#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
CHERP	10523	broad.mit.edu	37	19	16640580	16640580	+	Silent	SNP	T	T	C	rs528619775	byFrequency	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr19:16640580T>C	ENST00000198939.6	-	8	1077	c.1041A>G	c.(1039-1041)caA>caG	p.Q347Q	CTD-3222D19.2_ENST00000409035.1_Intron|CHERP_ENST00000546361.2_Silent_p.Q336Q					calcium homeostasis endoplasmic reticulum protein									p.Q336Q(2)		endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						gctgctgctgttgctgctgct	0.667													T|||	23	0.00459265	0.0129	0.0043	5008	,	,		16097	0.001		0.001	False		,,,				2504	0.001					ENST00000546361.2																			2	Substitution - coding silent(2)	p.Q336Q(2)	lung(2)	endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						c.(1006-1008)caA>caG		calcium homeostasis endoplasmic reticulum protein							21.0	29.0	26.0					19																	16640580		2193	4293	6486	SO:0001819	synonymous_variant	10523				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding	g.chr19:16640580T>C	U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"""G patch domain containing"""	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.1041A>G	19.37:g.16640580T>C						CHERP_ENST00000198939.6_Silent_p.Q347Q|CTD-3222D19.2_ENST00000409035.1_Intron	p.Q336Q	NM_006387.5	NP_006378.3	Q8IWX8	CHERP_HUMAN			8	1159	-			336			Gln-rich.			Silent	SNP	ENST00000198939.6	37	c.1008A>G																																																																																					0.667	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387		3	24	0	0	0	1	0	3	24				
CHERP	10523	broad.mit.edu	37	19	16640583	16640583	+	Silent	SNP	C	C	T			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr19:16640583C>T	ENST00000198939.6	-	8	1074	c.1038G>A	c.(1036-1038)caG>caA	p.Q346Q	CTD-3222D19.2_ENST00000409035.1_Intron|CHERP_ENST00000546361.2_Silent_p.Q335Q					calcium homeostasis endoplasmic reticulum protein											endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						gctgctgttgctgctgctgct	0.667																																						ENST00000546361.2																			0				endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						c.(1003-1005)caG>caA		calcium homeostasis endoplasmic reticulum protein							21.0	29.0	26.0					19																	16640583		2194	4294	6488	SO:0001819	synonymous_variant	10523				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding	g.chr19:16640583C>T	U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"""G patch domain containing"""	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.1038G>A	19.37:g.16640583C>T						CHERP_ENST00000198939.6_Silent_p.Q346Q|CTD-3222D19.2_ENST00000409035.1_Intron	p.Q335Q	NM_006387.5	NP_006378.3	Q8IWX8	CHERP_HUMAN			8	1156	-			335			Gln-rich.			Silent	SNP	ENST00000198939.6	37	c.1005G>A																																																																																					0.667	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387		3	25	0	0	0	1	0	3	25				
GGT3P	2679	broad.mit.edu	37	22	18778612	18778612	+	RNA	SNP	C	C	T	rs1055042	byFrequency	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr22:18778612C>T	ENST00000412448.1	-	0	793							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene						glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)										GCGGCCACGGCAGCCCTGGTG	0.637																																						ENST00000412448.1																			0																																																			0							g.chr22:18778612C>T			22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421		"""Gamma-glutamyltransferases"""	4252	pseudogene	pseudogene			"""gamma-glutamyltransferase 3"""	GGT3		8104871, 18357469	Standard	NR_003267		Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161		22.37:g.18778612C>T														0	793	-									RNA	SNP	ENST00000412448.1	37																																																																																						0.637	GGT3P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341281.1	NR_003267		4	11	0	0	0	1	0	4	11				
TUBB8P7	197331	broad.mit.edu	37	16	90162298	90162298	+	RNA	SNP	C	C	T	rs566020585		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr16:90162298C>T	ENST00000564451.1	+	0	1651				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		TGCTGACTGGCTCCCCAACAA	0.502																																						ENST00000567960.1																			0																																																			0							g.chr16:90162298C>T			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162298C>T						TUBB8P7_ENST00000564451.1_RNA								0	1034	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.502	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		6	202	0	0	0	1	0	6	202				
FRG1B	284802	broad.mit.edu	37	20	29628251	29628251	+	Missense_Mutation	SNP	A	A	G			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr20:29628251A>G	ENST00000278882.3	+	6	633	c.253A>G	c.(253-255)Aat>Gat	p.N85D	FRG1B_ENST00000439954.2_Missense_Mutation_p.N90D|FRG1B_ENST00000358464.4_Missense_Mutation_p.N85D			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	85								p.N85D(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTTGGCCTCAAATAGCTGCTT	0.358																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.N85D(2)	kidney(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(253-255)Aat>Gat																																						SO:0001583	missense	0							g.chr20:29628251A>G			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.253A>G	20.37:g.29628251A>G	ENSP00000278882:p.Asn85Asp					FRG1B_ENST00000439954.2_Missense_Mutation_p.N90D|FRG1B_ENST00000358464.4_Missense_Mutation_p.N85D	p.N85D							6	633	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.253A>G		.	.	.	.	.	.	.	.	.	.	a	15.78	2.933773	0.52866	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.50277	0.75	2.08	2.08	0.27032	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	.	.	.	0.45390	D	0.998378	B;B	0.26809	0.086;0.16	B;B	0.40329	0.326;0.253	T	0.51553	-0.8691	9	0.66056	D	0.02	.	8.0833	0.30758	1.0:0.0:0.0:0.0	.	90;85	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	D	85;90;85	ENSP00000408863:N90D	ENSP00000278882:N85D	N	+	1	0	FRG1B	28241912	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	8.047000	0.89440	1.208000	0.43306	0.347000	0.21830	AAT		0.358	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		9	111	0	0	0	1	0	9	111				
KRTAP4-6	81871	broad.mit.edu	37	17	39296167	39296167	+	Silent	SNP	A	A	G			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr17:39296167A>G	ENST00000345847.4	-	1	572	c.573T>C	c.(571-573)atT>atC	p.I191I		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	191						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GGCAGGTGGAAATGACACAGG	0.627																																						ENST00000345847.4																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						c.(571-573)atT>atC		keratin associated protein 4-6																																				SO:0001819	synonymous_variant	81871					keratin filament		g.chr17:39296167A>G	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.573T>C	17.37:g.39296167A>G							p.I191I	NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN			1	572	-			187					Q9BYR1	Silent	SNP	ENST00000345847.4	37	c.573T>C	CCDS54125.1																																																																																				0.627	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1			3	10	0	0	0	1	0	3	10				
CCDC178	374864	broad.mit.edu	37	18	30795529	30795529	+	Missense_Mutation	SNP	G	G	A	rs185692505	byFrequency	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr18:30795529G>A	ENST00000383096.3	-	19	2245	c.2063C>T	c.(2062-2064)aCa>aTa	p.T688I	CCDC178_ENST00000402325.1_Missense_Mutation_p.T688I|CCDC178_ENST00000406524.2_Missense_Mutation_p.T688I|CCDC178_ENST00000583930.1_Missense_Mutation_p.T688I|CCDC178_ENST00000579947.1_Missense_Mutation_p.T688I|CCDC178_ENST00000403303.1_Missense_Mutation_p.T688I|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000300227.8_Missense_Mutation_p.T650I			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	688																	TATTTCAAGTGTCTGATCAAA	0.209													G|||	5	0.000998403	0.0	0.0014	5008	,	,		13256	0.0		0.004	False		,,,				2504	0.0					ENST00000383096.3																			0											c.(2062-2064)aCa>aTa		coiled-coil domain containing 178		G	ILE/THR,ILE/THR	1,4205		0,1,2102	17.0	17.0	17.0		2063,1949	-8.3	0.0	18		17	22,8374		0,22,4176	yes	missense,missense	C18orf34	NM_001105528.1,NM_198995.2	89,89	0,23,6278	AA,AG,GG		0.262,0.0238,0.1825	benign,benign	688/868,650/830	30795529	23,12579	2103	4198	6301	SO:0001583	missense	374864							g.chr18:30795529G>A	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2063C>T	18.37:g.30795529G>A	ENSP00000372576:p.Thr688Ile					CCDC178_ENST00000402325.1_Missense_Mutation_p.T688I|CCDC178_ENST00000403303.1_Missense_Mutation_p.T688I|CCDC178_ENST00000583930.1_Missense_Mutation_p.T688I|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Missense_Mutation_p.T688I|CCDC178_ENST00000579947.1_Missense_Mutation_p.T688I|CCDC178_ENST00000300227.8_Missense_Mutation_p.T650I	p.T688I							19	2245	-								A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	c.2063C>T	CCDS42424.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	0.890	-0.725930	0.03158	2.38E-4	0.00262	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.14266	2.58;2.58;2.56;2.58;2.52	4.14	-8.29	0.01009	.	.	.	.	.	T	0.03390	0.0098	N	0.11201	0.11	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.35475	-0.9787	9	0.32370	T	0.25	1.4221	5.4573	0.16598	0.1445:0.0953:0.5149:0.2453	.	688;688;688;650;688	F8W7A7;Q5BJE1-3;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;CR034_HUMAN	I	688;688;650;688;688	ENSP00000385591:T688I;ENSP00000372576:T688I;ENSP00000300227:T650I;ENSP00000385867:T688I;ENSP00000385234:T688I	ENSP00000300227:T650I	T	-	2	0	C18orf34	29049527	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.043000	0.00157	-2.793000	0.00355	-1.628000	0.00784	ACA		0.209	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		4	8	0	0	0	1	0	4	8				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			3	32	0	0	0	1	0	3	32				
KCNJ4	3761	broad.mit.edu	37	22	38823832	38823832	+	Silent	SNP	A	A	C			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr22:38823832A>C	ENST00000303592.3	-	2	564	c.306T>G	c.(304-306)ggT>ggG	p.G102G	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	102	Poly-Gly.|Val/Gly/Ala/Pro stretch.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					CTCCGCCACCAcccgccgccg	0.687																																						ENST00000303592.3																			0				endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						c.(304-306)ggT>ggG		potassium inwardly-rectifying channel, subfamily J, member 4							27.0	26.0	26.0					22																	38823832		2199	4298	6497	SO:0001819	synonymous_variant	3761				synaptic transmission	basolateral plasma membrane|voltage-gated potassium channel complex	inward rectifier potassium channel activity|PDZ domain binding	g.chr22:38823832A>C	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.306T>G	22.37:g.38823832A>C							p.G102G	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	IRK4_HUMAN			2	564	-	Melanoma(58;0.0286)		102			Poly-Gly.|Val/Gly/Ala/Pro stretch.		Q14D44	Silent	SNP	ENST00000303592.3	37	c.306T>G	CCDS13971.1																																																																																				0.687	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		8	28	0	0	0	1	0	8	28				
TUBB8P7	197331	broad.mit.edu	37	16	90162304	90162304	+	RNA	SNP	A	A	G			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr16:90162304A>G	ENST00000564451.1	+	0	1657				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		CTGGCTCCCCAACAACGTAAA	0.502																																						ENST00000567960.1																			0																																																			0							g.chr16:90162304A>G			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162304A>G						TUBB8P7_ENST00000564451.1_RNA								0	1040	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.502	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	199	0	0	0	1	0	4	199				
RP11-423O2.5	0	broad.mit.edu	37	1	142803493	142803493	+	lincRNA	SNP	T	T	C	rs80149641		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr1:142803493T>C	ENST00000423385.1	-	0	1472																											TGTACATTTATTATTGATTTA	0.323																																						ENST00000423385.1																			0																																																			0							g.chr1:142803493T>C																													1.37:g.142803493T>C														0	1472	-									RNA	SNP	ENST00000423385.1	37																																																																																						0.323	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			8	61	0	0	0	1	0	8	61				
TVP23C	201158	broad.mit.edu	37	17	15441469	15441469	+	Intron	SNP	C	C	T	rs568909748	byFrequency	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr17:15441469C>T	ENST00000225576.3	-	5	558				TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000584811.1_Splice_Site|TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000583206.1_5'Flank|TVP23C_ENST00000428082.2_Splice_Site|TVP23C_ENST00000519970.1_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)							integral component of membrane (GO:0016021)											TCCAGTGTTCCGCAAAAGACA	0.393													c|||	3	0.000599042	0.0015	0.0	5008	,	,		17476	0.001		0.0	False		,,,				2504	0.0					ENST00000584811.1																			0											c.e7-2		trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)																																				SO:0001627	intron_variant	201158							g.chr17:15441469C>T	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.462+7629G>A	17.37:g.15441469C>T						TVP23C_ENST00000225576.3_Intron|TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000428082.2_Splice_Site								7	1815	-								Q3LIC7	Splice_Site	SNP	ENST00000225576.3	37		CCDS11170.1	.	.	.	.	.	.	.	.	.	.	c	13.58	2.280351	0.40294	.	.	ENSG00000175106	ENST00000438826	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0583	0.25111	0.0:0.1033:0.0:0.8967	.	.	.	.	.	-1	.	.	.	-	.	.	FAM18B2	15382194	1.000000	0.71417	0.996000	0.52242	0.698000	0.40448	1.919000	0.40015	0.852000	0.35287	-0.352000	0.07741	.		0.393	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301		4	59	0	0	0	1	0	4	59				
SPEN	23013	broad.mit.edu	37	1	16255142	16255143	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr1:16255142_16255143delGA	ENST00000375759.3	+	11	2611_2612	c.2407_2408delGA	c.(2407-2409)gagfs	p.E803fs		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	803	Arg-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGAGAGAGTGGAGAGAGAGAGA	0.431																																						ENST00000375759.3																			0				NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149						c.(2407-2409)gfs		spen family transcriptional repressor																																				SO:0001589	frameshift_variant	23013				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding	g.chr1:16255142_16255143delGA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2407_2408delGA	1.37:g.16255152_16255153delGA	ENSP00000364912:p.Glu803fs						p.E803fs	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	11	2611_2612	+		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)	803			Arg-rich.		Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Frame_Shift_Del	DEL	ENST00000375759.3	37	c.2407_2408delGA	CCDS164.1																																																																																				0.431	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		7	116						7	116	---	---	---	---
MBD4	8930	broad.mit.edu	37	3	129155548	129155548	+	Frame_Shift_Del	DEL	T	T	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr3:129155548delT	ENST00000249910.1	-	3	1114	c.939delA	c.(937-939)aaafs	p.K313fs	MBD4_ENST00000503197.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000429544.2_Frame_Shift_Del_p.K313fs|MBD4_ENST00000393278.2_Intron|MBD4_ENST00000509587.1_Intron|MBD4_ENST00000507208.1_Frame_Shift_Del_p.K313fs	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	313					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						ATGATCTTTCTTTTTTTTTTA	0.373								Base excision repair (BER), DNA glycosylases																														ENST00000429544.2																			0				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						c.(937-939)aafs	Base excision repair (BER), DNA glycosylases	methyl-CpG binding domain protein 4				7,57,4198		0,0,7,1,55,2068	71.0	78.0	76.0			3.4	0.0	3		77	22,69,8159		0,0,22,0,69,4034	no	codingComplex	MBD4	NM_003925.1		0,0,29,1,124,6102	A1A1,A1A2,A1R,A2A2,A2R,RR		1.103,1.5016,1.2388			129155548	29,126,12357	2202	4299	6501	SO:0001589	frameshift_variant	8930				depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding	g.chr3:129155548delT	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.939delA	3.37:g.129155548delT	ENSP00000249910:p.Lys313fs					MBD4_ENST00000503197.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000393278.2_Intron|MBD4_ENST00000249910.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000507208.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000509587.1_Intron	p.K313fs	NM_001276270.1	NP_001263199.1	O95243	MBD4_HUMAN			3	1134	-			313					B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Frame_Shift_Del	DEL	ENST00000249910.1	37	c.939delA	CCDS3058.1																																																																																				0.373	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		10	115						10	115	---	---	---	---
LINC00937	389634	broad.mit.edu	37	12	8519552	8519554	+	lincRNA	DEL	CCA	CCA	-	rs370335955|rs36094839|rs571647407		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr12:8519552_8519554delCCA	ENST00000544461.1	-	0	1081				AC092865.1_ENST00000408177.1_RNA|RP11-113C12.4_ENST00000537764.1_RNA					long intergenic non-protein coding RNA 937																		TACCAGCTTCccaccaccaccac	0.473														457	0.091254	0.1309	0.085	5008	,	,		17620	0.002		0.172	False		,,,				2504	0.0511					ENST00000544461.1																			0																																																			0							g.chr12:8519552_8519554delCCA	BC073935		12p13.31	2013-05-30			ENSG00000226091	ENSG00000226091		"""Long non-coding RNAs"""	48629	non-coding RNA	RNA, long non-coding							Standard	NR_024420		Approved				OTTHUMG00000168663		12.37:g.8519561_8519563delCCA						RP11-113C12.4_ENST00000537764.1_RNA								0	1081	-									RNA	DEL	ENST00000544461.1	37																																																																																						0.473	LINC00937-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000400511.1			8	39						8	39	---	---	---	---
TPTE2P1	646405	broad.mit.edu	37	13	25525716	25525716	+	RNA	DEL	A	A	-	rs200495212	byFrequency	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr13:25525716delA	ENST00000429698.1	-	0	282							Q5T6R2	TPT2L_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 1																		TGGAAGAAACAAAAAAAAGAA	0.383													AAAAAAA|AAAAAAAA|AAAAAAA|insertion	774	0.154553	0.1256	0.1571	5008	,	,		14949	0.2123		0.162	False		,,,				2504	0.1247					ENST00000429698.1																			0																																																			0							g.chr13:25525716delA			13q12.12-q12.13	2012-10-03			ENSG00000253771	ENSG00000253771			35196	pseudogene	pseudogene							Standard	NR_026730		Approved		uc010tdh.2	Q5T6R2	OTTHUMG00000016596		13.37:g.25525716delA														0	282	-								B3KST4|B4DMH9	RNA	DEL	ENST00000429698.1	37																																																																																						0.383	TPTE2P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000044206.1			5	1						5	1	---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71275774	71275776	+	In_Frame_Del	DEL	CCT	CCT	-	rs397840789|rs201322413		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr14:71275774_71275776delCCT	ENST00000554752.2	-	1	112_114	c.113_115delAGG	c.(112-117)gaggcg>gcg	p.E38del	RP6-65G23.3_ENST00000557691.1_lincRNA|MAP3K9_ENST00000381250.4_In_Frame_Del_p.E38del|MAP3K9_ENST00000555993.2_In_Frame_Del_p.E38del	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	38	Ala-rich.|Poly-Glu.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.E38delE(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GCCGCCGCCGcctcctcctcctc	0.773																																					GBM(114;411 1587 13539 28235 50070)	ENST00000554752.2																			1	Deletion - In frame(1)	p.E38delE(1)	ovary(1)	breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46						c.(112-117)gcg>g		mitogen-activated protein kinase kinase kinase 9																																				SO:0001651	inframe_deletion	4293				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity	g.chr14:71275774_71275776delCCT	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.113_115delAGG	14.37:g.71275783_71275785delCCT	ENSP00000451612:p.Glu38del					MAP3K9_ENST00000381250.4_In_Frame_Del_p.EA38del|MAP3K9_ENST00000555993.2_In_Frame_Del_p.EA38del	p.EA38del			P80192	M3K9_HUMAN		all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)	1	112_114	-			38			Ala-rich.|Poly-Glu.		A3KN85|Q0D2G7|Q6EH31|Q9H2N5	In_Frame_Del	DEL	ENST00000554752.2	37	c.113_115delAGG																																																																																					0.773	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			2	4						2	4	---	---	---	---
KRT10	3858	broad.mit.edu	37	17	38978766	38978768	+	In_Frame_Del	DEL	TCC	TCC	-	rs148510452|rs556262610	byFrequency	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr17:38978766_38978768delTCC	ENST00000269576.5	-	1	79_81	c.70_72delGGA	c.(70-72)ggadel	p.G24del	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	24	Gly-rich.|Head.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ctcctccacatcctcctcctcct	0.547																																						ENST00000269576.5																			0				NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11						c.(70-72)del		keratin 10			,,,	689,7,3556		198,0,293,0,7,1628					,,,	3.0	0.1		dbSNP_134	51	1494,8,6750		368,0,758,0,8,2992	no	intron,intron,intron,codingComplex	KRT10,TMEM99	NM_145274.3,NM_001195387.1,NM_001195386.1,NM_000421.3	,,,	566,0,1051,0,15,4620	A1A1,A1A2,A1R,A2A2,A2R,RR		18.2016,16.3688,17.5784	,,,	,,,		2183,15,10306				SO:0001651	inframe_deletion	3858				epidermis development		protein binding|structural constituent of epidermis	g.chr17:38978766_38978768delTCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.70_72delGGA	17.37:g.38978775_38978777delTCC	ENSP00000269576:p.Gly24del					TMEM99_ENST00000496847.1_Intron|TMEM99_ENST00000301665.3_Intron	p.G24del	NM_000421.3	NP_000412.3	P13645	K1C10_HUMAN			1	79_81	-		Breast(137;0.000301)	24	Missing (in Ref. 1; AAA60544).		Gly-rich.|Head.		Q14664|Q8N175	In_Frame_Del	DEL	ENST00000269576.5	37	c.70_72delGGA	CCDS11377.1																																																																																				0.547	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		7	25						7	25	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11085835	11085837	+	RNA	DEL	CAT	CAT	-	rs199904990		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr21:11085835_11085837delCAT	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccaccatcaccatcaccaccacc	0.586																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11085835_11085837delCAT	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11085835_11085837delCAT												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	DEL	ENST00000470054.1	37																																																																																						0.586	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		2	4						2	4	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11085940	11085942	+	RNA	DEL	CAC	CAC	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr21:11085940_11085942delCAC	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccaccaccatcaccaccaccacc	0.532																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11085940_11085942delCAC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11085949_11085951delCAC												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	DEL	ENST00000470054.1	37																																																																																						0.532	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		2	4						2	4	---	---	---	---
