*1 COSMIC NP NP 151 ccRCC-32 KIDNEY c.1396G>T p.E466* COSMIC NP NP 152 ccRCC-5 KIDNEY c.2412delG p.R805fs*11 COSMIC NP NP 153 ccRCC-62 KIDNEY c.1984delC p.L662fs*102 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 PF02375 JmjN 15 48 4.3e-15 PF01388 ARID 77 165 4.5e-23 PF00628 PHD 326 372 6.2e-12 PB006766 Pfam-B_6766 340 378 7.9e-09 PF02373 JmjC 501 617 2.7e-43 PF02928 zf-C5HC2 707 760 1.1e-16 PF08429 PLU-1 771 1100 1.9e-99 PF00628 PHD 1187 1249 1.3e-06 PB000113 Pfam-B_113 1206 1322 1e-38 PB012821 Pfam-B_12821 1417 1482 8.6e-41 2. Superfamily Domains:Domain ID Start Site End Site E-value 0047105 385 436 4.94e-37 0046063 60 181 6.54e-32 0050474 312 379 3.99e-17 0050470 1181 1258 4.65e-12 -
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 KDM5C KDM5C KDM5C ENSP00000364528 P41229 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt P41229 KDM5C ENSP00000364528 KDM5C P41229 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM5C ENSP00000364528 314690 P41229 PA35964
