#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
ATP1A4	480	broad.mit.edu	37	1	160141222	160141222	+	Missense_Mutation	SNP	G	G	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr1:160141222G>A	ENST00000368081.4	+	11	2144	c.1673G>A	c.(1672-1674)cGt>cAt	p.R558H	ATP1A4_ENST00000418334.1_3'UTR	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	558					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.R558H(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTGGGGGAACGTGTGCTAGGT	0.443																																						ENST00000368081.4																			1	Substitution - Missense(1)	p.R558H(1)	prostate(1)	breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75						c.(1672-1674)cGt>cAt		ATPase, Na+/K+ transporting, alpha 4 polypeptide							70.0	70.0	70.0					1																	160141222		2203	4300	6503	SO:0001583	missense	480				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity	g.chr1:160141222G>A	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1673G>A	1.37:g.160141222G>A	ENSP00000357060:p.Arg558His					ATP1A4_ENST00000418334.1_3'UTR	p.R558H	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.111)		11	2144	+	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		558					Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	37	c.1673G>A	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.782396	0.70222	.	.	ENSG00000132681	ENST00000368081	D	0.92545	-3.06	4.43	4.43	0.53597	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.96849	0.8971	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97585	1.0113	10	0.87932	D	0	.	14.9387	0.70978	0.0:0.0:1.0:0.0	.	558	Q13733	AT1A4_HUMAN	H	558	ENSP00000357060:R558H	ENSP00000357060:R558H	R	+	2	0	ATP1A4	158407846	1.000000	0.71417	0.706000	0.30403	0.410000	0.31052	9.633000	0.98432	2.458000	0.83093	0.655000	0.94253	CGT		0.443	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		12	20	0	0	0	1	0	12	20				
AVL9	23080	broad.mit.edu	37	7	32582854	32582854	+	Silent	SNP	C	C	T	rs367575541		TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr7:32582854C>T	ENST00000318709.4	+	2	416	c.195C>T	c.(193-195)ggC>ggT	p.G65G	AVL9_ENST00000404479.1_Silent_p.G65G|AVL9_ENST00000409301.1_Silent_p.G65G	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	65					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)		p.G65G(2)		endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TACCAGATGGCGCACACAACT	0.423																																						ENST00000318709.4																			2	Substitution - coding silent(2)	p.G65G(2)	endometrium(2)	endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						c.(193-195)ggC>ggT		AVL9 homolog (S. cerevisiase)		C		0,4406		0,0,2203	174.0	143.0	154.0		195	-5.2	1.0	7		154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AVL9	NM_015060.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		65/649	32582854	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23080					integral to membrane		g.chr7:32582854C>T	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.195C>T	7.37:g.32582854C>T						AVL9_ENST00000404479.1_Silent_p.G65G|AVL9_ENST00000409301.1_Silent_p.G65G	p.G65G	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN			2	416	+			65					Q92573	Silent	SNP	ENST00000318709.4	37	c.195C>T	CCDS34613.1																																																																																				0.423	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		5	82	0	0	0	1	0	5	82				
FAM86EP	348926	broad.mit.edu	37	4	3954857	3954857	+	RNA	SNP	C	C	A	rs17410899		TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr4:3954857C>A	ENST00000313946.8	-	0	135				AC226119.5_ENST00000281228.8_RNA					family with sequence similarity 86, member E, pseudogene																		AATATCCCGCCGCAGCTCAGA	0.488																																						ENST00000281228.8																			0																																																			0							g.chr4:3954857C>A			4p16.3	2011-07-01			ENSG00000251669	ENSG00000251669			28017	pseudogene	pseudogene						12477932	Standard	NR_024253		Approved		uc011bvu.2		OTTHUMG00000159867		4.37:g.3954857C>A						FAM86EP_ENST00000313946.8_RNA								0	141	-									RNA	SNP	ENST00000313946.8	37																																																																																						0.488	FAM86EP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357822.1			3	54	1	0	0.00024832	1	0.00024832	3	54				
HDLBP	3069	broad.mit.edu	37	2	242187753	242187753	+	Missense_Mutation	SNP	C	C	G			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr2:242187753C>G	ENST00000391975.1	-	13	1750	c.1523G>C	c.(1522-1524)cGt>cCt	p.R508P	HDLBP_ENST00000391976.2_Missense_Mutation_p.R508P|HDLBP_ENST00000310931.4_Missense_Mutation_p.R508P|HDLBP_ENST00000476807.1_5'UTR|HDLBP_ENST00000427183.2_Missense_Mutation_p.R475P	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	508	KH 5. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)	p.R508H(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		ATCCTTGGTACGCTCATTTTC	0.458																																						ENST00000391975.1																			1	Substitution - Missense(1)	p.R508H(1)	endometrium(1)	breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						c.(1522-1524)cGt>cCt		high density lipoprotein binding protein							121.0	116.0	118.0					2																	242187753		2203	4300	6503	SO:0001583	missense	3069				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding	g.chr2:242187753C>G		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.1523G>C	2.37:g.242187753C>G	ENSP00000375836:p.Arg508Pro					HDLBP_ENST00000476807.1_5'UTR|HDLBP_ENST00000391976.2_Missense_Mutation_p.R508P|HDLBP_ENST00000310931.4_Missense_Mutation_p.R508P|HDLBP_ENST00000427183.2_Missense_Mutation_p.R475P	p.R508P	NM_203346.3	NP_976221.1	Q00341	VIGLN_HUMAN		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)	13	1750	-		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)	508			KH 5.		B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	37	c.1523G>C	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.439095	0.83885	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183;ENST00000452931	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;1.93	6.17	3.46	0.39613	K Homology (1);K Homology, type 1 (1);	0.044585	0.85682	D	0.000000	T	0.61048	0.2316	M	0.76002	2.32	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.935	T	0.60974	-0.7156	10	0.52906	T	0.07	-7.9844	11.7143	0.51643	0.0:0.8105:0.0:0.1895	.	475;508	E7EM71;Q00341	.;VIGLN_HUMAN	P	508;508;508;475;17	ENSP00000375836:R508P;ENSP00000375837:R508P;ENSP00000312042:R508P;ENSP00000399139:R475P;ENSP00000388876:R17P	ENSP00000312042:R508P	R	-	2	0	HDLBP	241836426	1.000000	0.71417	0.492000	0.27490	0.990000	0.78478	7.755000	0.85180	0.502000	0.28037	0.655000	0.94253	CGT		0.458	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		15	29	0	0	0	1	0	15	29				
FRG1B	284802	broad.mit.edu	37	20	29628236	29628236	+	Missense_Mutation	SNP	G	G	C			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr20:29628236G>C	ENST00000278882.3	+	6	618	c.238G>C	c.(238-240)Gct>Cct	p.A80P	FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	80								p.A80P(8)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGGGAAAATGGCTTTGTTGGC	0.363																																						ENST00000278882.3																			8	Substitution - Missense(8)	p.A80P(8)	prostate(4)|kidney(4)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(238-240)Gct>Cct																																						SO:0001583	missense	284802							g.chr20:29628236G>C			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.238G>C	20.37:g.29628236G>C	ENSP00000278882:p.Ala80Pro					FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P	p.A80P							6	618	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.238G>C		.	.	.	.	.	.	.	.	.	.	g	15.73	2.920277	0.52653	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.57595	0.39	2.08	2.08	0.27032	Actin cross-linking (1);	0.052409	0.85682	D	0.000000	T	0.68952	0.3057	.	.	.	0.80722	D	1	D;D	0.64830	0.994;0.988	D;D	0.85130	0.997;0.993	T	0.72766	-0.4194	9	0.87932	D	0	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	85;80	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	P	80;85;80	ENSP00000408863:A85P	ENSP00000278882:A80P	A	+	1	0	FRG1B	28241897	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	8.494000	0.90477	1.475000	0.48197	0.423000	0.28283	GCT		0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		3	84	0	0	0	1	0	3	84				
SLC20A1	6574	broad.mit.edu	37	2	113405018	113405018	+	Missense_Mutation	SNP	A	A	G	rs191761952		TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr2:113405018A>G	ENST00000272542.3	+	3	991	c.452A>G	c.(451-453)aAg>aGg	p.K151R	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	151					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						GAGGGTGTCAAGTGGTCTGAA	0.433													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16736	0.0		0.0	False		,,,				2504	0.0					ENST00000272542.3																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						c.(451-453)aAg>aGg		solute carrier family 20 (phosphate transporter), member 1							189.0	195.0	193.0					2																	113405018		2203	4300	6503	SO:0001583	missense	6574				phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity	g.chr2:113405018A>G		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"""Solute carriers"""	10946	protein-coding gene	gene with protein product	"""gibbon ape leukemia virus receptor 1"""	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.452A>G	2.37:g.113405018A>G	ENSP00000272542:p.Lys151Arg						p.K151R	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN			3	991	+			151					Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	37	c.452A>G	CCDS2099.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	15.30	2.791212	0.50102	.	.	ENSG00000144136	ENST00000272542	D	0.90620	-2.7	5.49	3.12	0.35913	.	0.137480	0.64402	N	0.000004	D	0.86497	0.5947	L	0.49350	1.555	0.48901	D	0.999723	B	0.16166	0.016	B	0.23018	0.043	T	0.80398	-0.1399	10	0.72032	D	0.01	-23.7647	8.2015	0.31428	0.8346:0.0:0.1654:0.0	.	151	Q8WUM9	S20A1_HUMAN	R	151	ENSP00000272542:K151R	ENSP00000272542:K151R	K	+	2	0	SLC20A1	113121489	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.227000	0.42972	0.391000	0.25143	0.533000	0.62120	AAG		0.433	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		52	79	0	0	0	1	0	52	79				
MAP4	4134	broad.mit.edu	37	3	47958222	47958222	+	Silent	SNP	G	G	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr3:47958222G>A	ENST00000360240.6	-	7	1613	c.1095C>T	c.(1093-1095)gcC>gcT	p.A365A	MAP4_ENST00000395734.3_Silent_p.A365A|MAP4_ENST00000426837.2_Silent_p.A382A|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	365	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	CCTTGGAAGGGGCTAAGTCCA	0.478																																						ENST00000426837.2																			0				breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32						c.(1144-1146)gcC>gcT		microtubule-associated protein 4							177.0	177.0	177.0					3																	47958222		2203	4300	6503	SO:0001819	synonymous_variant	4134				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity	g.chr3:47958222G>A		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1095C>T	3.37:g.47958222G>A						MAP4_ENST00000360240.6_Silent_p.A365A|MAP4_ENST00000395734.3_Silent_p.A365A|MAP4_ENST00000383737.4_Intron	p.A382A			P27816	MAP4_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	8	1233	-			365			17 X 14 AA tandem repeats.		Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Silent	SNP	ENST00000360240.6	37	c.1146C>T	CCDS33750.1																																																																																				0.478	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		4	85	0	0	0	1	0	4	85				
TUBB8P7	197331	broad.mit.edu	37	16	90161618	90161618	+	RNA	SNP	C	C	T	rs13338202	byFrequency	TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr16:90161618C>T	ENST00000564451.1	+	0	971				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.D118D(2)									CAGTGATGGACGTTGTCAGAA	0.607													.|||	94	0.01877	0.0469	0.0173	5008	,	,		18765	0.0		0.0169	False		,,,				2504	0.0031					ENST00000564451.1																			2	Substitution - coding silent(2)	p.D118D(2)	kidney(2)																																																197331							g.chr16:90161618C>T			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90161618C>T						TUBB8P7_ENST00000567960.1_RNA								0	971	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.607	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		5	27	0	0	0	1	0	5	27				
MAP4	4134	broad.mit.edu	37	3	47958225	47958225	+	Silent	SNP	T	T	C			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr3:47958225T>C	ENST00000360240.6	-	7	1610	c.1092A>G	c.(1090-1092)ttA>ttG	p.L364L	MAP4_ENST00000395734.3_Silent_p.L364L|MAP4_ENST00000426837.2_Silent_p.L381L|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	364	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.L364L(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TGGAAGGGGCTAAGTCCATTT	0.478																																						ENST00000426837.2																			2	Substitution - coding silent(2)	p.L364L(2)	kidney(2)	breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32						c.(1141-1143)ttA>ttG		microtubule-associated protein 4							179.0	179.0	179.0					3																	47958225		2203	4300	6503	SO:0001819	synonymous_variant	4134				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity	g.chr3:47958225T>C		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1092A>G	3.37:g.47958225T>C						MAP4_ENST00000360240.6_Silent_p.L364L|MAP4_ENST00000395734.3_Silent_p.L364L|MAP4_ENST00000383737.4_Intron	p.L381L			P27816	MAP4_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	8	1230	-			364			17 X 14 AA tandem repeats.		Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Silent	SNP	ENST00000360240.6	37	c.1143A>G	CCDS33750.1																																																																																				0.478	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		4	88	0	0	0	1	0	4	88				
LOC101927209	101927209	broad.mit.edu	37	1	142713944	142713944	+	lincRNA	SNP	C	C	T	rs199960649		TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr1:142713944C>T	ENST00000610091.1	-	0	1714																											TGATTACCTCCGAAGTTAAAG	0.308																																						ENST00000369381.2																			0																																																			101927209							g.chr1:142713944C>T																													1.37:g.142713944C>T														0	661	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.308	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			4	27	0	0	0	1	0	4	27				
PRRC2B	84726	broad.mit.edu	37	9	134357838	134357838	+	Silent	SNP	G	G	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr9:134357838G>A	ENST00000357304.4	+	20	5119	c.5064G>A	c.(5062-5064)caG>caA	p.Q1688Q	PRRC2B_ENST00000405995.1_Silent_p.Q994Q|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.Q994Q	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1688							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						CCTCCTCGCAGCGCAGCTCCC	0.612																																						ENST00000357304.4																			0				cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						c.(5062-5064)caG>caA		proline-rich coiled-coil 2B							113.0	119.0	117.0					9																	134357838		1968	4153	6121	SO:0001819	synonymous_variant	84726						protein binding	g.chr9:134357838G>A	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5064G>A	9.37:g.134357838G>A						PRRC2B_ENST00000405995.1_Silent_p.Q994Q|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.Q994Q	p.Q1688Q	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN			20	5119	+			1688					O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	c.5064G>A	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	8.652	0.898417	0.17686	.	.	ENSG00000130723	ENST00000451855	.	.	.	4.92	4.02	0.46733	.	.	.	.	.	T	0.58623	0.2135	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55121	-0.8190	4	.	.	.	-33.0147	8.5002	0.33152	0.1752:0.0:0.8248:0.0	.	.	.	.	T	421	.	.	A	+	1	0	PRRC2B	133347659	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	3.101000	0.50283	1.068000	0.40764	0.561000	0.74099	GCG		0.612	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				9	87	0	0	0	1	0	9	87				
NKX6-3	157848	broad.mit.edu	37	8	41504197	41504197	+	Frame_Shift_Del	DEL	C	C	-			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr8:41504197delC	ENST00000524115.2	-	2	182	c.179delG	c.(178-180)cgcfs	p.R61fs		NM_152568.2	NP_689781.1	A6NJ46	NKX63_HUMAN	NK6 homeobox 3	191					cell fate determination (GO:0001709)|glandular epithelial cell differentiation (GO:0002067)|negative regulation of epithelial cell differentiation (GO:0030857)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(1)	1	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CTTGGTCCTGCGGTTCTGGAA	0.677																																						ENST00000524115.2																			0				lung(1)	1						c.(178-180)ccfs		NK6 homeobox 3							11.0	9.0	9.0					8																	41504197		2033	4016	6049	SO:0001589	frameshift_variant	157848					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr8:41504197delC	AK057898	CCDS6118.1	8p11.21	2014-08-12	2007-07-09		ENSG00000165066	ENSG00000165066		"""Homeoboxes / ANTP class : NKL subclass"""	26328	protein-coding gene	gene with protein product		610772	"""NK6 transcription factor related, locus 3 (Drosophila)"""			16326147	Standard	XM_005273422		Approved	FLJ25169	uc003xoa.2	A6NJ46	OTTHUMG00000164083	ENST00000524115.2:c.179delG	8.37:g.41504197delC	ENSP00000429553:p.Arg61fs						p.R61fs	NM_152568.2	NP_689781.1	A6NJ46	NKX63_HUMAN	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)		2	182	-	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	191					Q96LR0	Frame_Shift_Del	DEL	ENST00000524115.2	37	c.179delG	CCDS6118.1																																																																																				0.677	NKX6-3-002	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000377166.2	NM_152568		2	4						2	4	---	---	---	---
RP11-445N18.7	0	broad.mit.edu	37	10	45648292	45648292	+	RNA	DEL	G	G	-			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr10:45648292delG	ENST00000427229.2	+	0	1681																											TCAGAGAAATGGAATGGTTGC	0.323																																						ENST00000427229.2																			0																																																			0							g.chr10:45648292delG																													10.37:g.45648292delG														0	1681	+									RNA	DEL	ENST00000427229.2	37																																																																																						0.323	RP11-445N18.7-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000470688.1			2	4						2	4	---	---	---	---
TRAV9-2	28677	broad.mit.edu	37	14	22409539	22409540	+	RNA	INS	-	-	T	rs2178778|rs200693606|rs367992314|rs374912343|rs371270332	byFrequency	TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr14:22409539_22409540insT	ENST00000390441.2	+	0	102									T cell receptor alpha variable 9-2																		ctctctctctctTTTTTTTTTT	0.426																																						ENST00000390441.2																			0																																																			28677							g.chr14:22409539_22409540insT	AE000659		14q11.2	2012-02-07			ENSG00000211793	ENSG00000211793		"""T cell receptors / TRA locus"""	12154	other	T cell receptor gene						8188290	Standard	NG_001332		Approved				OTTHUMG00000170637		14.37:g.22409550_22409550dupT														0	102	+									RNA	INS	ENST00000390441.2	37																																																																																						0.426	TRAV9-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000409885.1	NG_001332		3	5						3	5	---	---	---	---
STAG2	10735	broad.mit.edu	37	X	123171406	123171407	+	Frame_Shift_Ins	INS	-	-	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chrX:123171406_123171407insA	ENST00000371160.1	+	6	608_609	c.318_319insA	c.(319-321)aagfs	p.K107fs	STAG2_ENST00000354548.5_Frame_Shift_Ins_p.K38fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Ins_p.K107fs|STAG2_ENST00000371157.3_Frame_Shift_Ins_p.K107fs|STAG2_ENST00000371145.3_Frame_Shift_Ins_p.K107fs|STAG2_ENST00000371144.3_Frame_Shift_Ins_p.K107fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	107					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TAGAATCATACAAGCATGACCG	0.327																																						ENST00000371160.1																			0				breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						c.(316-321)taagcafs		stromal antigen 2																																				SO:0001589	frameshift_variant	10735				cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding	g.chrX:123171406_123171407insA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.320dupA	X.37:g.123171408_123171408dupA	ENSP00000360202:p.Lys107fs					STAG2_ENST00000371144.3_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000371157.3_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371145.3_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000218089.9_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000354548.5_Frame_Shift_Ins_p.A38fs	p.A107fs			Q8N3U4	STAG2_HUMAN			6	608_609	+			107					B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Ins	INS	ENST00000371160.1	37	c.318_319insA	CCDS14607.1																																																																																				0.327	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		47	62						47	62	---	---	---	---
