#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
NBPF10	100132406	broad.mit.edu	37	1	145302714	145302714	+	Silent	SNP	A	A	G	rs9424867	byFrequency	TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr1:145302714A>G	ENST00000369339.3	+	5	592	c.339A>G	c.(337-339)ttA>ttG	p.L113L	NBPF10_ENST00000342960.5_Silent_p.L384L|NBPF10_ENST00000369338.1_Silent_p.L113L|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	384						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L113L(3)|p.L384L(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGGAGAAGTTACGGGAAGGGA	0.527																																						ENST00000342960.5																			6	Substitution - coding silent(6)	p.L113L(3)|p.L384L(3)	prostate(2)|kidney(2)|central_nervous_system(2)	NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(1150-1152)ttA>ttG		neuroblastoma breakpoint family, member 10																																				SO:0001819	synonymous_variant	100132406							g.chr1:145302714A>G	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.339A>G	1.37:g.145302714A>G						NBPF10_ENST00000369338.1_Silent_p.L113L|NBPF10_ENST00000369339.2_Silent_p.L113L|RP11-458D21.5_ENST00000468030.1_3'UTR	p.L384L	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	8	1187	+	all_hematologic(923;0.032)		384					Q5RHC0|Q9NWN6	Silent	SNP	ENST00000369339.3	37	c.1152A>G																																																																																					0.527	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703		7	198	0	0	0	0.000157383	0	7	198				
BMS1P20	96610	broad.mit.edu	37	22	22661474	22661474	+	RNA	SNP	C	C	T	rs537933406	byFrequency	TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr22:22661474C>T	ENST00000426066.1	+	0	364					NR_027293.1				BMS1 pseudogene 20																		CCCTCAGATGCGTCTGAAGAA	0.493													.|||	30	0.00599042	0.0136	0.0029	5008	,	,		25183	0.0		0.002	False		,,,				2504	0.0082					ENST00000426066.1																			0																																																			0							g.chr22:22661474C>T			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661474C>T								NR_027293.1						0	364	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.493	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			7	63	0	0	0	0.000442599	0	7	63				
MAGED2	10916	broad.mit.edu	37	X	54841696	54841696	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chrX:54841696C>T	ENST00000375068.1	+	12	1635	c.1402C>T	c.(1402-1404)Ccc>Tcc	p.P468S	MAGED2_ENST00000347546.4_Missense_Mutation_p.P450S|MAGED2_ENST00000375060.1_Missense_Mutation_p.P383S|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375058.1_Missense_Mutation_p.P468S|MAGED2_ENST00000375062.4_Missense_Mutation_p.P383S|MAGED2_ENST00000396224.1_Missense_Mutation_p.P468S|MAGED2_ENST00000218439.4_Missense_Mutation_p.P468S|MAGED2_ENST00000375053.2_Missense_Mutation_p.P468S			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	468	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					membrane (GO:0016020)		p.P468S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						AAAGAAGGATCCCAAGGAATG	0.458																																						ENST00000375068.1																			1	Substitution - Missense(1)	p.P468S(1)	skin(1)	breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						c.(1402-1404)Ccc>Tcc		melanoma antigen family D, 2							47.0	47.0	47.0					X																	54841696		2202	4294	6496	SO:0001583	missense	10916							g.chrX:54841696C>T	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1402C>T	X.37:g.54841696C>T	ENSP00000364209:p.Pro468Ser					MAGED2_ENST00000375053.2_Missense_Mutation_p.P468S|MAGED2_ENST00000375060.1_Missense_Mutation_p.P383S|MAGED2_ENST00000396224.1_Missense_Mutation_p.P468S|MAGED2_ENST00000375062.4_Missense_Mutation_p.P383S|MAGED2_ENST00000347546.3_Missense_Mutation_p.P412S|MAGED2_ENST00000343474.6_Missense_Mutation_p.P450S|MAGED2_ENST00000375058.1_Missense_Mutation_p.P468S|MAGED2_ENST00000218439.4_Missense_Mutation_p.P468S	p.P468S			Q9UNF1	MAGD2_HUMAN			12	1635	+			468			MAGE.		A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	c.1402C>T	CCDS14362.1	.	.	.	.	.	.	.	.	.	.	C	17.30	3.355027	0.61293	.	.	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.38722	3.64;3.64;3.76;3.6;1.12;3.64;3.64;1.12;3.64	4.73	4.73	0.59995	.	0.000000	0.45361	D	0.000366	T	0.62612	0.2442	M	0.73753	2.245	0.48395	D	0.999646	D;P	0.76494	0.999;0.76	D;P	0.67900	0.954;0.674	T	0.67964	-0.5534	10	0.87932	D	0	.	14.0723	0.64868	0.0:1.0:0.0:0.0	.	383;468	Q5H907;Q9UNF1	.;MAGD2_HUMAN	S	468;468;412;450;383;468;468;383;468	ENSP00000364209:P468S;ENSP00000364193:P468S;ENSP00000336962:P412S;ENSP00000340290:P450S;ENSP00000364202:P383S;ENSP00000218439:P468S;ENSP00000364198:P468S;ENSP00000364200:P383S;ENSP00000379526:P468S	ENSP00000218439:P468S	P	+	1	0	MAGED2	54858421	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.334000	0.59291	2.098000	0.63641	0.513000	0.50165	CCC		0.458	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		4	70	0	0	0	1.23904e-05	0	4	70				
C22orf31	25770	broad.mit.edu	37	22	29456530	29456530	+	Missense_Mutation	SNP	G	G	C			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr22:29456530G>C	ENST00000216071.4	-	2	356	c.305C>G	c.(304-306)tCg>tGg	p.S102W		NM_015370.1	NP_056185.1	O95567	CV031_HUMAN	chromosome 22 open reading frame 31	102										cervix(1)|endometrium(1)|kidney(17)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	27						TAATCTCTTCGAGAGTTTTCC	0.483																																						ENST00000216071.4																			0				cervix(1)|endometrium(1)|kidney(17)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	27						c.(304-306)tCg>tGg		chromosome 22 open reading frame 31							109.0	101.0	103.0					22																	29456530		2203	4300	6503	SO:0001583	missense	25770							g.chr22:29456530G>C	AL035364	CCDS13848.1	22q12.1	2006-07-05			ENSG00000100249	ENSG00000100249			26931	protein-coding gene	gene with protein product						15461802	Standard	XM_005261490		Approved	HS747E2A, bK747E2.1	uc003aej.1	O95567	OTTHUMG00000151011	ENST00000216071.4:c.305C>G	22.37:g.29456530G>C	ENSP00000216071:p.Ser102Trp						p.S102W	NM_015370.1	NP_056185.1	O95567	CV031_HUMAN			2	356	-			102					A0AV97	Missense_Mutation	SNP	ENST00000216071.4	37	c.305C>G	CCDS13848.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.822836	0.32237	.	.	ENSG00000100249	ENST00000216071	T	0.33865	1.39	4.91	-0.893	0.10567	.	1.417790	0.04670	N	0.410474	T	0.38639	0.1048	L	0.27053	0.805	0.09310	N	1	D	0.62365	0.991	P	0.57911	0.829	T	0.34104	-0.9842	10	0.59425	D	0.04	1.8066	5.525	0.16953	0.1638:0.3362:0.5:0.0	.	102	O95567	CV031_HUMAN	W	102	ENSP00000216071:S102W	ENSP00000216071:S102W	S	-	2	0	C22orf31	27786530	0.000000	0.05858	0.010000	0.14722	0.916000	0.54674	-0.117000	0.10708	0.013000	0.14918	0.585000	0.79938	TCG		0.483	C22orf31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320952.1	NM_015370		3	141	0	0	0	6.4e-05	0	3	141				
VPS51	738	broad.mit.edu	37	11	64878010	64878010	+	Missense_Mutation	SNP	G	G	C			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr11:64878010G>C	ENST00000279281.3	+	8	2027	c.1935G>C	c.(1933-1935)aaG>aaC	p.K645N	TM7SF2_ENST00000540748.1_5'Flank|AP003068.9_ENST00000528887.1_RNA|VPS51_ENST00000527646.1_3'UTR|TM7SF2_ENST00000279263.7_5'Flank|TM7SF2_ENST00000345348.5_5'Flank	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	645					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											ACTCCAGCAAGAGGACTTTCT	0.637											OREG0021071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000279281.3																			0											c.(1933-1935)aaG>aaC		vacuolar protein sorting 51 homolog (S. cerevisiae)							99.0	108.0	105.0					11																	64878010		2201	4297	6498	SO:0001583	missense	738							g.chr11:64878010G>C	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"""fat-free homolog (zebrafish)"""	615738	"""chromosome 11 open reading frame 3"", ""chromosome 11 open reading frame 2"""	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.1935G>C	11.37:g.64878010G>C	ENSP00000279281:p.Lys645Asn		OREG0021071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1079	VPS51_ENST00000527646.1_3'UTR	p.K645N	NM_013265.2	NP_037397.2					8	2027	+								Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Missense_Mutation	SNP	ENST00000279281.3	37	c.1935G>C	CCDS8093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	4.005779|4.005779	0.74932|0.74932	.|.	.|.	ENSG00000149823|ENSG00000149823	ENST00000279281;ENST00000530673|ENST00000526856	.|.	.|.	.|.	4.77|4.77	0.647|0.647	0.17796|0.17796	.|.	0.053764|.	0.64402|.	D|.	0.000001|.	T|T	0.56775|0.56775	0.2008|0.2008	L|L	0.57536|0.57536	1.79|1.79	0.53005|0.53005	D|D	0.999969|0.999969	P|.	0.45634|.	0.863|.	P|.	0.45276|.	0.475|.	T|T	0.50659|0.50659	-0.8802|-0.8802	9|5	0.30854|.	T|.	0.27|.	-6.0758|-6.0758	6.7776|6.7776	0.23628|0.23628	0.5474:0.0:0.4526:0.0|0.5474:0.0:0.4526:0.0	.|.	645|.	Q9UID3|.	FFR_HUMAN|.	N|T	645;19|143	.|.	ENSP00000279281:K645N|.	K|R	+|+	3|2	2|0	C11orf2|C11orf2	64634586|64634586	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	0.854000|0.854000	0.27791|0.27791	0.276000|0.276000	0.22118|0.22118	-0.339000|-0.339000	0.08088|0.08088	AAG|AGA		0.637	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265		4	193	0	0	0	0.00024832	0	4	193				
LRRC32	2615	broad.mit.edu	37	11	76371702	76371702	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr11:76371702C>T	ENST00000407242.2	-	3	1177	c.935G>A	c.(934-936)cGc>cAc	p.R312H	LRRC32_ENST00000260061.5_Missense_Mutation_p.R312H|LRRC32_ENST00000404995.1_Missense_Mutation_p.R312H|LRRC32_ENST00000464145.1_Intron|AP001189.4_ENST00000447519.1_RNA	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	312					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GGAAAGGGGGCGGCCGCTGGC	0.622																																						ENST00000407242.2																			0				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						c.(934-936)cGc>cAc		leucine rich repeat containing 32							18.0	23.0	21.0					11																	76371702		2200	4292	6492	SO:0001583	missense	2615					integral to plasma membrane		g.chr11:76371702C>T	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"""glycoprotein A repetitions predominant"""	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.935G>A	11.37:g.76371702C>T	ENSP00000384126:p.Arg312His					LRRC32_ENST00000464145.1_Intron|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Missense_Mutation_p.R312H|LRRC32_ENST00000404995.1_Missense_Mutation_p.R312H	p.R312H	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN			3	1177	-			312					Q86V06	Missense_Mutation	SNP	ENST00000407242.2	37	c.935G>A	CCDS8245.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.361592	0.01235	.	.	ENSG00000137507	ENST00000260061;ENST00000407242;ENST00000404995	T;T;T	0.04502	3.61;3.61;3.61	4.55	-1.38	0.09027	.	1.521110	0.03962	N	0.290140	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42932	-0.9422	10	0.12430	T	0.62	.	0.0462	0.00010	0.2789:0.194:0.2344:0.2927	.	312	Q14392	LRC32_HUMAN	H	312	ENSP00000260061:R312H;ENSP00000384126:R312H;ENSP00000385766:R312H	ENSP00000260061:R312H	R	-	2	0	LRRC32	76049350	0.000000	0.05858	0.001000	0.08648	0.074000	0.17049	-0.728000	0.04925	-0.007000	0.14345	-0.474000	0.04947	CGC		0.622	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		7	44	0	0	0	0.000157383	0	7	44				
PRAMEF11	440560	broad.mit.edu	37	1	12887606	12887606	+	Missense_Mutation	SNP	C	C	G	rs58074988	byFrequency	TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr1:12887606C>G	ENST00000535591.1	-	3	446	c.251G>C	c.(250-252)tGc>tCc	p.C84S		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	84					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.C84S(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						ATTGAGGAAGCACCCATGGGC	0.483																																						ENST00000535591.1																			1	Substitution - Missense(1)	p.C84S(1)	endometrium(1)	NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						c.(250-252)tGc>tCc		PRAME family member 11																																				SO:0001583	missense	440560							g.chr1:12887606C>G	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.251G>C	1.37:g.12887606C>G	ENSP00000439551:p.Cys84Ser						p.C84S	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN			3	446	-			84						Missense_Mutation	SNP	ENST00000535591.1	37	c.251G>C	CCDS53268.1	.	.	.	.	.	.	.	.	.	.	.	8.676	0.903882	0.17760	.	.	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.18016	2.24;2.24	1.48	-0.635	0.11512	.	1.371720	0.04624	N	0.402516	T	0.15825	0.0381	L	0.54908	1.71	0.09310	N	1	P	0.44816	0.844	B	0.41764	0.366	T	0.23904	-1.0175	10	0.16896	T	0.51	.	3.692	0.08350	0.2835:0.4381:0.2784:0.0	rs58074988	84	O60813	PRA11_HUMAN	S	84;125;84	ENSP00000439551:C84S;ENSP00000391839:C84S	ENSP00000328783:C125S	C	-	2	0	PRAMEF11	12810193	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.358000	0.07641	-0.176000	0.10707	-1.934000	0.00508	TGC		0.483	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341		6	483	0	0	0	6.40141e-05	0	6	483				
PRRG3	79057	broad.mit.edu	37	X	150869382	150869382	+	Silent	SNP	C	C	T			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chrX:150869382C>T	ENST00000370353.3	+	4	963	c.573C>T	c.(571-573)ccC>ccT	p.P191P	PRRG3_ENST00000538575.1_Silent_p.P191P			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	191						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					CCACCCCTCCCCCCTCCTACG	0.647																																						ENST00000370353.3																			0				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24						c.(571-573)ccC>ccT		proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)							56.0	45.0	49.0					X																	150869382		2203	4300	6503	SO:0001819	synonymous_variant	79057					extracellular region|integral to membrane	calcium ion binding	g.chrX:150869382C>T	AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.573C>T	X.37:g.150869382C>T						PRRG3_ENST00000538575.1_Silent_p.P191P	p.P191P			Q9BZD7	TMG3_HUMAN			4	963	+	Acute lymphoblastic leukemia(192;6.56e-05)		191					A1A523|A1A575|Q8N2N6	Silent	SNP	ENST00000370353.3	37	c.573C>T	CCDS14699.1																																																																																				0.647	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	NM_024082		4	63	0	0	0	1.23904e-05	0	4	63				
STK36	27148	broad.mit.edu	37	2	219561866	219561866	+	Silent	SNP	A	A	G			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr2:219561866A>G	ENST00000295709.3	+	23	2970	c.2691A>G	c.(2689-2691)gcA>gcG	p.A897A	STK36_ENST00000440309.1_Silent_p.A897A|STK36_ENST00000392105.3_Silent_p.A876A|STK36_ENST00000392106.2_Silent_p.A876A	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		AGGCATCTGCACAGGAAGGGG	0.537																																						ENST00000295709.3																			0				biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52						c.(2689-2691)gcA>gcG		serine/threonine kinase 36							122.0	129.0	126.0					2																	219561866		2203	4300	6503	SO:0001819	synonymous_variant	27148				cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding	g.chr2:219561866A>G	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.2691A>G	2.37:g.219561866A>G						STK36_ENST00000440309.1_Silent_p.A897A|STK36_ENST00000392105.3_Silent_p.A876A|STK36_ENST00000392106.2_Silent_p.A876A	p.A897A	NM_015690.4	NP_056505.2	Q9NRP7	STK36_HUMAN		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)	23	2970	+		Renal(207;0.0915)	897						Silent	SNP	ENST00000295709.3	37	c.2691A>G	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	A	9.591	1.126267	0.20959	.	.	ENSG00000163482	ENST00000431040	.	.	.	5.12	-3.92	0.04155	.	.	.	.	.	T	0.28764	0.0713	.	.	.	0.20975	N	0.999812	.	.	.	.	.	.	T	0.36601	-0.9741	4	.	.	.	8.2973	8.025	0.30431	0.3516:0.4546:0.1938:0.0	.	.	.	.	R	90	.	.	H	+	2	0	STK36	219270110	0.000000	0.05858	0.165000	0.22776	0.955000	0.61496	-0.576000	0.05854	-0.455000	0.07054	0.533000	0.62120	CAC		0.537	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			5	235	0	0	0	3.59834e-05	0	5	235				
RP11-146E13.4	0	broad.mit.edu	37	14	19857036	19857036	+	lincRNA	SNP	A	A	G	rs374719458		TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr14:19857036A>G	ENST00000548109.1	+	0	72																											CTGGATAATAAAGTTCATCTC	0.373																																						ENST00000548109.1																			0																																																			0							g.chr14:19857036A>G																													14.37:g.19857036A>G														0	72	+									RNA	SNP	ENST00000548109.1	37																																																																																						0.373	RP11-146E13.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000409408.1			5	129	0	0	0	1.23904e-05	0	5	129				
RP11-156P1.2	0	broad.mit.edu	37	17	45127107	45127107	+	IGR	SNP	C	C	G	rs374963948		TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr17:45127107C>G	ENST00000571841.1	+	0	889				RP11-156P1.3_ENST00000575173.1_RNA|LRRC37A17P_ENST00000570478.1_RNA																							CCTTCGTTCACCCAAGAGCAT	0.592																																						ENST00000575173.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr17:45127107C>G																													17.37:g.45127107C>G														0	418	-									RNA	SNP	ENST00000571841.1	37																																																																																						0.592	RP11-156P1.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000440447.1			5	113	0	0	0	1.23904e-05	0	5	113				
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	A	G			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr1:145367739A>G	ENST00000342960.5	+	83	10370	c.10335A>G	c.(10333-10335)aaA>aaG	p.K3445K	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	750						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.K3445K(4)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.413																																						ENST00000342960.5																			4	Substitution - coding silent(4)	p.K3445K(4)	prostate(3)|kidney(1)	NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(10333-10335)aaA>aaG		neuroblastoma breakpoint family, member 10																																				SO:0001819	synonymous_variant	100132406							g.chr1:145367739A>G	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.10335A>G	1.37:g.145367739A>G						NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron	p.K3445K	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	83	10370	+	all_hematologic(923;0.032)		3445					Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	c.10335A>G	CCDS53355.1																																																																																				0.413	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703		3	153	0	0	0	6.4e-05	0	3	153				
PRUNE2	158471	broad.mit.edu	37	9	79322343	79322343	+	Missense_Mutation	SNP	C	C	T	rs368679517		TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr9:79322343C>T	ENST00000376718.3	-	8	4970	c.4847G>A	c.(4846-4848)cGc>cAc	p.R1616H	PRUNE2_ENST00000428286.1_Missense_Mutation_p.R1257H	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1616					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGGAGTTTTGCGATCAAAGCT	0.353																																						ENST00000428286.1																			0				endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						c.(3769-3771)cGc>cAc		prune homolog 2 (Drosophila)		C	HIS/ARG	1,3135		0,1,1567	65.0	59.0	61.0		4847	-5.6	0.0	9		61	0,7164		0,0,3582	no	missense	PRUNE2	NM_015225.2	29	0,1,5149	TT,TC,CC		0.0,0.0319,0.0097	benign	1616/3089	79322343	1,10299	1568	3582	5150	SO:0001583	missense	158471				apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity	g.chr9:79322343C>T	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4847G>A	9.37:g.79322343C>T	ENSP00000365908:p.Arg1616His					PRUNE2_ENST00000376718.3_Missense_Mutation_p.R1616H	p.R1257H			Q8WUY3	PRUN2_HUMAN			8	4970	-			1616					B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	c.3770G>A	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.890648	0.00527	3.19E-4	0.0	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.39406	1.08;1.08	5.91	-5.58	0.02512	.	1.613590	0.03194	N	0.173709	T	0.08626	0.0214	N	0.00289	-1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29274	-1.0017	10	0.06494	T	0.89	4.1937	3.9404	0.09325	0.1079:0.1256:0.4463:0.3201	.	1616	Q8WUY3	PRUN2_HUMAN	H	1616;1257;1615	ENSP00000365908:R1616H;ENSP00000397425:R1257H	ENSP00000365908:R1616H	R	-	2	0	PRUNE2	78512163	0.049000	0.20398	0.000000	0.03702	0.165000	0.22458	-0.101000	0.10973	-0.749000	0.04747	-0.290000	0.09829	CGC		0.353	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		4	56	0	0	0	0.00024832	0	4	56				
CHD2	1106	broad.mit.edu	37	15	93545433	93545434	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr15:93545433_93545434insA	ENST00000394196.4	+	33	5232_5233	c.4164_4165insA	c.(4165-4167)aaafs	p.K1389fs	CHD2_ENST00000557381.1_Frame_Shift_Ins_p.K1389fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1389					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			AAAGTCCAATgaaaaaaaaaca	0.337																																						ENST00000394196.4																			0				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47						c.(4162-4167)ataaaafs		chromodomain helicase DNA binding protein 2																																				SO:0001589	frameshift_variant	1106				regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding	g.chr15:93545433_93545434insA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4173dupA	15.37:g.93545442_93545442dupA	ENSP00000377747:p.Lys1389fs					CHD2_ENST00000557381.1_Frame_Shift_Ins_p.IK1388fs	p.IK1388fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)		33	5232_5233	+	Lung NSC(78;0.00976)|all_lung(78;0.016)		1388					C6G482|Q96IP5	Frame_Shift_Ins	INS	ENST00000394196.4	37	c.4164_4165insA	CCDS10374.2																																																																																				0.337	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		8	159						8	159	---	---	---	---
PRR25	388199	broad.mit.edu	37	16	863356	863372	+	Frame_Shift_Del	DEL	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC	-	rs367751056|rs199580467|rs371962006|rs200304320|rs138733834	byFrequency	TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr16:863356_863372delGGACGCCGGACCGACAC	ENST00000301698.1	+	3	704_720	c.704_720delGGACGCCGGACCGACAC	c.(703-720)aggacgccggaccgacacfs	p.RTPDRH235fs		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	235										large_intestine(1)|lung(1)|skin(1)	3						GGACCGGCAAGGACGCCGGACCGACACGGCCTCCCCA	0.714														1307	0.260982	0.6876	0.2622	5008	,	,		14975	0.0675		0.0755	False		,,,				2504	0.0736					ENST00000301698.1																			0				large_intestine(1)|lung(1)|skin(1)	3						c.(703-720)afs		proline rich 25																																				SO:0001589	frameshift_variant	388199							g.chr16:863356_863372delGGACGCCGGACCGACAC	BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.704_720delGGACGCCGGACCGACAC	16.37:g.863356_863372delGGACGCCGGACCGACAC	ENSP00000301698:p.Arg235fs						p.RTPDRH235fs	NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN			3	704_720	+			235						Frame_Shift_Del	DEL	ENST00000301698.1	37	c.704_720delGGACGCCGGACCGACAC	CCDS45372.1																																																																																				0.714	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638		8	7						8	7	---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7751764	7751765	+	Frame_Shift_Ins	INS	-	-	C			TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr17:7751764_7751765insC	ENST00000448097.2	+	11	2489_2490	c.2158_2159insC	c.(2158-2160)gccfs	p.A720fs	KDM6B_ENST00000254846.5_Frame_Shift_Ins_p.A720fs			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	720	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						AGCAGGCGTGGCCCCCCAACCC	0.584																																						ENST00000254846.5																			0				central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						c.(2158-2160)cccfs		lysine (K)-specific demethylase 6B																																				SO:0001589	frameshift_variant	23135				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	g.chr17:7751764_7751765insC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.2164dupC	17.37:g.7751770_7751770dupC	ENSP00000412513:p.Ala720fs					KDM6B_ENST00000448097.2_Frame_Shift_Ins_p.P720fs	p.P720fs	NM_001080424.1	NP_001073893.1	O15054	KDM6B_HUMAN			11	2547_2548	+			720			Pro-rich.		C9IZ40|Q96G33	Frame_Shift_Ins	INS	ENST00000448097.2	37	c.2158_2159insC																																																																																					0.584	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		11	195						11	195	---	---	---	---
AC008132.13	0	broad.mit.edu	37	22	18842473	18842473	+	Intron	DEL	G	G	-	rs66480106	byFrequency	TCGA-EM-A2CP-01A-11D-A17V-08	TCGA-EM-A2CP-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8cd6882-be27-4742-bc63-3227d31bf704	e6101d92-5616-476e-8b38-8b6847ae3d48	g.chr22:18842473delG	ENST00000412938.1	+	4	2208																											AGCTGCTGGTGGGGAGGTCTT	0.647													?|GGGG|GGG|unsure	2225	0.444289	0.2716	0.4467	5008	,	,		25744	0.5079		0.5099	False		,,,				2504	0.5429					ENST00000412938.1																			0																																																	SO:0001627	intron_variant	0							g.chr22:18842473delG																												ENST00000412938.1:c.2209-830G>-	22.37:g.18842473delG														0	2208	+									RNA	DEL	ENST00000412938.1	37																																																																																						0.647	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000471615.1			7	15						7	15	---	---	---	---
