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: KDM4C |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 09-12737 HAEMATOPOIETIC AND LYMPHOID TISSUE c.3124A>G p.T1042A COSMIC PASSENGER/OTHER Benign 2 1946219 LUNG c.1948C>T p.L650L COSMIC NP NP 3 587336 LARGE INTESTINE c.2651C>T p.T884M COSMIC PASSENGER/OTHER Probably Damaging 4 587336 LARGE INTESTINE c.658C>T p.R220* COSMIC NP NP 5 587342 LARGE INTESTINE c.2167G>A p.V723I COSMIC PASSENGER/OTHER Benign 6 587376 LARGE INTESTINE c.802G>T p.E268* COSMIC NP NP 7 8033610 PANCREAS c.2025C>T p.V675V COSMIC NP NP 8 CLL152 HAEMATOPOIETIC AND LYMPHOID TISSUE c.519A>T p.V173V COSMIC NP NP 9 DLBCL-PatientC HAEMATOPOIETIC AND LYMPHOID TISSUE c.2380A>G p.T794A COSMIC PASSENGER/OTHER Benign 10 HCC31T LIVER c.286G>T p.V96L COSMIC PASSENGER/OTHER Benign 11 HCC71T LIVER c.3146A>C p.Q1049P COSMIC PASSENGER/OTHER Possibly Damaging 12 HN_62506 UPPER AERODIGESTIVE TRACT c.1050A>G p.P350P COSMIC NP NP 13 ICGC_0067 PANCREAS c.2025C>T p.V675V COSMIC NP NP 14 KM12 LARGE INTESTINE c.3107C>T p.A1036V COSMIC PASSENGER/OTHER Benign 15 LAU50_1 SKIN c.2778C>T p.I926I COSMIC NP NP 16 LAU50_2 SKIN c.2778C>T p.I926I COSMIC NP NP 17 LC_C9 LUNG c.1233G>C p.K411N COSMIC PASSENGER/OTHER Benign 18 LUAD-E00918 LUNG c.2104C>T p.P702S COSMIC PASSENGER/OTHER Probably Damaging 19 LUAD-FH5PJ LUNG c.513G>T p.E171D COSMIC PASSENGER/OTHER Benign 20 LUAD-NYU1219 LUNG c.1492G>A p.E498K COSMIC PASSENGER/OTHER Benign 21 LUAD_E00565 LUNG c.1520G>C p.W507S COSMIC PASSENGER/OTHER Benign 22 LUAD_E00565 LUNG c.2131G>T p.G711* COSMIC NP NP 23 PD6754a NS c.2301A>G p.Q767Q COSMIC NP NP 24 S00472 LUNG c.1589G>C p.S530T COSMIC PASSENGER/OTHER Benign 25 SJMB016 CENTRAL NERVOUS SYSTEM c.843delT p.F281fs*35 COSMIC NP NP 26 SJMB016 CENTRAL NERVOUS SYSTEM c.845A>T p.N282I COSMIC PASSENGER/OTHER Probably Damaging 27 SJMB043 CENTRAL NERVOUS SYSTEM c.3125C>A p.T1042N COSMIC PASSENGER/OTHER Possibly Damaging 28 SJMB087 CENTRAL NERVOUS SYSTEM c.2939G>C p.R980T COSMIC PASSENGER/OTHER Probably Damaging 29 TCGA-18-3407-01 LUNG c.3054G>T p.G1018G COSMIC NP NP 30 TCGA-20-1686-01 OVARY c.2034G>A p.S678S COSMIC NP NP 31 TCGA-24-2293-01 OVARY c.2352A>T p.E784D COSMIC PASSENGER/OTHER Probably Damaging 32 TCGA-33-4532-01 LUNG c.1301C>T p.S434F COSMIC PASSENGER/OTHER Benign 33 TCGA-33-4566-01 LUNG c.1936G>T p.A646S COSMIC PASSENGER/OTHER Probably Damaging 34 TCGA-34-5928-01 LUNG c.1260G>A p.V420V COSMIC NP NP 35 TCGA-35-4123-01 LUNG c.2344G>C p.V782L COSMIC PASSENGER/OTHER Benign 36 TCGA-38-4632-01 LUNG c.408A>T p.A136A COSMIC NP NP 37 TCGA-44-7660-01 LUNG c.1766A>T p.Q589L COSMIC PASSENGER/OTHER Benign 38 TCGA-44-8119-01 LUNG c.300G>T p.R100S COSMIC PASSENGER/OTHER Possibly Damaging 39 TCGA-50-5045-01 LUNG c.2293C>T p.L765F COSMIC PASSENGER/OTHER Probably Damaging 40 TCGA-50-6594-01 LUNG c.2372C>T p.P791L COSMIC PASSENGER/OTHER Benign 41 TCGA-55-8089-01 LUNG c.3120C>A p.Y1040* COSMIC NP NP 42 TCGA-63-5128-01 LUNG c.2083G>T p.E695* COSMIC NP NP 43 TCGA-69-7980-01 LUNG c.753A>G p.V251V COSMIC NP NP 44 TCGA-73-4668-01 LUNG c.851G>T p.G284V COSMIC PASSENGER/OTHER Probably Damaging 45 TCGA-75-5147-01 LUNG c.1557G>C p.E519D COSMIC PASSENGER/OTHER Possibly Damaging 46 TCGA-78-7155-01 LUNG c.1932C>T p.H644H COSMIC NP NP 47 TCGA-78-7539-01 LUNG c.1497A>T p.K499N COSMIC PASSENGER/OTHER Benign 48 TCGA-91-6849-01 LUNG c.1614C>T p.G538G COSMIC NP NP 49 TCGA-A2-A0CU-01 BREAST c.84G>A p.E28E COSMIC NP NP 50 TCGA-A2-A0YH-01 BREAST c.690A>T p.P230P COSMIC NP NP 51 TCGA-A5-A0VP-01 ENDOMETRIUM c.2343G>A p.A781A COSMIC NP NP 52 TCGA-A6-2672-01 LARGE INTESTINE c.1715G>A p.R572H COSMIC PASSENGER/OTHER Possibly Damaging 53 TCGA-A6-6141-01 LARGE INTESTINE c.1186G>A p.D396N COSMIC PASSENGER/OTHER Benign 54 TCGA-A8-A07P-01 BREAST c.362G>A p.R121H COSMIC PASSENGER/OTHER Probably Damaging 55 TCGA-AA-3502-01 LARGE INTESTINE c.1392A>T p.I464I COSMIC NP NP 56 TCGA-AA-3549-01 LARGE INTESTINE c.155C>T p.P52L COSMIC PASSENGER/OTHER Probably Damaging 57 TCGA-AA-3663-01 LARGE INTESTINE c.2303C>T p.T768M COSMIC PASSENGER/OTHER Probably Damaging 58 TCGA-AA-3712-01 LARGE INTESTINE c.2352A>G p.E784E COSMIC NP NP 59 TCGA-AA-3811-01 LARGE INTESTINE c.2640C>T p.S880S COSMIC NP NP 60 TCGA-AA-3984-01 LARGE INTESTINE c.375G>T p.K125N COSMIC PASSENGER/OTHER Probably Damaging 61 TCGA-AA-A01R-01 LARGE INTESTINE c.2608G>A p.V870M COSMIC PASSENGER/OTHER Benign 62 TCGA-AA-A022-01 LARGE INTESTINE c.658C>T p.R220* COSMIC NP NP 63 TCGA-AG-A002-01 LARGE INTESTINE c.2029A>G p.T677A COSMIC PASSENGER/OTHER Benign 64 TCGA-AG-A002-01 LARGE INTESTINE c.659G>A p.R220Q COSMIC PASSENGER/OTHER Probably Damaging 65 TCGA-AP-A051-01 ENDOMETRIUM c.472G>A p.V158I COSMIC PASSENGER/OTHER Benign 66 TCGA-AP-A056-01 ENDOMETRIUM c.2156C>G p.A719G COSMIC PASSENGER/OTHER Possibly Damaging 67 TCGA-AP-A059-01 ENDOMETRIUM c.1320G>T p.V440V COSMIC NP NP 68 TCGA-AP-A059-01 ENDOMETRIUM c.180C>T p.C60C COSMIC NP NP 69 TCGA-AP-A0LM-01 ENDOMETRIUM c.173G>T p.R58I COSMIC PASSENGER/OTHER Benign 70 TCGA-AP-A0LM-01 ENDOMETRIUM c.1841C>T p.A614V COSMIC PASSENGER/OTHER Probably Damaging 71 TCGA-AP-A0LM-01 ENDOMETRIUM c.1868C>T p.T623M COSMIC PASSENGER/OTHER Probably Damaging 72 TCGA-AP-A0LM-01 ENDOMETRIUM c.2885T>C p.I962T COSMIC PASSENGER/OTHER Benign 73 TCGA-AU-6004-01 LARGE INTESTINE c.2352A>G p.E784E COSMIC NP NP 74 TCGA-AX-A05U-01 ENDOMETRIUM c.3108C>T p.A1036A COSMIC NP NP 75 TCGA-AX-A05Z-01 ENDOMETRIUM c.2356C>T p.R786* COSMIC NP NP 76 TCGA-AX-A0J0-01 ENDOMETRIUM c.2412G>A p.Q804Q COSMIC NP NP 77 TCGA-B0-4945-01 KIDNEY c.90C>A p.N30K COSMIC PASSENGER/OTHER Probably Damaging 78 TCGA-B5-A0JY-01 ENDOMETRIUM c.1494G>T p.E498D COSMIC PASSENGER/OTHER Benign 79 TCGA-B5-A0JY-01 ENDOMETRIUM c.802G>A p.E268K COSMIC PASSENGER/OTHER Probably Damaging 80 TCGA-B5-A0JZ-01 ENDOMETRIUM c.2249C>T p.A750V COSMIC PASSENGER/OTHER Benign 81 TCGA-B5-A11E-01 ENDOMETRIUM c.1136C>T p.T379I COSMIC PASSENGER/OTHER Benign 82 TCGA-B5-A11E-01 ENDOMETRIUM c.2137A>C p.S713R COSMIC PASSENGER/OTHER Probably Damaging 83 TCGA-B8-4622-01 KIDNEY c.2250G>A p.A750A COSMIC NP NP 84 TCGA-BH-A0BG-01 BREAST c.1888G>T p.A630S COSMIC PASSENGER/OTHER Probably Damaging 85 TCGA-BS-A0UV-01 ENDOMETRIUM c.1869G>A p.T623T COSMIC NP NP 86 TCGA-CJ-5675-01 KIDNEY c.492A>G p.E164E COSMIC NP NP 87 TCGA-CZ-5459-01 KIDNEY c.2160G>A p.K720K COSMIC NP NP 88 TCGA-D1-A0ZU-01 ENDOMETRIUM c.2661G>A p.T887T COSMIC NP NP 89 TCGA-D1-A103-01 ENDOMETRIUM c.2778C>T p.I926I COSMIC NP NP 90 TCGA-D1-A103-01 ENDOMETRIUM c.362G>A p.R121H COSMIC PASSENGER/OTHER Probably Damaging 91 TCGA-D1-A16N-01 ENDOMETRIUM c.886G>T p.V296F COSMIC PASSENGER/OTHER Possibly Damaging 92 TCGA-D1-A17H-01 ENDOMETRIUM c.1602C>A p.S534R COSMIC PASSENGER/OTHER Benign 93 TCGA-D8-A1JK-01 BREAST c.1439T>A p.I480K COSMIC PASSENGER/OTHER Benign 94 TCGA-D8-A1X6-01 BREAST c.145G>C p.V49L COSMIC PASSENGER/OTHER Benign 95 TCGA-DK-A1AC-01 URINARY TRACT c.3059G>C p.R1020T COSMIC PASSENGER/OTHER Benign 96 TCGA-DK-A3IM-01 URINARY TRACT c.2547G>A p.E849E COSMIC NP NP 97 TCGA-DM-A1D8-01 LARGE INTESTINE c.2352A>G p.E784E COSMIC NP NP 98 TCGA-DS-A0VM-01 CERVIX c.389T>C p.V130A COSMIC PASSENGER/OTHER Probably Damaging 99 TCGA-E2-A14S-01 BREAST c.1186G>A p.D396N COSMIC PASSENGER/OTHER Benign 100 TCGA-G4-6588-01 LARGE INTESTINE c.1148C>A p.P383H COSMIC PASSENGER/OTHER Benign 101 YUBAN SKIN c.640C>T p.P214S COSMIC PASSENGER/OTHER Probably Damaging 102 YUDAB SKIN c.2293C>T p.L765F COSMIC PASSENGER/OTHER Probably Damaging 103 YUDEXA SKIN c.1987G>A p.E663K COSMIC PASSENGER/OTHER Benign 104 YURUS SKIN c.2767C>T p.P923S COSMIC PASSENGER/OTHER Probably Damaging 105 ccRCC-97 KIDNEY c.2386A>G p.I796V COSMIC PASSENGER/OTHER Benign 106 pfg016T STOMACH c.681_682insT p.S231fs*7 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 17 51 9.1e-13 PB008394 Pfam-B_8394 47 143 2.8e-60 PF02373 JmjC 177 293 1e-43 PB014467 Pfam-B_14467 478 674 4.2e-101 PB013227 Pfam-B_13227 631 707 4.2e-07 PF13831 PHD_2 712 747 1.9e-12 PF13832 zf-HC5HC2H_2 753 864 9.9e-36 PB005109 Pfam-B_5109 890 1018 2.5e-18 PB002825 Pfam-B_2825 964 1035 3.8e-15 PB010616 Pfam-B_10616 1023 1049 1.4e-09 2. Superfamily Domains:Domain ID Start Site End Site E-value 0047105 63 331 3.98e-40 0052883 879 935 8.65e-22 0054623 936 991 7.15e-16 0050463 711 749 5.98e-05 -
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 KDM4C KDM4C KDM4C ENSP00000370707 Q9H3R0 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9H3R0 KDM4C ENSP00000370707 KDM4C Q9H3R0 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM4C ENSP00000370707 605469 Q9H3R0 PA164721503
