#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_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
RPL13AP3	645683	broad.mit.edu	37	14	56232970	56232970	+	lincRNA	SNP	T	T	C	rs2184557	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr14:56232970T>C	ENST00000554458.1	+	0	75				RPL13AP3_ENST00000494676.1_RNA																							CGTGGCTAAGTAGTTACTGCT	0.587													C|||	3286	0.65615	0.9221	0.4914	5008	,	,		16651	0.756		0.3678	False		,,,				2504	0.6074					ENST00000554458.1																			0																																																			0							g.chr14:56232970T>C																													14.37:g.56232970T>C						RPL13AP3_ENST00000494676.1_RNA								0	75	+									RNA	SNP	ENST00000554458.1	37																																																																																						0.587	RP11-813I20.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000411474.1			3	24	0	0	0	1	0	3	24				
RPL13AP3	645683	broad.mit.edu	37	14	56233069	56233069	+	lincRNA	SNP	G	G	T	rs10144431	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr14:56233069G>T	ENST00000554458.1	+	0	75				RPL13AP3_ENST00000494676.1_RNA																							GGCTTTCCTCGGCAAGCGGAT	0.562													T|||	1986	0.396565	0.4781	0.3329	5008	,	,		17497	0.2937		0.3489	False		,,,				2504	0.4867					ENST00000554458.1																			0																																																			0							g.chr14:56233069G>T																													14.37:g.56233069G>T						RPL13AP3_ENST00000494676.1_RNA								0	75	+									RNA	SNP	ENST00000554458.1	37																																																																																						0.562	RP11-813I20.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000411474.1			3	30	1	0	0.115264	1	0.118219	3	30				
SERPINA10	51156	broad.mit.edu	37	14	94756943	94756943	+	5'UTR	SNP	G	G	C	rs45505795	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr14:94756943G>C	ENST00000393096.1	-	0	453				SERPINA10_ENST00000554173.1_5'UTR|SERPINA10_ENST00000261994.4_5'UTR|SERPINA10_ENST00000554723.1_Silent_p.S36S	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10						blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GATCGGCTGCGGAGGCCAAGG	0.562													G|||	43	0.00858626	0.0	0.0043	5008	,	,		19077	0.0		0.0308	False		,,,				2504	0.0092					ENST00000554723.1																			0				haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33						c.(106-108)tcC>tcG		serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10		G	,	28,4378		0,28,2175	21.0	23.0	23.0		,	2.2	0.0	14	dbSNP_127	23	265,8333		4,257,4038	no	utr-5,utr-5	SERPINA10	NM_001100607.1,NM_016186.2	,	4,285,6213	CC,CG,GG		3.0821,0.6355,2.2532	,	,	94756943	293,12711	2203	4299	6502	SO:0001623	5_prime_UTR_variant	51156				regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity	g.chr14:94756943G>C	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"""Serine (or cysteine) peptidase inhibitors"""	15996	protein-coding gene	gene with protein product		605271	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"""			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.-13C>G	14.37:g.94756943G>C						SERPINA10_ENST00000393096.1_5'UTR|SERPINA10_ENST00000554173.1_5'UTR|SERPINA10_ENST00000261994.4_5'UTR	p.S36S			Q9UK55	ZPI_HUMAN		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	2	526	-		all_cancers(154;0.105)	0					A5Z2A5|Q6UWX9|Q86U20	Silent	SNP	ENST00000393096.1	37	c.108C>G	CCDS9923.1																																																																																				0.562	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		3	22	0	0	0	1	0	3	22				
TYW1B	441250	broad.mit.edu	37	7	72093914	72093914	+	RNA	SNP	C	C	A	rs374211694		TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr7:72093914C>A	ENST00000435769.2	-	0	1698				TYW1B_ENST00000438125.1_RNA|TYW1B_ENST00000343721.5_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)						tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)										ACACGAGCTGCGCGTAGGCCT	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		17625	0.0		0.0	False		,,,				2504	0.001					ENST00000438125.1																			0													tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)							62.0	67.0	65.0					7																	72093914		692	1591	2283			441250				tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity	g.chr7:72093914C>A	BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149			33908	protein-coding gene	gene with protein product	"""radical S-adenosyl methionine and flavodoxin domains 1"", ""non-protein coding RNA 69"", ""long intergenic non-protein coding RNA 69"""		"""tRNA-yW synthesizing protein 1 homolog B (non-protein coding)"""				Standard	NM_001145440		Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067		7.37:g.72093914C>A										Q6NUM6	TYW1B_HUMAN			0	1188	-								A6NG09|B4DFY2|Q3KQX2	RNA	SNP	ENST00000435769.2	37																																																																																						0.527	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347346.2	NM_001145440		3	19	1	0	1	1	1	3	19				
TRAV6	6956	broad.mit.edu	37	14	22236771	22236771	+	RNA	SNP	C	C	T	rs11623408	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr14:22236771C>T	ENST00000390428.3	+	0	43									T cell receptor alpha variable 6																		GTCTACATTTCAGGCCACATT	0.468													C|||	777	0.155152	0.1172	0.1455	5008	,	,		21523	0.1171		0.2406	False		,,,				2504	0.1646					ENST00000390428.3																			0															C		572,3278		33,506,1386	248.0	246.0	247.0			-2.3	0.0	14	dbSNP_120	247	1972,6282		227,1518,2382	no	intergenic				260,2024,3768	TT,TC,CC		23.8914,14.8571,21.0178			22236771	2544,9560	1925	4127	6052			0							g.chr14:22236771C>T	Z49060		14q11.2	2012-02-07			ENSG00000211780	ENSG00000211780		"""T cell receptors / TRA locus"""	12144	other	T cell receptor gene				TCRAV5S1		8188290, 8530018	Standard	NG_001332		Approved				OTTHUMG00000168984		14.37:g.22236771C>T														0	43	+									RNA	SNP	ENST00000390428.3	37																																																																																						0.468	TRAV6-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000401882.1	NG_001332		6	149	0	0	0	1	0	6	149				
ATXN2L	11273	broad.mit.edu	37	16	28846948	28846948	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr16:28846948A>C	ENST00000336783.4	+	21	2931	c.2764A>C	c.(2764-2766)Acg>Ccg	p.T922P	ATXN2L_ENST00000395547.2_Missense_Mutation_p.T922P|ATXN2L_ENST00000340394.8_Missense_Mutation_p.T922P|ATXN2L_ENST00000325215.6_Missense_Mutation_p.T922P|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000564304.1_Missense_Mutation_p.T928P|ATXN2L_ENST00000570200.1_Missense_Mutation_p.T922P|ATXN2L_ENST00000382686.4_Missense_Mutation_p.T922P	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	922					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						CCTGACAGGCACGCCGCCCTC	0.672																																						ENST00000336783.4																			0				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						c.(2764-2766)Acg>Ccg		ataxin 2-like							39.0	39.0	39.0					16																	28846948		2197	4299	6496	SO:0001583	missense	11273					membrane		g.chr16:28846948A>C		CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2764A>C	16.37:g.28846948A>C	ENSP00000338718:p.Thr922Pro					ATXN2L_ENST00000340394.8_Missense_Mutation_p.T922P|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000564304.1_Missense_Mutation_p.T928P|ATXN2L_ENST00000570200.1_Missense_Mutation_p.T922P|ATXN2L_ENST00000395547.2_Missense_Mutation_p.T922P|ATXN2L_ENST00000325215.6_Missense_Mutation_p.T922P|ATXN2L_ENST00000382686.4_Missense_Mutation_p.T922P	p.T922P	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN			21	2931	+			922					A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Missense_Mutation	SNP	ENST00000336783.4	37	c.2764A>C	CCDS10641.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.557872	0.65425	.	.	ENSG00000168488	ENST00000340394;ENST00000395547;ENST00000336783;ENST00000382686;ENST00000325215	T;T;T;T;T	0.70986	-0.41;-0.53;-0.48;-0.43;-0.45	5.82	5.82	0.92795	.	0.070599	0.64402	D	0.000020	T	0.77177	0.4092	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D;D	0.76494	0.998;0.998;0.999;0.999;0.998;0.999	D;D;D;D;D;D	0.80764	0.987;0.987;0.994;0.994;0.987;0.994	T	0.75510	-0.3292	10	0.33940	T	0.23	-10.331	15.1603	0.72778	1.0:0.0:0.0:0.0	.	922;922;922;922;922;922	Q63ZY4;Q8WWM7;Q8WWM7-2;Q8WWM7-4;A8K1R6;Q8WWM7-3	.;ATX2L_HUMAN;.;.;.;.	P	922	ENSP00000341459:T922P;ENSP00000378917:T922P;ENSP00000338718:T922P;ENSP00000372133:T922P;ENSP00000315650:T922P	ENSP00000315650:T922P	T	+	1	0	ATXN2L	28754449	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.024000	0.76443	2.222000	0.72286	0.383000	0.25322	ACG		0.672	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		15	34	0	0	0	1	0	15	34				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|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)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|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)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		57	63	0	0	0	1	0	57	63				
TMEM79	84283	broad.mit.edu	37	1	156255560	156255560	+	Silent	SNP	G	G	A	rs140033065	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr1:156255560G>A	ENST00000405535.2	+	2	714	c.543G>A	c.(541-543)ccG>ccA	p.P181P	TMEM79_ENST00000495881.1_3'UTR|SMG5_ENST00000368267.5_5'Flank|SMG5_ENST00000361813.5_5'Flank|TMEM79_ENST00000295694.5_Silent_p.P181P|TMEM79_ENST00000357501.2_Intron	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	181					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					TGGTGAGGCCGCCTGGCTGTT	0.682													G|||	5	0.000998403	0.0	0.0	5008	,	,		12551	0.0		0.004	False		,,,				2504	0.001					ENST00000405535.2																			0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21						c.(541-543)ccG>ccA		transmembrane protein 79		G		5,4395		0,5,2195	39.0	45.0	43.0		543	-11.3	0.0	1	dbSNP_134	43	29,8569		1,27,4271	no	coding-synonymous	TMEM79	NM_032323.2		1,32,6466	AA,AG,GG		0.3373,0.1136,0.2616		181/395	156255560	34,12964	2200	4299	6499	SO:0001819	synonymous_variant	84283					integral to membrane		g.chr1:156255560G>A	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"""mattrin"""	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.543G>A	1.37:g.156255560G>A						TMEM79_ENST00000357501.2_Intron|TMEM79_ENST00000295694.5_Silent_p.P181P|TMEM79_ENST00000495881.1_3'UTR	p.P181P	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN			2	714	+	Hepatocellular(266;0.158)		181					B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	37	c.543G>A	CCDS1138.1																																																																																				0.682	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		8	76	0	0	0	1	0	8	76				
ACSS2	55902	broad.mit.edu	37	20	33501967	33501967	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr20:33501967C>T	ENST00000360596.2	+	6	923	c.712C>T	c.(712-714)Cag>Tag	p.Q238*	ACSS2_ENST00000336325.4_Nonsense_Mutation_p.Q188*|ACSS2_ENST00000253382.5_Nonsense_Mutation_p.Q238*|ACSS2_ENST00000476922.1_Intron	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	238					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCAGAAGTGTCAGGAGAAGTA	0.537																																						ENST00000360596.2																			0				cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21						c.(712-714)Cag>Tag		acyl-CoA synthetase short-chain family member 2	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)						97.0	102.0	100.0					20																	33501967		2203	4300	6503	SO:0001587	stop_gained	55902				ethanol oxidation|lipid biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	acetate-CoA ligase activity|ATP binding|protein binding	g.chr20:33501967C>T	AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"""Acyl-CoA synthetase family"""	15814	protein-coding gene	gene with protein product		605832	"""acetyl-Coenzyme A synthetase 2 (ADP forming)"""	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.712C>T	20.37:g.33501967C>T	ENSP00000353804:p.Gln238*					ACSS2_ENST00000253382.5_Nonsense_Mutation_p.Q238*|ACSS2_ENST00000476922.1_Intron|ACSS2_ENST00000336325.4_Nonsense_Mutation_p.Q188*	p.Q238*	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN			6	923	+			238					A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Nonsense_Mutation	SNP	ENST00000360596.2	37	c.712C>T	CCDS13243.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953305	0.92660	.	.	ENSG00000131069	ENST00000336325;ENST00000360596;ENST00000374693;ENST00000253382	.	.	.	5.24	5.24	0.73138	.	0.424663	0.26808	N	0.022386	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-16.1784	8.8531	0.35212	0.2073:0.6595:0.1332:0.0	.	.	.	.	X	188;238;238;238	.	ENSP00000253382:Q238X	Q	+	1	0	ACSS2	32965628	1.000000	0.71417	0.990000	0.47175	0.979000	0.70002	2.841000	0.48223	2.729000	0.93468	0.655000	0.94253	CAG		0.537	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677		3	31	0	0	0	1	0	3	31				
CRACR2A	84766	broad.mit.edu	37	12	3788151	3788151	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr12:3788151T>C	ENST00000252322.1	-	6	922	c.454A>G	c.(454-456)Atg>Gtg	p.M152V	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.M152V|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.M152V	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		152					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TCTTCGCCCATGTCGCCCAGA	0.532																																						ENST00000440314.2																			0				breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24						c.(454-456)Atg>Gtg		EF-hand calcium binding domain 4B							206.0	166.0	179.0					12																	3788151		2203	4300	6503	SO:0001583	missense	84766				activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding	g.chr12:3788151T>C																												ENST00000252322.1:c.454A>G	12.37:g.3788151T>C	ENSP00000252322:p.Met152Val					EFCAB4B_ENST00000444507.1_Missense_Mutation_p.M152V|EFCAB4B_ENST00000252322.1_Missense_Mutation_p.M152V	p.M152V	NM_001144958.1	NP_001138430.1	Q9BSW2	EFC4B_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)		6	927	-			152					B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	c.454A>G	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	T	0.707	-0.788760	0.02884	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.59638	0.25;2.71;2.73	4.38	-3.17	0.05202	.	0.956485	0.08808	N	0.890749	T	0.37019	0.0988	L	0.39020	1.185	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.19353	-1.0308	10	0.26408	T	0.33	-3.7883	0.9736	0.01421	0.1506:0.174:0.309:0.3664	.	152;152;152	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	V	152	ENSP00000409382:M152V;ENSP00000412496:M152V;ENSP00000252322:M152V	ENSP00000252322:M152V	M	-	1	0	EFCAB4B	3658412	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.193000	0.09573	-0.824000	0.04295	0.459000	0.35465	ATG		0.532	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			48	74	0	0	0	1	0	48	74				
TOPORS	10210	broad.mit.edu	37	9	32541435	32541435	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr9:32541435G>A	ENST00000360538.2	-	3	3204	c.3088C>T	c.(3088-3090)Cgg>Tgg	p.R1030W	TOPORS_ENST00000379858.1_Missense_Mutation_p.R965W	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	1030					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		AATGATGTCCGTGGCGATGGC	0.393																																						ENST00000360538.2																			0				large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12						c.(3088-3090)Cgg>Tgg		topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase							100.0	96.0	98.0					9																	32541435		2203	4300	6503	SO:0001583	missense	10210				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding	g.chr9:32541435G>A	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.3088C>T	9.37:g.32541435G>A	ENSP00000353735:p.Arg1030Trp					TOPORS_ENST00000379858.1_Missense_Mutation_p.R965W	p.R1030W	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)	3	3204	-			1030					O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	c.3088C>T	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116162	0.56505	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.19105	2.17;2.19	4.72	1.55	0.23275	.	0.000000	0.38897	N	0.001523	T	0.23611	0.0571	N	0.19112	0.55	0.29347	N	0.865591	D	0.89917	1.0	D	0.69654	0.965	T	0.03344	-1.1046	10	0.87932	D	0	-6.5977	5.7977	0.18396	0.0923:0.0:0.4041:0.5035	.	1030	Q9NS56	TOPRS_HUMAN	W	1030;965	ENSP00000353735:R1030W;ENSP00000369187:R965W	ENSP00000353735:R1030W	R	-	1	2	TOPORS	32531435	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.026000	0.30103	0.674000	0.31244	0.650000	0.86243	CGG		0.393	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		4	62	0	0	0	1	0	4	62				
TAF6L	10629	broad.mit.edu	37	11	62543326	62543326	+	Missense_Mutation	SNP	C	C	T	rs76769410	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr11:62543326C>T	ENST00000294168.3	+	2	272	c.71C>T	c.(70-72)aCg>aTg	p.T24M	TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	24					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						GCGGAGAGCACGGGCCTGGAG	0.637													C|||	13	0.00259585	0.0015	0.0014	5008	,	,		18124	0.0		0.008	False		,,,				2504	0.002					ENST00000294168.3																			0				endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						c.(70-72)aCg>aTg		TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa		C	MET/THR	9,4393	16.8+/-37.8	0,9,2192	69.0	68.0	68.0		71	3.9	1.0	11	dbSNP_131	68	78,8520	45.4+/-104.0	2,74,4223	yes	missense	TAF6L	NM_006473.3	81	2,83,6415	TT,TC,CC		0.9072,0.2045,0.6692	possibly-damaging	24/623	62543326	87,12913	2201	4299	6500	SO:0001583	missense	10629				chromatin remodeling|histone H3 acetylation|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	histone deacetylase complex|STAGA complex	DNA binding|protein binding|transcription coactivator activity	g.chr11:62543326C>T	BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"""TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.71C>T	11.37:g.62543326C>T	ENSP00000294168:p.Thr24Met					TMEM223_ENST00000527073.1_Intron	p.T24M	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN			2	272	+			24					B2RAT0|Q96HA6	Missense_Mutation	SNP	ENST00000294168.3	37	c.71C>T	CCDS8035.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	12.19	1.864603	0.32977	0.002045	0.009072	ENSG00000162227	ENST00000294168;ENST00000526261;ENST00000529509	T;T;T	0.42131	0.98;0.98;0.98	4.78	3.86	0.44501	Histone-fold (2);TATA box binding protein associated factor (TAF) (2);	0.211038	0.39615	N	0.001303	T	0.15478	0.0373	N	0.11427	0.14	0.80722	D	1	B;B	0.22146	0.013;0.065	B;B	0.17098	0.006;0.017	T	0.04522	-1.0945	10	0.37606	T	0.19	1.1681	7.4374	0.27164	0.0:0.8078:0.0:0.1922	.	24;24	B4DVM4;Q9Y6J9	.;TAF6L_HUMAN	M	24	ENSP00000294168:T24M;ENSP00000435116:T24M;ENSP00000434662:T24M	ENSP00000294168:T24M	T	+	2	0	TAF6L	62299902	0.996000	0.38824	0.963000	0.40424	0.968000	0.65278	3.349000	0.52217	1.364000	0.46038	0.561000	0.74099	ACG		0.637	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473		4	57	0	0	0	1	0	4	57				
KMT2A	4297	broad.mit.edu	37	11	118362606	118362606	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr11:118362606A>C	ENST00000389506.5	+	15	4958	c.4958A>C	c.(4957-4959)aAt>aCt	p.N1653T	KMT2A_ENST00000534358.1_Missense_Mutation_p.N1656T|KMT2A_ENST00000354520.4_Missense_Mutation_p.N1615T			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1653					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										GCTTTGTTGAATTCTCGGACT	0.473																																						ENST00000534358.1																			0											c.(4966-4968)aAt>aCt		lysine (K)-specific methyltransferase 2A							52.0	51.0	51.0					11																	118362606		2200	4296	6496	SO:0001583	missense	4297							g.chr11:118362606A>C	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.4958A>C	11.37:g.118362606A>C	ENSP00000374157:p.Asn1653Thr					KMT2A_ENST00000389506.5_Missense_Mutation_p.N1653T|KMT2A_ENST00000354520.4_Missense_Mutation_p.N1615T	p.N1656T	NM_001197104.1|NM_005933.3	NP_001184033.1|NP_005924.2					15	4990	+								E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	c.4967A>C	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.362840	0.61403	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313;ENST00000392873	D;D;D;D	0.90324	-1.61;-1.62;-1.55;-2.65	5.75	5.75	0.90469	Bromodomain (1);	0.000000	0.85682	D	0.000000	D	0.93077	0.7796	L	0.47716	1.5	0.80722	D	1	D;D	0.67145	0.972;0.996	P;D	0.65140	0.875;0.932	D	0.93666	0.6986	10	0.66056	D	0.02	.	16.0681	0.80903	1.0:0.0:0.0:0.0	.	1656;1653	E9PQG7;Q03164	.;MLL1_HUMAN	T	1656;1653;1615;563;365	ENSP00000436786:N1656T;ENSP00000374157:N1653T;ENSP00000346516:N1615T;ENSP00000376612:N365T	ENSP00000346516:N1615T	N	+	2	0	MLL	117867816	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.891000	0.69782	2.188000	0.69820	0.528000	0.53228	AAT		0.473	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		5	51	0	0	0	1	0	5	51				
CCDC136	64753	broad.mit.edu	37	7	128445518	128445518	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr7:128445518G>T	ENST00000297788.4	+	6	1255	c.888G>T	c.(886-888)atG>atT	p.M296I	CCDC136_ENST00000464832.1_Missense_Mutation_p.M346I|CCDC136_ENST00000487361.1_Missense_Mutation_p.M296I|CCDC136_ENST00000378685.4_Missense_Mutation_p.M334I	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	296	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						ATCCTGAAATGCAGTTGTTAC	0.502																																						ENST00000297788.4																			0				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						c.(886-888)atG>atT		coiled-coil domain containing 136							129.0	129.0	129.0					7																	128445518		2006	4180	6186	SO:0001583	missense	64753					integral to membrane	protein binding	g.chr7:128445518G>T		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.888G>T	7.37:g.128445518G>T	ENSP00000297788:p.Met296Ile					CCDC136_ENST00000487361.1_Missense_Mutation_p.M296I|CCDC136_ENST00000378685.4_Missense_Mutation_p.M334I|CCDC136_ENST00000464832.1_Missense_Mutation_p.M346I	p.M296I	NM_022742.4	NP_073579.4	Q96JN2	CC136_HUMAN			6	1255	+			296			Glu-rich.		A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	37	c.888G>T	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.863|7.863	0.726402|0.726402	0.15439|0.15439	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000494552|ENST00000378685;ENST00000464832;ENST00000487361;ENST00000297788;ENST00000397697;ENST00000320524	.|T;T;T;T	.|0.74106	.|1.0;0.98;-0.81;1.55	5.65|5.65	-0.858|-0.858	0.10689|0.10689	.|.	.|0.660669	.|0.16047	.|N	.|0.232148	T|T	0.57607|0.57607	0.2065|0.2065	L|L	0.38531|0.38531	1.155|1.155	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.25904	.|0.012;0.137;0.009	.|B;B;B	.|0.21546	.|0.015;0.035;0.008	T|T	0.42068|0.42068	-0.9473|-0.9473	5|10	.|0.32370	.|T	.|0.25	-1.0407|-1.0407	6.7498|6.7498	0.23482|0.23482	0.0792:0.1419:0.5989:0.1801|0.0792:0.1419:0.5989:0.1801	.|.	.|296;296;334	.|C9JE17;Q96JN2;Q96JN2-3	.|.;CC136_HUMAN;.	F|I	173|334;346;296;296;296;296	.|ENSP00000367956:M334I;ENSP00000419515:M346I;ENSP00000420509:M296I;ENSP00000297788:M296I	.|ENSP00000297788:M296I	C|M	+|+	2|3	0|0	CCDC136|CCDC136	128232754|128232754	0.000000|0.000000	0.05858|0.05858	0.016000|0.016000	0.15963|0.15963	0.684000|0.684000	0.39900|0.39900	-0.168000|-0.168000	0.09925|0.09925	-0.140000|-0.140000	0.11394|0.11394	0.655000|0.655000	0.94253|0.94253	TGC|ATG		0.502	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		38	66	1	0	1.90571e-15	1	2.00601e-15	38	66				
MED15	51586	broad.mit.edu	37	22	20909296	20909296	+	Silent	SNP	G	G	C			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr22:20909296G>C	ENST00000263205.7	+	5	381	c.312G>C	c.(310-312)cgG>cgC	p.R104R	MED15_ENST00000542773.1_Intron|MED15_ENST00000425759.2_Intron|MED15_ENST00000541476.1_Silent_p.R78R|MED15_ENST00000406969.1_Silent_p.R78R|MED15_ENST00000292733.7_Silent_p.R104R|MED15_ENST00000382974.2_Intron	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	104					gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			TGCCTCCTCGGGGCCCGGGAC	0.647																																						ENST00000263205.7																			0				central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25						c.(310-312)cgG>cgC		mediator complex subunit 15							40.0	43.0	42.0					22																	20909296		2203	4300	6503	SO:0001819	synonymous_variant	51586				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding	g.chr22:20909296G>C	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.312G>C	22.37:g.20909296G>C						MED15_ENST00000425759.2_Intron|MED15_ENST00000542773.1_Intron|MED15_ENST00000292733.7_Silent_p.R104R|MED15_ENST00000382974.2_Intron|MED15_ENST00000541476.1_Silent_p.R78R|MED15_ENST00000406969.1_Silent_p.R78R	p.R104R	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)		5	381	+	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	104					D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	37	c.312G>C	CCDS33602.1																																																																																				0.647	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		5	50	0	0	0	1	0	5	50				
CD5	921	broad.mit.edu	37	11	60885869	60885869	+	Missense_Mutation	SNP	T	T	C	rs142251832		TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr11:60885869T>C	ENST00000347785.3	+	3	483	c.317T>C	c.(316-318)aTc>aCc	p.I106T		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	106	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		AGCTCAATCATCTGCTACGGA	0.562																																						ENST00000347785.3																			0				central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						c.(316-318)aTc>aCc		CD5 molecule		T	THR/ILE	0,4406		0,0,2203	205.0	185.0	192.0		317	-3.7	0.0	11	dbSNP_134	192	3,8595	3.0+/-9.4	0,3,4296	no	missense	CD5	NM_014207.3	89	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	benign	106/496	60885869	3,13001	2203	4299	6502	SO:0001583	missense	921				cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity	g.chr11:60885869T>C	X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"""CD molecules"""	1685	protein-coding gene	gene with protein product		153340	"""CD5 antigen (p56-62)"""	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.317T>C	11.37:g.60885869T>C	ENSP00000342681:p.Ile106Thr						p.I106T	NM_014207.3	NP_055022.2	P06127	CD5_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)	3	483	+		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)	106			SRCR 1.		A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	c.317T>C	CCDS8000.1	.	.	.	.	.	.	.	.	.	.	T	2.549	-0.304490	0.05495	0.0	3.49E-4	ENSG00000110448	ENST00000347785;ENST00000544014	T;T	0.34275	1.37;1.37	3.85	-3.67	0.04476	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	2.223100	0.01902	N	0.039273	T	0.24547	0.0595	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.11329	0.006	T	0.19386	-1.0307	10	0.20046	T	0.44	-0.5178	11.0793	0.48051	0.0:0.3933:0.0:0.6067	.	106	P06127	CD5_HUMAN	T	106	ENSP00000342681:I106T;ENSP00000440899:I106T	ENSP00000342681:I106T	I	+	2	0	CD5	60642445	0.007000	0.16637	0.001000	0.08648	0.002000	0.02628	-0.456000	0.06754	-1.218000	0.02601	-1.139000	0.01908	ATC		0.562	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207		10	191	0	0	0	1	0	10	191				
BRCC3	79184	broad.mit.edu	37	X	154305462	154305462	+	Silent	SNP	T	T	A			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chrX:154305462T>A	ENST00000369462.1	+	4	238	c.213T>A	c.(211-213)atT>atA	p.I71I	BRCC3_ENST00000369459.2_Silent_p.I71I|BRCC3_ENST00000330045.7_Silent_p.I71I|MTCP1_ENST00000362018.2_Intron|BRCC3_ENST00000340647.4_Silent_p.I72I|BRCC3_ENST00000399042.1_Silent_p.I71I	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	71	MPN.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCGTCAGAATTGTTCACATTC	0.413																																						ENST00000369462.1																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22						c.(211-213)atT>atA		BRCA1/BRCA2-containing complex, subunit 3							109.0	94.0	98.0					X																	154305462		1885	4100	5985	SO:0001819	synonymous_variant	79184				double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|positive regulation of DNA repair|response to X-ray	BRCA1-A complex|BRISC complex|nuclear ubiquitin ligase complex	enzyme regulator activity|metal ion binding|metallopeptidase activity|polyubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chrX:154305462T>A	X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515			24185	protein-coding gene	gene with protein product	"""Lys-63-specific deubiquitinase"""	300617	"""chromosome X open reading frame 53"""	CXorf53		1303175, 14636569	Standard	NM_024332		Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000369462.1:c.213T>A	X.37:g.154305462T>A						BRCC3_ENST00000330045.7_Silent_p.I71I|MTCP1_ENST00000362018.2_Intron|BRCC3_ENST00000399042.1_Silent_p.I71I|BRCC3_ENST00000369459.2_Silent_p.I71I|BRCC3_ENST00000340647.4_Silent_p.I72I	p.I71I	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN			4	238	+	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)		71					A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	Silent	SNP	ENST00000369462.1	37	c.213T>A	CCDS56611.1																																																																																				0.413	BRCC3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058788.4	NM_024332		20	30	0	0	0	1	0	20	30				
GOLGA2P9	440518	broad.mit.edu	37	19	22785299	22785299	+	RNA	SNP	T	T	G	rs11670278	byFrequency	TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr19:22785299T>G	ENST00000599738.1	+	0	0				AC011467.1_ENST00000408863.1_RNA|RN7SL860P_ENST00000473738.2_RNA|CTC-457E21.3_ENST00000600260.1_RNA																							CCCTGCAGGGTGCCATGGAGA	0.632													G|||	1469	0.293331	0.4834	0.2565	5008	,	,		16838	0.2679		0.1431	False		,,,				2504	0.2434					ENST00000600260.1																			0																																																			0							g.chr19:22785299T>G																													19.37:g.22785299T>G								NR_033899.1						0	1475	+									RNA	SNP	ENST00000599738.1	37																																																																																						0.632	CTC-457E21.6-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000464575.1			4	25	0	0	0	1	0	4	25				
FAM131C	348487	broad.mit.edu	37	1	16388993	16388993	+	Splice_Site	SNP	C	C	T			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr1:16388993C>T	ENST00000375662.4	-	3	358		c.e3+1		FAM131C_ENST00000494078.1_Splice_Site	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C											large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGTGCACTGACCTGCCAAGGA	0.607																																						ENST00000375662.4																			0				large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8						c.e3+1		family with sequence similarity 131, member C							19.0	21.0	20.0					1																	16388993		1904	4109	6013	SO:0001630	splice_region_variant	348487							g.chr1:16388993C>T		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.174+1G>A	1.37:g.16388993C>T						FAM131C_ENST00000494078.1_Splice_Site		NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)	3	358	-		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)						Q5T5Q5|Q8N3X3|Q8N9P9	Splice_Site	SNP	ENST00000375662.4	37		CCDS41270.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.201980	0.58234	.	.	ENSG00000185519	ENST00000375662	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4058	0.60913	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM131C	16261580	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	2.444000	0.44890	2.239000	0.73571	0.561000	0.74099	.		0.607	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	Intron	3	5	0	0	0	1	0	3	5				
LOC101927533	101927533	broad.mit.edu	37	2	65894933	65894934	+	lincRNA	DEL	AA	AA	-			TCGA-EL-A3ZH-01A-31D-A23M-08	TCGA-EL-A3ZH-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cc31e6b-07a9-4f0e-b3f3-9005473057fa	14208ab1-4d73-4805-9538-8f63d23152a3	g.chr2:65894933_65894934delAA	ENST00000377977.3	+	0	862				AC007389.4_ENST00000583614.1_RNA																							TCAGAGGTTTAAAAAAAAAAAA	0.52																																						ENST00000377977.3																			0																																																			0							g.chr2:65894933_65894934delAA																													2.37:g.65894943_65894944delAA														0	862	+									RNA	DEL	ENST00000377977.3	37																																																																																						0.520	AC074391.1-010	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470883.1			2	4						2	4	---	---	---	---
