#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
YTHDC2	64848	hgsc.bcm.edu	37	5	112927842	112927843	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr5:112927842_112927843insT	ENST00000161863.4	+	28	4392_4393	c.4179_4180insT	c.(4180-4182)aacfs	p.N1394fs		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1394	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.N1394fs*1(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		CATGGAATGACAACAAGAAAGT	0.391																																					p.D1393fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.4179_4180insT	5						.																																			112955742	SO:0001589	frameshift_variant	64848	exon28			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	Exception_encountered	5.37:g.112927842_112927843insT	ENSP00000161863:p.Asn1394fs		112955741	NM_022828	B2RP66	Frame_Shift_Ins	INS	ENST00000161863.4	37	CCDS4113.1																																																																																				0.391	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
PKD1L1	168507	hgsc.bcm.edu	37	7	47860768	47860768	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr7:47860768T>C	ENST00000289672.2	-	46	6921	c.6871A>G	c.(6871-6873)Atc>Gtc	p.I2291V		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2291					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.I2291V(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AGCATGAGGATGTCCATGGAA	0.378																																					p.I2291V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6871G	7						.						83.0	77.0	79.0					7																	47860768		2203	4300	6503	47827293	SO:0001583	missense	168507	exon46			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6871A>G	7.37:g.47860768T>C	ENSP00000289672:p.Ile2291Val		47827293	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.674357	0.29693	.	.	ENSG00000158683	ENST00000289672	T	0.18657	2.2	5.27	-1.83	0.07833	.	1.592510	0.03401	N	0.203333	T	0.12390	0.0301	N	0.25647	0.755	0.09310	N	1	B	0.18166	0.026	B	0.10450	0.005	T	0.24941	-1.0146	10	0.05525	T	0.97	-7.6636	7.0451	0.25040	0.0:0.4951:0.1533:0.3516	.	2291	Q8TDX9	PK1L1_HUMAN	V	2291	ENSP00000289672:I2291V	ENSP00000289672:I2291V	I	-	1	0	PKD1L1	47827293	0.000000	0.05858	0.000000	0.03702	0.821000	0.46438	-0.577000	0.05847	-0.471000	0.06891	0.528000	0.53228	ATC		0.378	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
DLX5	1749	hgsc.bcm.edu	37	7	96653612	96653612	+	Silent	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr7:96653612G>A	ENST00000222598.4	-	1	797	c.324C>T	c.(322-324)taC>taT	p.Y108Y	DLX5_ENST00000493764.1_5'UTR|DLX5_ENST00000486603.2_Silent_p.Y108Y	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	108					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.Y108Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					GGACGCGGTTGTAGGCGCCGC	0.637																																					p.Y108Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C324T	7						.						45.0	43.0	44.0					7																	96653612		2203	4300	6503	96491548	SO:0001819	synonymous_variant	1749	exon1				CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"""Homeoboxes / ANTP class : NKL subclass"""	2918	protein-coding gene	gene with protein product		600028	"""distal-less homeo box 5"""			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.324C>T	7.37:g.96653612G>A			96491548	NM_005221	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																				0.637	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2		
CLMN	79789	hgsc.bcm.edu	37	14	95669375	95669375	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr14:95669375C>T	ENST00000298912.4	-	9	2424	c.2311G>A	c.(2311-2313)Gag>Aag	p.E771K		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	771					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.E771K(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		GCCTCCTCCTCCCTGGAGTCC	0.567																																					p.E771K												.	.	1	Substitution - Missense(1)	skin(1)	c.G2311A	14						.						37.0	38.0	38.0					14																	95669375		2203	4300	6503	94739128	SO:0001583	missense	79789	exon9			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2311G>A	14.37:g.95669375C>T	ENSP00000298912:p.Glu771Lys		94739128	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129497	0.77549	.	.	ENSG00000165959	ENST00000298912	D	0.94232	-3.38	5.22	4.32	0.51571	.	0.352007	0.20750	N	0.086363	D	0.89908	0.6851	L	0.55481	1.735	0.80722	D	1	B	0.17852	0.024	B	0.13407	0.009	D	0.85369	0.1112	10	0.25106	T	0.35	.	11.2904	0.49247	0.0:0.9125:0.0:0.0875	.	771	Q96JQ2	CLMN_HUMAN	K	771	ENSP00000298912:E771K	ENSP00000298912:E771K	E	-	1	0	CLMN	94739128	0.132000	0.22450	0.752000	0.31206	0.620000	0.37586	1.278000	0.33179	2.438000	0.82558	0.555000	0.69702	GAG		0.567	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
SEZ6L	23544	hgsc.bcm.edu	37	22	26688743	26688743	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr22:26688743C>A	ENST00000248933.6	+	2	561	c.466C>A	c.(466-468)Ctc>Atc	p.L156I	SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000404234.3_Missense_Mutation_p.L156I|SEZ6L_ENST00000343706.4_Missense_Mutation_p.L156I|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000529632.2_Missense_Mutation_p.L156I|SEZ6L_ENST00000360929.3_Missense_Mutation_p.L156I			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	156	O-glycosylated at one site.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.L156I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GGGCCTAGATCTCCTCTCCTC	0.662																																					p.L156I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C466A	22						.						44.0	41.0	42.0					22																	26688743		2203	4300	6503	25018743	SO:0001583	missense	23544	exon2			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.466C>A	22.37:g.26688743C>A	ENSP00000248933:p.Leu156Ile		25018743	NM_001184776	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	6.953	0.545655	0.13312	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706	T;T;T;T;T	0.27720	1.9;2.02;2.08;1.9;1.65	2.02	0.956	0.19608	.	0.447569	0.13544	U	0.379972	T	0.13457	0.0326	N	0.08118	0	0.20074	N	0.999937	B;B;B;B;B;B	0.28291	0.015;0.015;0.103;0.206;0.007;0.007	B;B;B;B;B;B	0.24269	0.01;0.01;0.024;0.052;0.006;0.006	T	0.25779	-1.0122	10	0.25106	T	0.35	.	8.4456	0.32841	0.0:0.7567:0.2433:0.0	.	156;156;156;156;156;156	B7ZLJ8;B7ZLJ6;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	I	156	ENSP00000384772:L156I;ENSP00000437037:L156I;ENSP00000354185:L156I;ENSP00000248933:L156I;ENSP00000342661:L156I	ENSP00000248933:L156I	L	+	1	0	SEZ6L	25018743	0.000000	0.05858	0.007000	0.13788	0.050000	0.14768	-0.224000	0.09164	0.434000	0.26340	0.508000	0.49915	CTC		0.662	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
PRODH2	58510	hgsc.bcm.edu	37	19	36297981	36297981	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr19:36297981G>A	ENST00000301175.3	-	6	885	c.868C>T	c.(868-870)Ctc>Ttc	p.L290F		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	290					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGGCCCGGAGGTGCTGGTTC	0.602																																					p.L290F												.	.	0			c.C868T	19						.						25.0	29.0	27.0					19																	36297981		2140	4171	6311	40989821	SO:0001583	missense	58510	exon6			U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.868C>T	19.37:g.36297981G>A	ENSP00000301175:p.Leu290Phe		40989821	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673860	0.47781	.	.	ENSG00000250799	ENST00000301175	T	0.32753	1.44	5.11	5.11	0.69529	Proline dehydrogenase (1);	.	.	.	.	T	0.29223	0.0727	L	0.35854	1.095	0.80722	D	1	P	0.41978	0.767	P	0.45138	0.471	T	0.01062	-1.1464	9	0.17832	T	0.49	.	14.2251	0.65853	0.0:0.0:1.0:0.0	.	290	Q9UF12	PROD2_HUMAN	F	290	ENSP00000301175:L290F	ENSP00000301175:L290F	L	-	1	0	PRODH2	40989821	0.890000	0.30428	0.936000	0.37596	0.846000	0.48090	1.795000	0.38784	2.826000	0.97356	0.655000	0.94253	CTC		0.602	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
PIK3CD	5293	hgsc.bcm.edu	37	1	9777133	9777133	+	Silent	SNP	G	G	A	rs149279787		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr1:9777133G>A	ENST00000377346.4	+	7	1092	c.897G>A	c.(895-897)ccG>ccA	p.P299P	PIK3CD_ENST00000543390.1_5'Flank|PIK3CD_ENST00000361110.2_Silent_p.P264P|PIK3CD_ENST00000536656.1_Silent_p.P264P	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	299					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.P299P(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	TCCAGAAACCGCGTGCCAAAC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.P299P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G897A	1						.	G		2,4404	4.2+/-10.8	0,2,2201	128.0	116.0	120.0		897	-9.9	0.0	1	dbSNP_134	120	0,8600		0,0,4300	no	coding-synonymous	PIK3CD	NM_005026.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		299/1045	9777133	2,13004	2203	4300	6503	9699720	SO:0001819	synonymous_variant	5293	exon7				CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.897G>A	1.37:g.9777133G>A			9699720	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Silent	SNP	ENST00000377346.4	37	CCDS104.1																																																																																				0.617	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026	
DDOST	1650	hgsc.bcm.edu	37	1	20978950	20978950	+	Silent	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr1:20978950G>A	ENST00000375048.3	-	11	1398	c.1293C>T	c.(1291-1293)agC>agT	p.S431S	PINK1-AS_ENST00000451424.1_RNA|DDOST_ENST00000415136.2_Silent_p.S394S|DDOST_ENST00000602624.2_Silent_p.S414S	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	431					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.S431S(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TGGAGAAGGCGCTGGCGTAGT	0.602																																					p.S431S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1293T	1						.						59.0	58.0	59.0					1																	20978950		2203	4300	6503	20851537	SO:0001819	synonymous_variant	1650	exon11			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"""oligosaccharyltransferase subunit 48"""	602202	"""dolichyl-diphosphooligosaccharide-protein glycosyltransferase"", ""dolichyl-diphosphooligosaccharide--protein glycosyltransferase"""			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.1293C>T	1.37:g.20978950G>A			20851537	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																				0.602	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204419032	204419032	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr1:204419032C>T	ENST00000367187.3	-	14	2736	c.2180G>A	c.(2179-2181)cGg>cAg	p.R727Q	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R727Q	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	727	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)	p.R727Q(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			AGGCACCCGCCGCTGCTTATT	0.627																																					p.R727Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2180A	1						.						23.0	27.0	26.0					1																	204419032		2203	4300	6503	202685655	SO:0001583	missense	5287	exon14			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2180G>A	1.37:g.204419032C>T	ENSP00000356155:p.Arg727Gln		202685655	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848435	0.91277	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.77358	-1.09;-1.09	4.88	3.96	0.45880	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.223973	0.35378	N	0.003248	T	0.73094	0.3543	L	0.49778	1.585	0.32741	N	0.507687	B;P	0.35780	0.426;0.52	B;B	0.38056	0.264;0.237	T	0.79569	-0.1749	10	0.62326	D	0.03	.	11.9068	0.52717	0.0:0.9122:0.0:0.0878	.	727;727	F5GWN5;O00750	.;P3C2B_HUMAN	Q	727	ENSP00000356155:R727Q;ENSP00000400561:R727Q	ENSP00000356155:R727Q	R	-	2	0	PIK3C2B	202685655	1.000000	0.71417	0.997000	0.53966	0.836000	0.47400	4.506000	0.60428	1.033000	0.39918	0.305000	0.20034	CGG		0.627	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
KIF18A	81930	hgsc.bcm.edu	37	11	28057931	28057931	+	Missense_Mutation	SNP	A	A	C			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr11:28057931A>C	ENST00000263181.6	-	14	2519	c.2229T>G	c.(2227-2229)aaT>aaG	p.N743K		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	743					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.N743K(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TTTTCAGACAATTATCACTGT	0.348																																					p.N743K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2229G	11						.						150.0	145.0	147.0					11																	28057931		2202	4298	6500	28014507	SO:0001583	missense	81930	exon14			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"""Kinesins"""	29441	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 99"""	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2229T>G	11.37:g.28057931A>C	ENSP00000263181:p.Asn743Lys		28014507	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	37	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.718996	0.30503	.	.	ENSG00000121621	ENST00000263181	T	0.71934	-0.61	5.67	1.87	0.25490	.	0.665589	0.15988	N	0.234993	T	0.54191	0.1843	L	0.57536	1.79	0.09310	N	1	P	0.35433	0.501	B	0.25140	0.058	T	0.44847	-0.9301	10	0.05959	T	0.93	.	8.0859	0.30771	0.6799:0.0:0.3201:0.0	.	743	Q8NI77	KI18A_HUMAN	K	743	ENSP00000263181:N743K	ENSP00000263181:N743K	N	-	3	2	KIF18A	28014507	0.010000	0.17322	0.005000	0.12908	0.007000	0.05969	0.245000	0.18142	0.400000	0.25396	0.533000	0.62120	AAT		0.348	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217	
SLC22A9	114571	hgsc.bcm.edu	37	11	63149671	63149671	+	Frame_Shift_Del	DEL	A	A	-	rs564236291|rs76547355|rs78765214	byFrequency	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	A	A	A	A	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr11:63149671delA	ENST00000279178.3	+	6	1244	c.995delA	c.(994-996)caafs	p.Q332fs	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	332					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						GAGGCAGCACAAAAAAAAAAA	0.398														181	0.0361422	0.0651	0.0187	5008	,	,		18548	0.0109		0.0139	False		,,,				2504	0.0583				p.Q332fs												.	.	0			c.995delA	11						.						133.0	130.0	131.0					11																	63149671		2201	4298	6499	62906247	SO:0001589	frameshift_variant	114571	exon6			AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"""Solute carriers"""	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.995delA	11.37:g.63149671delA	ENSP00000279178:p.Gln332fs		62906247	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Frame_Shift_Del	DEL	ENST00000279178.3	37	CCDS8043.1																																																																																				0.398	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866	
WNT11	7481	hgsc.bcm.edu	37	11	75898130	75898130	+	Silent	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr11:75898130C>T	ENST00000322563.3	-	5	1168	c.1044G>A	c.(1042-1044)gtG>gtA	p.V348V		NM_004626.2	NP_004617.2	O96014	WNT11_HUMAN	wingless-type MMTV integration site family, member 11	348					adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|bone mineralization (GO:0030282)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cloacal septation (GO:0060197)|embryonic skeletal system development (GO:0048706)|lung-associated mesenchyme development (GO:0060484)|mesonephric duct development (GO:0072177)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroendocrine cell differentiation (GO:0061101)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway (GO:0035567)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta2 production (GO:0032915)|protein localization to cell surface (GO:0034394)|protein phosphorylation (GO:0006468)|response to nutrient levels (GO:0031667)|tight junction assembly (GO:0070830)|ureteric bud morphogenesis (GO:0060675)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|protein kinase activator activity (GO:0030295)|Ras GTPase activator activity (GO:0005099)|transcription regulatory region DNA binding (GO:0044212)	p.V348V(1)		breast(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20						CATAGCGCTCCACGGTACGCT	0.652																																					p.V348V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1044A	11						.						109.0	81.0	91.0					11																	75898130		2200	4292	6492	75575778	SO:0001819	synonymous_variant	7481	exon5			Y12692	CCDS8242.1	11q13.5	2008-02-05			ENSG00000085741	ENSG00000085741		"""Wingless-type MMTV integration sites"""	12776	protein-coding gene	gene with protein product		603699				9757009	Standard	NM_004626		Approved		uc001oxe.3	O96014	OTTHUMG00000165264	ENST00000322563.3:c.1044G>A	11.37:g.75898130C>T			75575778	NM_004626	B2R8Z6|Q14DE8|Q8WZ98	Silent	SNP	ENST00000322563.3	37	CCDS8242.1																																																																																				0.652	WNT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383083.1	NM_004626	
TRPC6	7225	hgsc.bcm.edu	37	11	101353851	101353851	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr11:101353851C>T	ENST00000344327.3	-	5	1763	c.1339G>A	c.(1339-1341)Gca>Aca	p.A447T	TRPC6_ENST00000532133.1_Missense_Mutation_p.A447T|TRPC6_ENST00000360497.4_Missense_Mutation_p.A392T|TRPC6_ENST00000348423.4_Missense_Mutation_p.A331T	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	447					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.A447T(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		AAGGAGGCTGCGTGTGCTACA	0.418																																					p.A447T	Colon(166;1315 1927 11094 12848 34731)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1339A	11						.						105.0	95.0	98.0					11																	101353851		2203	4299	6502	100859061	SO:0001583	missense	7225	exon5			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12338	protein-coding gene	gene with protein product		603652	"""focal segmental glomerulosclerosis 2"""	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.1339G>A	11.37:g.101353851C>T	ENSP00000340913:p.Ala447Thr		100859061	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319186	0.60524	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.59169	0.2174	L	0.48218	1.51	0.80722	D	1	D;P;D	0.89917	1.0;0.905;1.0	D;B;D	0.91635	0.999;0.346;0.998	T	0.50931	-0.8769	10	0.27785	T	0.31	-0.7414	19.431	0.94765	0.0:1.0:0.0:0.0	.	392;331;447	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	T	447;447;331;392	ENSP00000340913:A447T;ENSP00000435574:A447T;ENSP00000343672:A331T;ENSP00000353687:A392T	ENSP00000340913:A447T	A	-	1	0	TRPC6	100859061	1.000000	0.71417	0.850000	0.33497	0.989000	0.77384	7.818000	0.86416	2.584000	0.87258	0.591000	0.81541	GCA		0.418	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
MAK	4117	hgsc.bcm.edu	37	6	10791978	10791978	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr6:10791978C>T	ENST00000313243.2	-	10	1628	c.1246G>A	c.(1246-1248)Gga>Aga	p.G416R	MAK_ENST00000354489.2_Missense_Mutation_p.G416R|RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000536370.1_3'UTR|MAK_ENST00000538030.1_Missense_Mutation_p.G416R|MAK_ENST00000474039.1_Missense_Mutation_p.G416R			P20794	MAK_HUMAN	male germ cell-associated kinase	416					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)	p.G416R(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				TGGGAGGCTCCGAAATCATAG	0.418																																					p.G416R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1246A	6						.						92.0	90.0	91.0					6																	10791978		2203	4300	6503	10899964	SO:0001583	missense	4117	exon9				CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1246G>A	6.37:g.10791978C>T	ENSP00000313021:p.Gly416Arg		10899964	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960823	0.74016	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.72505	-0.66;-0.66;-0.63	5.25	5.25	0.73442	.	0.197055	0.45126	D	0.000381	T	0.76884	0.4050	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	P	0.60345	0.873	T	0.77011	-0.2746	10	0.48119	T	0.1	.	17.4017	0.87461	0.0:1.0:0.0:0.0	.	416	P20794	MAK_HUMAN	R	416	ENSP00000313021:G416R;ENSP00000346484:G416R;ENSP00000442250:G416R	ENSP00000313021:G416R	G	-	1	0	MAK	10899964	0.999000	0.42202	0.955000	0.39395	0.594000	0.36715	2.814000	0.48010	2.603000	0.88011	0.655000	0.94253	GGA		0.418	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
SLC2A12	154091	hgsc.bcm.edu	37	6	134350498	134350498	+	Silent	SNP	G	G	A	rs377021554		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr6:134350498G>A	ENST00000275230.5	-	2	620	c.465C>T	c.(463-465)atC>atT	p.I155I		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	155					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.I155I(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		CAATCTCTGCGATGTAAACAC	0.448													G|||	1	0.000199681	0.0008	0.0	5008	,	,		23105	0.0		0.0	False		,,,				2504	0.0				p.I155I	Melanoma(122;1663 1672 14489 35294 41228)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C465T	6						.	G		1,4405	2.1+/-5.4	0,1,2202	110.0	110.0	110.0		465	-3.2	0.9	6		110	0,8600		0,0,4300	no	coding-synonymous	SLC2A12	NM_145176.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		155/618	134350498	1,13005	2203	4300	6503	134392191	SO:0001819	synonymous_variant	154091	exon2			AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"""Solute carriers"""	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.465C>T	6.37:g.134350498G>A			134392191	NM_145176	B3KV17|Q7Z6U3|Q96MR8	Silent	SNP	ENST00000275230.5	37	CCDS5169.1																																																																																				0.448	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1		
NRM	11270	hgsc.bcm.edu	37	6	30657088	30657088	+	Missense_Mutation	SNP	C	C	T	rs573111369		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr6:30657088C>T	ENST00000259953.4	-	4	823	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	PPP1R18_ENST00000488324.1_5'Flank|PPP1R18_ENST00000274853.3_5'Flank|PPP1R18_ENST00000399199.3_5'Flank|NRM_ENST00000470733.1_5'UTR|NRM_ENST00000376420.5_Intron|NRM_ENST00000376421.5_Missense_Mutation_p.V158I	NM_007243.2	NP_009174.1	Q8IXM6	NRM_HUMAN	nurim (nuclear envelope membrane protein)	158	Leu-rich.					integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.V158I(1)		large_intestine(1)|lung(2)	3						TAGTCAAAGACGAGAAGGATG	0.552													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20816	0.0		0.0	False		,,,				2504	0.0				p.V158I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G472A	6						.						57.0	46.0	50.0					6																	30657088		2186	4266	6452	30765067	SO:0001583	missense	11270	exon3			AF143676	CCDS4686.1, CCDS59498.1	6p21.3	2010-02-17			ENSG00000137404	ENSG00000137404			8003	protein-coding gene	gene with protein product						10402458, 17517639	Standard	NM_007243		Approved	NRM29	uc031sng.1	Q8IXM6	OTTHUMG00000031223	ENST00000259953.4:c.472G>A	6.37:g.30657088C>T	ENSP00000259953:p.Val158Ile		30765067	NM_007243	B0S7R0|B0S7R1|I3XIE2|I3XIE3|Q5JP57|Q5JP58|Q5JP59|Q5JP60|Q8WU45|Q9BSX3|Q9UN92	Missense_Mutation	SNP	ENST00000259953.4	37	CCDS4686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.581|6.581	0.475489|0.475489	0.12521|0.12521	.|.	.|.	ENSG00000137404|ENSG00000137404	ENST00000444096|ENST00000259953;ENST00000376421	.|T;T	.|0.26223	.|1.75;1.75	4.72|4.72	3.85|3.85	0.44370|0.44370	.|.	.|0.123897	.|0.52532	.|N	.|0.000066	T|T	0.01870|0.01870	0.0059|0.0059	N|N	0.00621|0.00621	-1.32|-1.32	0.34152|0.34152	D|D	0.667684|0.667684	.|B	.|0.13594	.|0.008	.|B	.|0.12156	.|0.007	T|T	0.42344|0.42344	-0.9457|-0.9457	5|10	.|0.10377	.|T	.|0.69	-3.6216|-3.6216	7.3878|7.3878	0.26893|0.26893	0.0:0.803:0.0:0.197|0.0:0.803:0.0:0.197	.|.	.|158	.|Q8IXM6	.|NRM_HUMAN	H|I	157|158	.|ENSP00000259953:V158I;ENSP00000365603:V158I	.|ENSP00000259953:V158I	R|V	-|-	2|1	0|0	NRM|NRM	30765067|30765067	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.705000|3.705000	0.54823|0.54823	1.128000|1.128000	0.42052|0.42052	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.552	NRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076466.2		
OGFRL1	79627	hgsc.bcm.edu	37	6	72006228	72006228	+	Silent	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr6:72006228C>T	ENST00000370435.4	+	5	644	c.510C>T	c.(508-510)aaC>aaT	p.N170N	RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	170						membrane (GO:0016020)	receptor activity (GO:0004872)	p.N170N(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						AAGGCTTGAACTTCTATGCCA	0.318																																					p.N170N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C510T	6						.						45.0	43.0	44.0					6																	72006228		2184	4268	6452	72062949	SO:0001819	synonymous_variant	79627	exon5				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.510C>T	6.37:g.72006228C>T			72062949	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	37	CCDS34482.1																																																																																				0.318	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576	
SYNE1	23345	hgsc.bcm.edu	37	6	152485429	152485429	+	Missense_Mutation	SNP	C	C	T	rs143842011		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr6:152485429C>T	ENST00000367255.5	-	131	24260	c.23659G>A	c.(23659-23661)Gtg>Atg	p.V7887M	SYNE1_ENST00000356820.4_Missense_Mutation_p.V2411M|SYNE1_ENST00000341594.5_Missense_Mutation_p.V7499M|SYNE1_ENST00000265368.4_Missense_Mutation_p.V7887M|SYNE1_ENST00000539504.1_Missense_Mutation_p.V42M|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.V7816M|SYNE1_ENST00000354674.4_Missense_Mutation_p.V42M|SYNE1_ENST00000423061.1_Missense_Mutation_p.V7816M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7887					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V7887M(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGCTGCTGCACGGCTACCAGG	0.557										HNSCC(10;0.0054)			C|||	1	0.000199681	0.0	0.0	5008	,	,		18263	0.0		0.0	False		,,,				2504	0.001				p.V2411M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G7231A	6						.	C	MET/VAL,MET/VAL	4,4402	8.1+/-20.4	0,4,2199	79.0	72.0	75.0		23446,23659	5.3	0.9	6	dbSNP_134	75	0,8600		0,0,4300	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	21,21	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging,probably-damaging	7816/8750,7887/8798	152485429	4,13002	2203	4300	6503	152527122	SO:0001583	missense	23345	exon46			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23659G>A	6.37:g.152485429C>T	ENSP00000356224:p.Val7887Met		152527122	NM_015293	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	29.8	5.038313	0.93630	9.08E-4	0.0	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.52983	1.33;0.64;1.33;1.33;1.33;1.33;1.33;1.33;1.33;0.64	5.34	5.34	0.76211	.	0.000000	0.49305	D	0.000154	T	0.60248	0.2254	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991	D;D;D;D;P	0.97110	1.0;1.0;1.0;1.0;0.832	T	0.63175	-0.6696	10	0.72032	D	0.01	.	19.033	0.92965	0.0:1.0:0.0:0.0	.	7887;7887;7816;7816;89	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	M	7887;42;533;7816;7887;7816;7499;2411;49;44;809;42	ENSP00000356224:V7887M;ENSP00000441052:V42M;ENSP00000356226:V533M;ENSP00000396024:V7816M;ENSP00000265368:V7887M;ENSP00000390975:V7816M;ENSP00000341887:V7499M;ENSP00000349276:V2411M;ENSP00000356220:V809M;ENSP00000346701:V42M	ENSP00000265368:V7887M	V	-	1	0	SYNE1	152527122	1.000000	0.71417	0.857000	0.33713	0.967000	0.64934	7.757000	0.85209	2.497000	0.84241	0.585000	0.79938	GTG		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PRPF8	10594	hgsc.bcm.edu	37	17	1579255	1579255	+	Silent	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr17:1579255C>T	ENST00000572621.1	-	17	2911	c.2646G>A	c.(2644-2646)aaG>aaA	p.K882K	PRPF8_ENST00000304992.6_Silent_p.K882K			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	882	Reverse transcriptase homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)	p.K882K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GGAGGTGACGCTTGATGCGGG	0.532																																					p.K882K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2646A	17						.						72.0	68.0	70.0					17																	1579255		2203	4300	6503	1526005	SO:0001819	synonymous_variant	10594	exon18			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.2646G>A	17.37:g.1579255C>T			1526005	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																				0.532	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
TP53	7157	hgsc.bcm.edu	37	17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	rs397516436		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr17:7578212G>A	ENST00000269305.4	-	6	826	c.637C>T	c.(637-639)Cga>Tga	p.R213*	TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R213*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACACTATGTCGAAAAGTGTTT	0.532		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R213X	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,central_nervous_system,brain,Substitution - Missense,+1	.	333	Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1)	large_intestine(89)|breast(45)|lung(37)|upper_aerodigestive_tract(30)|central_nervous_system(18)|skin(16)|oesophagus(15)|stomach(14)|ovary(14)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(9)|biliary_tract(8)|liver(8)|soft_tissue(5)|endometrium(5)|bone(4)|prostate(3)|thyroid(1)|pancreas(1)|autonomic_ganglia(1)	c.C637T	17	GRCh37	CM951226	TP53	M		.						132.0	118.0	123.0					17																	7578212		2203	4300	6503	7518937	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.637C>T	17.37:g.7578212G>A	ENSP00000269305:p.Arg213*		7518937	NM_001126114	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039727	0.97226	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.28	3.25	0.37280	.	0.057335	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5444	12.7263	0.57173	0.0:0.0:0.701:0.299	.	.	.	.	X	213;213;213;213;213;213;202;120;81;120;81	.	ENSP00000269305:R213X	R	-	1	2	TP53	7518937	0.971000	0.33674	0.123000	0.21794	0.957000	0.61999	1.659000	0.37387	0.702000	0.31825	0.563000	0.77884	CGA		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TRIM37	4591	hgsc.bcm.edu	37	17	57109344	57109344	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr17:57109344G>A	ENST00000262294.7	-	18	2120	c.1861C>T	c.(1861-1863)Cat>Tat	p.H621Y	TRIM37_ENST00000393066.3_Missense_Mutation_p.H621Y|TRIM37_ENST00000393065.2_Missense_Mutation_p.H587Y|TRIM37_ENST00000376149.3_Missense_Mutation_p.H499Y	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	621					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H621Y(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TCCAACAAATGTATTAAAATT	0.418									Mulibrey Nanism																												p.H621Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1861T	17						.						123.0	132.0	129.0					17																	57109344		2203	4300	6503	54464126	SO:0001583	missense	4591	exon18	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	7523	protein-coding gene	gene with protein product	"""RING-B-box-coiled-coil protein"""	605073	"""tripartite motif-containing 37"""	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1861C>T	17.37:g.57109344G>A	ENSP00000262294:p.His621Tyr		54464126	NM_001005207	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815843	0.90790	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.68025	1.46;1.46;-0.3;1.07	5.75	5.75	0.90469	.	0.051124	0.85682	D	0.000000	T	0.72366	0.3451	L	0.29908	0.895	0.51012	D	0.999904	D;D;D	0.62365	0.991;0.991;0.971	P;P;P	0.59056	0.851;0.851;0.572	T	0.74867	-0.3518	10	0.87932	D	0	-17.3392	19.938	0.97149	0.0:0.0:1.0:0.0	.	587;499;621	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	Y	621;621;499;587	ENSP00000376785:H621Y;ENSP00000262294:H621Y;ENSP00000365319:H499Y;ENSP00000376784:H587Y	ENSP00000262294:H621Y	H	-	1	0	TRIM37	54464126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.432000	0.90288	2.732000	0.93576	0.650000	0.86243	CAT		0.418	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294	
HID1	283987	hgsc.bcm.edu	37	17	72950430	72950430	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr17:72950430C>T	ENST00000425042.2	-	14	1744	c.1667G>A	c.(1666-1668)cGc>cAc	p.R556H		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	556					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)		p.R556H(1)									GCTGCGCTTGCGGATGATGGC	0.677																																					p.R556H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1667A	17						.						49.0	35.0	40.0					17																	72950430		2195	4288	6483	70462025	SO:0001583	missense	283987	exon14				CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"""downregulated in multiple cancer 1"""	605752	"""chromosome 17 open reading frame 28"""	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.1667G>A	17.37:g.72950430C>T	ENSP00000413520:p.Arg556His		70462025	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	37	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	C	34	5.294198	0.95546	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	4.47	4.47	0.54385	.	0.000000	0.85682	D	0.000000	D	0.85927	0.5811	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90168	0.4233	9	0.87932	D	0	-21.4586	17.1283	0.86720	0.0:1.0:0.0:0.0	.	556	Q8IV36	CQ028_HUMAN	H	328;556;328	.	ENSP00000317795:R328H	R	-	2	0	C17orf28	70462025	1.000000	0.71417	0.954000	0.39281	0.988000	0.76386	7.584000	0.82572	2.026000	0.59711	0.561000	0.74099	CGC		0.677	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
KRTAP15-1	254950	hgsc.bcm.edu	37	21	31812774	31812774	+	Silent	SNP	G	G	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr21:31812774G>T	ENST00000334067.3	+	1	178	c.129G>T	c.(127-129)ctG>ctT	p.L43L		NM_181623.1	NP_853654.1	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	43			L -> M (in dbSNP:rs2832873). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			intermediate filament (GO:0005882)		p.L43L(1)		kidney(1)|large_intestine(3)|lung(6)|skin(1)	11						CCTGCCAACTGGGCTCCTCTC	0.488																																					p.L43L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G129T	21						.						86.0	86.0	86.0					21																	31812774		2203	4300	6503	30734645	SO:0001819	synonymous_variant	254950	exon1			AP001708	CCDS13593.1	21q22.1	2008-05-21			ENSG00000186970	ENSG00000186970		"""Keratin associated proteins"""	18927	protein-coding gene	gene with protein product						12359730	Standard	NM_181623		Approved	KAP15.1	uc002yod.3	Q3LI76	OTTHUMG00000057784	ENST00000334067.3:c.129G>T	21.37:g.31812774G>T			30734645	NM_181623	Q2M3F4	Silent	SNP	ENST00000334067.3	37	CCDS13593.1																																																																																				0.488	KRTAP15-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128236.1		
ZNF423	23090	hgsc.bcm.edu	37	16	49670253	49670253	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr16:49670253C>T	ENST00000561648.1	-	4	2863	c.2810G>A	c.(2809-2811)cGg>cAg	p.R937Q	ZNF423_ENST00000563137.2_Missense_Mutation_p.R877Q|ZNF423_ENST00000562871.1_Missense_Mutation_p.R877Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.R877Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.R820Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.R820Q|ZNF423_ENST00000262383.2_Missense_Mutation_p.R937Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	937					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R937Q(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GAAGAAAGTCCGTGAACAAAC	0.597																																					p.R937Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2810A	16						.						76.0	63.0	67.0					16																	49670253		2198	4300	6498	48227754	SO:0001583	missense	23090	exon5			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2810G>A	16.37:g.49670253C>T	ENSP00000455426:p.Arg937Gln		48227754	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640974	0.87859	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.29142	1.58;1.58	4.81	4.81	0.61882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.55369	0.1916	M	0.72894	2.215	0.47407	D	0.999415	D	0.89917	1.0	D	0.73380	0.98	T	0.56962	-0.7892	9	.	.	.	-26.5821	17.8857	0.88854	0.0:1.0:0.0:0.0	.	937	Q2M1K9	ZN423_HUMAN	Q	937;820	ENSP00000262383:R937Q;ENSP00000442321:R820Q	.	R	-	2	0	ZNF423	48227754	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.487000	0.81328	2.234000	0.73211	0.561000	0.74099	CGG		0.597	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
TMPPE	643853	hgsc.bcm.edu	37	3	33135619	33135619	+	Silent	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr3:33135619G>A	ENST00000342462.4	-	2	259	c.69C>T	c.(67-69)tcC>tcT	p.S23S	GLB1_ENST00000307363.5_Intron|GLB1_ENST00000307377.8_Intron|TMPPE_ENST00000416695.2_Intron|GLB1_ENST00000399402.3_Intron|GLB1_ENST00000445488.2_Intron	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain	23						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.S23S(1)		breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						AGGCGATCATGGACACGAAGA	0.602																																					p.S23S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C69T	3						.						66.0	63.0	64.0					3																	33135619		2203	4300	6503	33110623	SO:0001819	synonymous_variant	643853	exon2			AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779	ENST00000342462.4:c.69C>T	3.37:g.33135619G>A			33110623	NM_001039770	B2RNG5|Q6ZRG1	Silent	SNP	ENST00000342462.4	37	CCDS33732.1																																																																																				0.602	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770	
TRA2B	6434	hgsc.bcm.edu	37	3	185635510	185635510	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr3:185635510C>T	ENST00000453386.2	-	9	1135	c.860G>A	c.(859-861)cGc>cAc	p.R287H	TRA2B_ENST00000382191.4_Missense_Mutation_p.R187H	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	287	Arg/Ser-rich (RS2 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R287H(1)		breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						GCTTTAATAGCGACCTGGGAA	0.338																																					p.R287H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G860A	3						.						86.0	91.0	89.0					3																	185635510		2203	4300	6503	187118204	SO:0001583	missense	6434	exon9			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"""RNA binding motif (RRM) containing"""	10781	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 156"""	602719	"""splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"""	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.860G>A	3.37:g.185635510C>T	ENSP00000416959:p.Arg287His		187118204	NM_004593	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Missense_Mutation	SNP	ENST00000453386.2	37	CCDS33905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.57|15.57	2.871579|2.871579	0.51695|0.51695	.|.	.|.	ENSG00000136527|ENSG00000136527	ENST00000259043;ENST00000414862|ENST00000453386;ENST00000382191	.|T;T	.|0.27402	.|1.83;1.67	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|1.623140	.|0.02892	.|N	.|0.134297	T|T	0.29588|0.29588	0.0738|0.0738	N|N	0.16656|0.16656	0.425|0.425	0.80722|0.80722	D|D	1|1	.|B;B	.|0.06786	.|0.001;0.001	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.05194|0.05194	-1.0900|-1.0900	5|10	.|0.28530	.|T	.|0.3	-2.1221|-2.1221	18.9107|18.9107	0.92483|0.92483	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|287;287	.|B2RDQ3;P62995	.|.;TRA2B_HUMAN	T|H	126;106|287;187	.|ENSP00000416959:R287H;ENSP00000371626:R187H	.|ENSP00000371626:R187H	A|R	-|-	1|2	0|0	TRA2B|TRA2B	187118204|187118204	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.863000|0.863000	0.49368|0.49368	4.054000|4.054000	0.57434|0.57434	2.751000|2.751000	0.94390|0.94390	0.591000|0.591000	0.81541|0.81541	GCT|CGC		0.338	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593	
WNK1	65125	hgsc.bcm.edu	37	12	970298	970298	+	Silent	SNP	A	A	G	rs112022175		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:970298A>G	ENST00000315939.6	+	7	2383	c.1740A>G	c.(1738-1740)gaA>gaG	p.E580E	WNK1_ENST00000535572.1_Silent_p.E580E|WNK1_ENST00000537687.1_Silent_p.E580E|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000340908.4_Silent_p.E173E|WNK1_ENST00000530271.2_Silent_p.E580E	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	580					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.E580E(2)|p.?(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AGGAGCAAGAAAAAAAAAAGC	0.473																																					p.E580E	Colon(19;451 567 6672 12618 28860)											.	.	3	Substitution - coding silent(2)|Unknown(1)	large_intestine(2)|skin(1)	c.A1740G	12						.						101.0	99.0	100.0					12																	970298		2203	4300	6503	840559	SO:0001819	synonymous_variant	65125	exon7			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1740A>G	12.37:g.970298A>G			840559	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																				0.473	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
CHD4	1108	hgsc.bcm.edu	37	12	6704571	6704571	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:6704571G>A	ENST00000357008.2	-	14	2213	c.2050C>T	c.(2050-2052)Cga>Tga	p.R684*	CHD4_ENST00000544040.1_Nonsense_Mutation_p.R677*|CHD4_ENST00000544484.1_Nonsense_Mutation_p.R681*|CHD4_ENST00000309577.6_Nonsense_Mutation_p.R684*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	684	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.R684*(1)		central_nervous_system(2)	2						TTGCCTGGTCGGCCTTCCTCA	0.502																																					p.R684X	Colon(32;586 792 4568 16848 45314)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2050T	12						.						142.0	119.0	126.0					12																	6704571		2203	4300	6503	6574832	SO:0001587	stop_gained	1108	exon14			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2050C>T	12.37:g.6704571G>A	ENSP00000349508:p.Arg684*		6574832	NM_001273	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	40	8.467431	0.98825	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	5.59	5.59	0.84812	.	0.138691	0.46758	D	0.000261	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0115	12.4852	0.55868	0.0:0.0:0.7234:0.2766	.	.	.	.	X	681;677;684;684;658	.	ENSP00000312419:R684X	R	-	1	2	CHD4	6574832	0.999000	0.42202	0.995000	0.50966	0.991000	0.79684	2.543000	0.45752	2.643000	0.89663	0.655000	0.94253	CGA		0.502	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12V	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35T	12						.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
IRAK4	51135	hgsc.bcm.edu	37	12	44176264	44176264	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:44176264C>A	ENST00000448290.2	+	9	1167	c.1096C>A	c.(1096-1098)Ccc>Acc	p.P366T	IRAK4_ENST00000440781.2_Missense_Mutation_p.P242T|IRAK4_ENST00000431837.1_Missense_Mutation_p.P242T|IRAK4_ENST00000551736.1_Missense_Mutation_p.P366T	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.P366T(1)				all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		AGAAATAACACCCAAATCTGA	0.368																																					p.P366T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1096A	12						.						72.0	71.0	72.0					12																	44176264		2203	4300	6503	42462531	SO:0001583	missense	51135	exon9			AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1096C>A	12.37:g.44176264C>A	ENSP00000390651:p.Pro366Thr		42462531	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251888	0.59212	.	.	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.62	2.82	0.32997	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113654	0.64402	D	0.000010	T	0.39118	0.1066	N	0.11560	0.145	0.36543	D	0.871396	B	0.33135	0.399	B	0.40659	0.336	T	0.25012	-1.0144	10	0.11485	T	0.65	-0.0011	4.1529	0.10247	0.1315:0.605:0.1269:0.1365	.	366	Q9NWZ3	IRAK4_HUMAN	T	242;242;366;366	ENSP00000408734:P242T;ENSP00000390327:P242T;ENSP00000390651:P366T;ENSP00000446490:P366T	ENSP00000390327:P242T	P	+	1	0	IRAK4	42462531	0.969000	0.33509	0.998000	0.56505	0.993000	0.82548	2.356000	0.44116	0.321000	0.23259	-0.237000	0.12165	CCC		0.368	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
TMEM117	84216	hgsc.bcm.edu	37	12	44782383	44782383	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:44782383G>T	ENST00000266534.3	+	8	1600	c.1473G>T	c.(1471-1473)caG>caT	p.Q491H	TMEM117_ENST00000536799.1_Missense_Mutation_p.Q387H|TMEM117_ENST00000546978.1_3'UTR|TMEM117_ENST00000551577.1_3'UTR	NM_032256.1	NP_115632.1	Q9H0C3	TM117_HUMAN	transmembrane protein 117	491						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.Q491H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|urinary_tract(1)	23	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		TGAGCTCACAGTTGAACGAAT	0.443																																					p.Q491H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1473T	12						.						166.0	158.0	161.0					12																	44782383		2203	4300	6503	43068650	SO:0001583	missense	84216	exon8			BC060798	CCDS8745.1, CCDS73462.1	12q12	2006-02-03				ENSG00000139173			25308	protein-coding gene	gene with protein product						11230166	Standard	NM_001286211		Approved	DKFZp434K2435	uc001rod.3	Q9H0C3	OTTHUMG00000169427	ENST00000266534.3:c.1473G>T	12.37:g.44782383G>T	ENSP00000266534:p.Gln491His		43068650	NM_032256		Missense_Mutation	SNP	ENST00000266534.3	37	CCDS8745.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.839373	0.00573	.	.	ENSG00000139173	ENST00000266534;ENST00000536799;ENST00000417623	T	0.42513	0.97	5.73	2.91	0.33838	.	0.144170	0.49305	N	0.000158	T	0.12774	0.0310	N	0.03115	-0.41	0.29072	N	0.883207	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26573	-1.0099	10	0.02654	T	1	-15.0365	1.6226	0.02716	0.1525:0.4734:0.1351:0.239	.	387;491	F5H3Q2;Q9H0C3	.;TM117_HUMAN	H	491;387;239	ENSP00000266534:Q491H	ENSP00000266534:Q491H	Q	+	3	2	TMEM117	43068650	0.798000	0.28890	0.935000	0.37517	0.695000	0.40330	-0.103000	0.10940	0.337000	0.23665	-0.153000	0.13522	CAG		0.443	TMEM117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403969.1	NM_032256	
DDIT3	1649	hgsc.bcm.edu	37	12	57910757	57910757	+	Silent	SNP	A	A	G			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:57910757A>G	ENST00000346473.3	-	4	524	c.345T>C	c.(343-345)gcT>gcC	p.A115A	DDIT3_ENST00000551116.1_Silent_p.A138A|DDIT3_ENST00000552740.1_Silent_p.A138A|MIR616_ENST00000385293.1_RNA|RN7SL312P_ENST00000582079.1_RNA|DDIT3_ENST00000547303.1_Silent_p.A115A	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	115	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.		A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A115A(1)	EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						GCTGCTTTCCAGCCCGGGCTG	0.542			T	FUS	liposarcoma																																p.A138A	GBM(112;1383 1547 7626 23045 28770)		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	DDIT3,large_intestine,colon,Substitution - Missense,-1	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T414C	12						.						142.0	151.0	148.0					12																	57910757		2203	4300	6503	56197024	SO:0001819	synonymous_variant	1649	exon4			BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"""C/EBP zeta"""	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.345T>C	12.37:g.57910757A>G			56197024	NM_001195055	F8VS99	Silent	SNP	ENST00000346473.3	37	CCDS8943.1																																																																																				0.542	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083	
SFSWAP	6433	hgsc.bcm.edu	37	12	132198667	132198667	+	Silent	SNP	T	T	C			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr12:132198667T>C	ENST00000261674.4	+	2	411	c.270T>C	c.(268-270)taT>taC	p.Y90Y	SFSWAP_ENST00000541286.1_Silent_p.Y90Y	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	90					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.Y90Y(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						ATGCTGAGTATTCCACGTGGA	0.458																																					p.Y90Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T270C	12						.						137.0	117.0	124.0					12																	132198667		2203	4300	6503	130764620	SO:0001819	synonymous_variant	6433	exon2			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.270T>C	12.37:g.132198667T>C			130764620	NM_004592	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1																																																																																				0.458	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
IMP3	55272	hgsc.bcm.edu	37	15	75931989	75931989	+	Missense_Mutation	SNP	T	T	C	rs200453864		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr15:75931989T>C	ENST00000314852.2	-	2	1464	c.521A>G	c.(520-522)aAt>aGt	p.N174S	CTD-2026K11.2_ENST00000564683.1_RNA|IMP3_ENST00000565349.1_5'Flank|IMP3_ENST00000403490.1_Missense_Mutation_p.N174S			Q8TCT8	SPP2A_HUMAN	IMP3, U3 small nucleolar ribonucleoprotein	0					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)	p.N174S(1)		large_intestine(1)	1						GCGCTCCTCATTGTACTCTAG	0.547													T|||	1	0.000199681	0.0	0.0	5008	,	,		20050	0.001		0.0	False		,,,				2504	0.0				p.N174S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A521G	15						.						99.0	85.0	90.0					15																	75931989		2197	4294	6491	73719044	SO:0001583	missense	55272	exon1			AB051628	CCDS10282.1	15q24	2014-02-19	2014-02-19	2005-07-14	ENSG00000177971	ENSG00000177971			14497	protein-coding gene	gene with protein product		612980	"""mitochondrial ribosomal protein S4"", ""chromosome 15 open reading frame 12"", ""IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""	MRPS4, C15orf12		11543634, 12655004	Standard	NM_018285		Approved	FLJ10968, BRMS2	uc010bkl.2	Q9NV31	OTTHUMG00000142840	ENST00000314852.2:c.521A>G	15.37:g.75931989T>C	ENSP00000326981:p.Asn174Ser		73719044	NM_018285	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000314852.2	37	CCDS10282.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	16.22	3.060326	0.55432	.	.	ENSG00000177971	ENST00000314852;ENST00000403490;ENST00000542473	T;T	0.40476	1.03;1.03	6.17	4.87	0.63330	RNA-binding S4 (2);	0.051204	0.85682	D	0.000000	T	0.49729	0.1574	M	0.90542	3.125	0.58432	D	0.999999	B	0.23937	0.094	B	0.25884	0.064	T	0.57254	-0.7843	10	0.59425	D	0.04	-15.2102	8.8492	0.35190	0.0:0.0932:0.0:0.9068	.	174	Q9NV31	IMP3_HUMAN	S	174;174;21	ENSP00000326981:N174S;ENSP00000385217:N174S	ENSP00000326981:N174S	N	-	2	0	IMP3	73719044	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	4.724000	0.61972	2.371000	0.80710	0.533000	0.62120	AAT		0.547	IMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286476.1	NM_018285	
EVC2	132884	hgsc.bcm.edu	37	4	5624468	5624468	+	Missense_Mutation	SNP	C	C	T	rs149854557		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr4:5624468C>T	ENST00000344408.5	-	14	2350	c.2297G>A	c.(2296-2298)cGt>cAt	p.R766H	EVC2_ENST00000344938.1_Missense_Mutation_p.R766H|EVC2_ENST00000310917.2_Missense_Mutation_p.R686H	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	766					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R766H(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						GGGCACCCCACGCTTGAGCAG	0.647																																					p.R686H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2057A	4						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	49.0	47.0	48.0		2057,2297	2.0	0.4	4	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	686/1229,766/1309	5624468	1,13005	2203	4300	6503	5675369	SO:0001583	missense	132884	exon14			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2297G>A	4.37:g.5624468C>T	ENSP00000342144:p.Arg766His		5675369	NM_001166136	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	9.512	1.105964	0.20632	0.0	1.16E-4	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74632	-0.86;-0.85;-0.86	5.32	1.95	0.26073	.	0.435130	0.24698	N	0.036337	T	0.59851	0.2224	L	0.51422	1.61	0.23568	N	0.997395	B	0.15719	0.014	B	0.08055	0.003	T	0.36504	-0.9745	10	0.15066	T	0.55	-9.7772	4.5016	0.11867	0.3113:0.4754:0.0:0.2133	.	766	Q86UK5	LBN_HUMAN	H	766;686;766	ENSP00000339954:R766H;ENSP00000311683:R686H;ENSP00000342144:R766H	ENSP00000311683:R686H	R	-	2	0	EVC2	5675369	0.676000	0.27567	0.383000	0.26132	0.377000	0.30045	1.072000	0.30678	0.504000	0.28082	0.462000	0.41574	CGT		0.647	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
FBXW7	55294	hgsc.bcm.edu	37	4	153250856	153250858	+	In_Frame_Del	DEL	TGT	TGT	-			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	TGT	TGT	TGT	-	TGT	TGT	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr4:153250856_153250858delTGT	ENST00000281708.4	-	8	2431_2433	c.1202_1204delACA	c.(1201-1206)aacact>act	p.N401del	FBXW7_ENST00000393956.3_In_Frame_Del_p.N225del|FBXW7_ENST00000296555.5_In_Frame_Del_p.N283del|FBXW7_ENST00000603548.1_In_Frame_Del_p.N401del|FBXW7_ENST00000603841.1_In_Frame_Del_p.N401del|FBXW7_ENST00000263981.5_In_Frame_Del_p.N321del	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	401					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.N401delN(2)|p.N162delN(1)|p.N321delN(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACTTTTAAAGTGTTGTCATCAGA	0.374			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.321_322del			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	.	.	5	Deletion - In frame(4)|Unknown(1)	large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)	c.962_964del	4						.																																			153470308	SO:0001651	inframe_deletion	55294	exon7			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1202_1204delACA	4.37:g.153250859_153250861delTGT	ENSP00000281708:p.Asn401del		153470306	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	In_Frame_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				0.374	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
TLL1	7092	hgsc.bcm.edu	37	4	166996031	166996031	+	Splice_Site	SNP	C	C	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr4:166996031C>A	ENST00000061240.2	+	17	2837	c.2190C>A	c.(2188-2190)gaC>gaA	p.D730E	TLL1_ENST00000507499.1_Splice_Site_p.D753E	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	730	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.|EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D730E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		CTTTGCTAGACAAAGATGAAT	0.403																																					p.D730E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2190A	4						.						153.0	129.0	137.0					4																	166996031		2203	4300	6503	167215481	SO:0001630	splice_region_variant	7092	exon17			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2189-1C>A	4.37:g.166996031C>A			167215481	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	37	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676725	0.47886	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	D;D	0.96427	-4.01;-1.85	5.59	1.92	0.25849	EGF-like calcium-binding, conserved site (1);CUB (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.96691	0.8920	L	0.59967	1.855	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.83275	0.996;0.984	D	0.94456	0.7672	10	0.45353	T	0.12	.	8.7137	0.34399	0.0:0.5518:0.0:0.4482	.	753;730	E9PD25;O43897	.;TLL1_HUMAN	E	730;753	ENSP00000061240:D730E;ENSP00000426082:D753E	ENSP00000061240:D730E	D	+	3	2	TLL1	167215481	1.000000	0.71417	0.998000	0.56505	0.251000	0.25915	1.216000	0.32443	0.106000	0.17784	0.557000	0.71058	GAC		0.403	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		Missense_Mutation
KLHL4	56062	hgsc.bcm.edu	37	X	86887365	86887365	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chrX:86887365G>A	ENST00000373119.4	+	7	1625	c.1480G>A	c.(1480-1482)Gaa>Aaa	p.E494K	KLHL4_ENST00000373114.4_Missense_Mutation_p.E494K	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	494						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.E494K(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GAATACAGTGGAATGTTTTAA	0.418																																					p.E494K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1480A	X						.						109.0	96.0	100.0					X																	86887365		2203	4300	6503	86774021	SO:0001583	missense	56062	exon7			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1480G>A	X.37:g.86887365G>A	ENSP00000362211:p.Glu494Lys		86774021	NM_057162	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	33	5.286038	0.95517	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	D;D	0.84516	-1.86;-1.86	5.32	5.32	0.75619	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.95360	0.8494	H	0.97732	4.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.97172	0.9845	10	0.87932	D	0	.	16.9539	0.86253	0.0:0.0:1.0:0.0	.	494;494	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	K	494	ENSP00000362211:E494K;ENSP00000362206:E494K	ENSP00000362206:E494K	E	+	1	0	KLHL4	86774021	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.225000	0.95219	2.211000	0.71520	0.506000	0.49869	GAA		0.418	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
HOXD4	3233	hgsc.bcm.edu	37	2	177017660	177017660	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr2:177017660C>T	ENST00000306324.3	+	2	1170	c.758C>T	c.(757-759)aCg>aTg	p.T253M	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	253					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T253M(1)		kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ACGGACCTGACGACCTTATAG	0.642																																					p.T253M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C758T	2						.						66.0	72.0	70.0					2																	177017660		2203	4300	6503	176725906	SO:0001583	missense	3233	exon2				CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"""Homeoboxes / ANTP class : HOXL subclass"""	5138	protein-coding gene	gene with protein product		142981	"""homeo box D4"""	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.758C>T	2.37:g.177017660C>T	ENSP00000302548:p.Thr253Met		176725906	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	37	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061367	0.76187	.	.	ENSG00000170166	ENST00000306324	D	0.90732	-2.72	5.67	5.67	0.87782	.	7.610600	0.00397	N	0.000055	D	0.96284	0.8788	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85608	0.1256	10	0.87932	D	0	.	19.7626	0.96329	0.0:1.0:0.0:0.0	.	253	P09016	HXD4_HUMAN	M	253	ENSP00000302548:T253M	ENSP00000302548:T253M	T	+	2	0	HOXD4	176725906	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.055000	0.71103	2.676000	0.91093	0.561000	0.74099	ACG		0.642	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2		
GLI2	2736	hgsc.bcm.edu	37	2	121726311	121726311	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr2:121726311G>A	ENST00000452319.1	+	6	725	c.665G>A	c.(664-666)cGg>cAg	p.R222Q	GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Missense_Mutation_p.R222Q					GLI family zinc finger 2									p.R222Q(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				TCCAGCCCGCGGGTGACGCCC	0.647																																					p.R222Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G665A	2						.						63.0	63.0	63.0					2																	121726311		2203	4300	6503	121442781	SO:0001583	missense	2736	exon5				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.665G>A	2.37:g.121726311G>A	ENSP00000390436:p.Arg222Gln		121442781	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207762	0.95033	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.70282	-0.47;-0.47	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.84579	0.5503	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.992	D	0.86643	0.1893	10	0.87932	D	0	.	18.2868	0.90117	0.0:0.0:1.0:0.0	.	222;222	P10070;Q0VGA0	GLI2_HUMAN;.	Q	222	ENSP00000390436:R222Q;ENSP00000354586:R222Q	ENSP00000354586:R222Q	R	+	2	0	GLI2	121442781	1.000000	0.71417	0.816000	0.32577	0.596000	0.36781	9.601000	0.98297	2.557000	0.86248	0.655000	0.94253	CGG		0.647	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
COL6A3	1293	hgsc.bcm.edu	37	2	238253585	238253585	+	Splice_Site	SNP	G	G	A	rs114248590	byFrequency	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr2:238253585G>A	ENST00000295550.4	-	35	7625	c.7173C>T	c.(7171-7173)taC>taT	p.Y2391Y	COL6A3_ENST00000353578.4_Splice_Site_p.Y2185Y|COL6A3_ENST00000346358.4_Splice_Site_p.Y2191Y|COL6A3_ENST00000347401.3_Splice_Site_p.Y2190Y|COL6A3_ENST00000472056.1_Splice_Site_p.Y1784Y|COL6A3_ENST00000409809.1_Splice_Site_p.Y2185Y	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2391	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Y2391Y(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TCAACTTACCGTAACAGCAAG	0.408													A|||	3	0.000599042	0.0008	0.0	5008	,	,		20521	0.001		0.0	False		,,,				2504	0.001				p.Y1784Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5352T	2						.						111.0	109.0	110.0					2																	238253585		2203	4300	6503	237918324	SO:0001630	splice_region_variant	1293	exon32			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7174+1C>T	2.37:g.238253585G>A			237918324	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.408	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	Silent
TNC	3371	hgsc.bcm.edu	37	9	117849482	117849482	+	Silent	SNP	G	G	A			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr9:117849482G>A	ENST00000350763.4	-	3	939	c.528C>T	c.(526-528)tgC>tgT	p.C176C	TNC_ENST00000542877.1_Silent_p.C176C|TNC_ENST00000537320.1_Silent_p.C176C|TNC_ENST00000345230.3_Silent_p.C176C|TNC_ENST00000341037.4_Silent_p.C176C|TNC_ENST00000535648.1_Silent_p.C176C|TNC_ENST00000346706.3_Silent_p.C176C|TNC_ENST00000340094.3_Silent_p.C176C|TNC_ENST00000423613.2_Silent_p.C176C	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	176	EGF-like 1; incomplete. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.C176C(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AGCCAGGTTCGCAGACACAGC	0.582																																					p.C176C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C528T	9						.						82.0	76.0	78.0					9																	117849482		2203	4300	6503	116889303	SO:0001819	synonymous_variant	3371	exon3				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.528C>T	9.37:g.117849482G>A			116889303	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.582	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
ITIH5	80760	hgsc.bcm.edu	37	10	7627983	7627983	+	Missense_Mutation	SNP	C	C	T	rs529878669		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr10:7627983C>T	ENST00000256861.6	-	8	1067	c.989G>A	c.(988-990)cGt>cAt	p.R330H	ITIH5_ENST00000397146.2_Missense_Mutation_p.R330H|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397145.2_Missense_Mutation_p.R330H|ITIH5_ENST00000446830.2_Missense_Mutation_p.R112H|ITIH5_ENST00000298441.6_Missense_Mutation_p.R116H	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	330	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R330H(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GATACTGAAACGGTCCTGGGG	0.473																																					p.R330H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G989A	10						.						148.0	127.0	134.0					10																	7627983		2203	4300	6503	7667989	SO:0001583	missense	80760	exon8					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.989G>A	10.37:g.7627983C>T	ENSP00000256861:p.Arg330His		7667989	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	0.568	-0.842188	0.02671	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08	5.3	-4.52	0.03472	von Willebrand factor, type A (3);	0.446927	0.26623	N	0.023357	T	0.72112	0.3420	.	.	.	0.20403	N	0.999908	B;B;B	0.12013	0.005;0.004;0.003	B;B;B	0.15052	0.012;0.003;0.002	T	0.55970	-0.8056	9	0.12103	T	0.63	-5.4197	13.2689	0.60150	0.0:0.2223:0.0:0.7777	.	330;330;116	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	H	330;330;116;112;330	ENSP00000256861:R330H;ENSP00000380333:R330H;ENSP00000298441:R116H;ENSP00000387969:R112H;ENSP00000380332:R330H	ENSP00000256861:R330H	R	-	2	0	ITIH5	7667989	0.017000	0.18338	0.009000	0.14445	0.699000	0.40488	-0.105000	0.10907	-1.191000	0.02695	-0.997000	0.02515	CGT		0.473	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
SGMS1	259230	hgsc.bcm.edu	37	10	52103403	52103403	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr10:52103403C>T	ENST00000361781.2	-	7	1431	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	SGMS1_ENST00000361543.2_Missense_Mutation_p.E158K|SGMS1_ENST00000492601.2_5'Flank|SGMS1_ENST00000429490.1_Intron	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	164					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)	p.E158K(1)		endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GGTACTCGTTCGTGGACGACC	0.493																																					p.E158K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G472A	10						.						59.0	53.0	55.0					10																	52103403		2203	4300	6503	51773409	SO:0001583	missense	259230	exon7			AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"""Sterile alpha motif (SAM) domain containing"""	29799	protein-coding gene	gene with protein product		611573	"""transmembrane protein 23"""	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.472G>A	10.37:g.52103403C>T	ENSP00000354829:p.Glu158Lys		51773409	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	37	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165193	0.94768	.	.	ENSG00000198964	ENST00000361781;ENST00000361543	T;T	0.60424	0.71;0.19	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.75686	0.3883	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.77768	-0.2464	10	0.87932	D	0	-14.4732	17.1838	0.86861	0.0:1.0:0.0:0.0	.	164	Q86VZ5	SMS1_HUMAN	K	158	ENSP00000354829:E158K;ENSP00000355235:E158K	ENSP00000355235:E158K	E	-	1	0	SGMS1	51773409	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.403000	0.79983	2.648000	0.89879	0.650000	0.86243	GAA		0.493	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156	
APC	324	hgsc.bcm.edu	37	5	112175001	112175002	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr5:112175001_112175002delAG	ENST00000457016.1	+	16	4090_4091	c.3710_3711delAG	c.(3709-3711)cagfs	p.Q1237fs	APC_ENST00000257430.4_Frame_Shift_Del_p.Q1237fs|APC_ENST00000508376.2_Frame_Shift_Del_p.Q1237fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1237	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1237fs*2(1)|p.S1238fs*1(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGTTCTGCACAGAGTAGAAGTG	0.411		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.1219_1219del	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	c.3656_3657del	5						.																																			112202901	SO:0001589	frameshift_variant	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3710_3711delAG	5.37:g.112175003_112175004delAG	ENSP00000413133:p.Gln1237fs		112202900	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.411	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
MYOT	9499	hgsc.bcm.edu	37	5	137213210	137213210	+	Splice_Site	SNP	G	G	A	rs150293853		TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3594-01A-02W-0831-10	TCGA-AG-3594-10A-01W-0831-10	g.chr5:137213210G>A	ENST00000239926.4	+	4	907	c.533G>A	c.(532-534)cGt>cAt	p.R178H	MYOT_ENST00000421631.2_5'UTR|MYOT_ENST00000509812.1_3'UTR|MYOT_ENST00000515645.1_Splice_Site_p.R63H|RP11-381K20.2_ENST00000514616.1_RNA	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	178					muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)	p.R178H(1)		cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCTCTAAAGCGTCTAACATAT	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		14939	0.0		0.001	False		,,,				2504	0.0				p.R178H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G533A	5						.	G	,HIS/ARG	0,4406		0,0,2203	77.0	77.0	77.0		,533	5.7	1.0	5	dbSNP_134	77	4,8596	3.7+/-12.6	0,4,4296	yes	utr-5,missense-near-splice	MYOT	NM_001135940.1,NM_006790.2	,29	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,probably-damaging	,178/499	137213210	4,13002	2203	4300	6503	137241109	SO:0001630	splice_region_variant	9499	exon4			AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"""Immunoglobulin superfamily / I-set domain containing"""	12399	protein-coding gene	gene with protein product		604103	"""titin immunoglobulin domain protein (myotilin)"", ""limb-girdle muscular dystrophy 1A (autosomal dominant)"""	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.532-1G>A	5.37:g.137213210G>A			137241109	NM_006790	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.39	3.614239	0.66672	0.0	4.65E-4	ENSG00000120729	ENST00000239926;ENST00000515645	T;T	0.72942	-0.7;-0.68	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000004	T	0.76212	0.3956	L	0.27053	0.805	0.40095	D	0.976309	D	0.89917	1.0	D	0.65874	0.939	T	0.76296	-0.3011	10	0.42905	T	0.14	.	19.8298	0.96631	0.0:0.0:1.0:0.0	.	178	Q9UBF9	MYOTI_HUMAN	H	178;63	ENSP00000239926:R178H;ENSP00000426281:R63H	ENSP00000239926:R178H	R	+	2	0	MYOT	137241109	1.000000	0.71417	0.999000	0.59377	0.327000	0.28475	6.020000	0.70826	2.687000	0.91594	0.591000	0.81541	CGT		0.398	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790	Missense_Mutation
