#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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
ADAR	103	hgsc.bcm.edu	37	1	154562826	154562826	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:154562826T>C	ENST00000368474.4	-	7	2529	c.2330A>G	c.(2329-2331)aAg>aGg	p.K777R	ADAR_ENST00000292205.5_Missense_Mutation_p.K820R|ADAR_ENST00000368471.3_Missense_Mutation_p.K482R	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	777	DRBM 3. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GCCTTGCTTCTTGCTGTGTGC	0.542																																					p.K777R		Atlas-SNP	.											.	ADAR	113	.	0			c.A2330G						PASS	.						99.0	92.0	94.0					1																	154562826		2203	4300	6503	SO:0001583	missense	103	exon7			TGCTTCTTGCTGT	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2330A>G	chr1.hg19:g.154562826T>C	ENSP00000357459:p.Lys777Arg	117.0	0.0	.		129.0	22.0	.	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	hg19	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	34	5.404549	0.96051	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.94	5.94	0.96194	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.93038	0.7784	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.997;0.999	D	0.94043	0.7311	10	0.87932	D	0	-29.5181	16.3951	0.83601	0.0:0.0:0.0:1.0	.	758;777;777	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	820;777;482;772	ENSP00000292205:K820R;ENSP00000357459:K777R;ENSP00000357456:K482R;ENSP00000431794:K772R	ENSP00000292205:K820R	K	-	2	0	ADAR	152829450	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.424000	0.80242	2.272000	0.75746	0.460000	0.39030	AAG	.	.	.	none		0.542	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
CACNA1S	779	hgsc.bcm.edu	37	1	201034981	201034981	+	Silent	SNP	G	G	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:201034981G>T	ENST00000362061.3	-	22	3064	c.2838C>A	c.(2836-2838)ggC>ggA	p.G946G	CACNA1S_ENST00000367338.3_Silent_p.G946G	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	946					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGAGCTGGACGCCGATGCAGG	0.622																																					p.G946G		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C2838A						PASS	.						85.0	70.0	75.0					1																	201034981		2203	4300	6503	SO:0001819	synonymous_variant	779	exon22			CTGGACGCCGATG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.2838C>A	chr1.hg19:g.201034981G>T		40.0	0.0	.		30.0	10.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	hg19	CCDS1407.1																																																																																			.	.	.	none		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
PARP9	83666	hgsc.bcm.edu	37	3	122247353	122247353	+	Missense_Mutation	SNP	A	A	C			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:122247353A>C	ENST00000360356.2	-	11	2650	c.2423T>G	c.(2422-2424)tTt>tGt	p.F808C	PARP9_ENST00000471785.1_Missense_Mutation_p.F773C|PARP9_ENST00000492382.1_Missense_Mutation_p.F353C|PARP9_ENST00000477522.2_Missense_Mutation_p.F773C	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	808	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		CATGCCACTAAAAATAACAAA	0.453																																					p.F808C		Atlas-SNP	.											.	PARP9	72	.	0			c.T2423G						PASS	.						118.0	108.0	111.0					3																	122247353		2203	4300	6503	SO:0001583	missense	83666	exon11			CCACTAAAAATAA	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.2423T>G	chr3.hg19:g.122247353A>C	ENSP00000353512:p.Phe808Cys	82.0	0.0	.		138.0	6.0	.	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	hg19	CCDS3014.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.879929	0.51801	.	.	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457	T;T;T;T	0.31769	1.8;1.48;1.69;1.69	4.7	4.7	0.59300	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.000000	0.52532	D	0.000063	T	0.48295	0.1492	M	0.80746	2.51	0.80722	D	1	D;D;D	0.64830	0.99;0.994;0.994	P;P;P	0.57468	0.796;0.766;0.821	T	0.51810	-0.8658	10	0.54805	T	0.06	.	8.7045	0.34345	0.8079:0.1921:0.0:0.0	.	808;353;773	Q8IXQ6;G5E9U8;Q8IXQ6-2	PARP9_HUMAN;.;.	C	808;353;773;773;731	ENSP00000353512:F808C;ENSP00000417664:F353C;ENSP00000419506:F773C;ENSP00000419001:F773C	ENSP00000353512:F808C	F	-	2	0	PARP9	123730043	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	3.138000	0.50570	2.108000	0.64289	0.533000	0.62120	TTT	.	.	.	none		0.453	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
HPS3	84343	hgsc.bcm.edu	37	3	148872995	148872995	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:148872995A>G	ENST00000296051.2	+	8	1642	c.1502A>G	c.(1501-1503)aAa>aGa	p.K501R	HPS3_ENST00000460120.1_Missense_Mutation_p.K336R	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	501					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CAGCTGTACAAAGAGATGGTA	0.348									Hermansky-Pudlak syndrome																												p.K501R		Atlas-SNP	.											.	HPS3	104	.	0			c.A1502G						PASS	.						136.0	141.0	140.0					3																	148872995		2203	4300	6503	SO:0001583	missense	84343	exon8	Familial Cancer Database	HPS, HPS1-8	TGTACAAAGAGAT	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.1502A>G	chr3.hg19:g.148872995A>G	ENSP00000296051:p.Lys501Arg	102.0	0.0	.		96.0	29.0	.	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	1.459	-0.562938	0.03939	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.64260	-0.09;-0.09	4.89	3.74	0.42951	.	0.205149	0.44902	N	0.000404	T	0.49474	0.1559	L	0.43923	1.385	0.25950	N	0.982762	B;B	0.22746	0.074;0.027	B;B	0.22386	0.039;0.013	T	0.35992	-0.9766	10	0.28530	T	0.3	-8.4607	7.6211	0.28185	0.8276:0.0:0.1724:0.0	.	336;501	G5E9V4;Q969F9	.;HPS3_HUMAN	R	501;336	ENSP00000296051:K501R;ENSP00000418230:K336R	ENSP00000296051:K501R	K	+	2	0	HPS3	150355685	1.000000	0.71417	0.999000	0.59377	0.018000	0.09664	2.513000	0.45494	1.000000	0.39049	-0.250000	0.11733	AAA	.	.	.	none		0.348	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
STPG2	285555	hgsc.bcm.edu	37	4	98633942	98633942	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr4:98633942A>T	ENST00000295268.3	-	10	1317	c.1228T>A	c.(1228-1230)Tta>Ata	p.L410I	STPG2_ENST00000506482.1_5'UTR	NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	410																	GATTTCCTTAAAACAGGATTG	0.348																																					p.L410I		Atlas-SNP	.											.	.	.	.	0			c.T1228A						PASS	.						98.0	101.0	100.0					4																	98633942		2203	4300	6503	SO:0001583	missense	285555	exon10			TCCTTAAAACAGG	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.1228T>A	chr4.hg19:g.98633942A>T	ENSP00000295268:p.Leu410Ile	136.0	0.0	.		112.0	39.0	.	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	hg19	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397643	0.25205	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.49139	0.79;2.73	4.85	2.3	0.28687	.	0.854661	0.09752	N	0.760480	T	0.32704	0.0838	L	0.27053	0.805	0.09310	N	0.999998	P	0.38300	0.626	B	0.40782	0.34	T	0.14868	-1.0457	10	0.23302	T	0.38	-8.0438	4.5761	0.12234	0.4933:0.3146:0.192:0.0	.	410	Q8N412	CD037_HUMAN	I	124;410	ENSP00000428346:L124I;ENSP00000295268:L410I	ENSP00000295268:L410I	L	-	1	2	C4orf37	98852965	0.779000	0.28652	0.948000	0.38648	0.774000	0.43823	0.556000	0.23438	1.930000	0.55929	0.528000	0.53228	TTA	.	.	.	none		0.348	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
RAB24	53917	hgsc.bcm.edu	37	5	176729807	176729807	+	Missense_Mutation	SNP	C	C	G			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr5:176729807C>G	ENST00000303251.6	-	3	630	c.211G>C	c.(211-213)Gag>Cag	p.E71Q	PRELID1_ENST00000303204.4_5'Flank|RAB24_ENST00000393611.2_Missense_Mutation_p.E71Q|RAB24_ENST00000303270.6_Missense_Mutation_p.E42Q|PRELID1_ENST00000503216.1_5'Flank	NM_001031677.2	NP_001026847.1	Q969Q5	RAB24_HUMAN	RAB24, member RAS oncogene family	71					autophagy (GO:0006914)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	autophagic vacuole (GO:0005776)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCATGGCCTCATAGCGCTCA	0.537																																					p.E71Q		Atlas-SNP	.											.	RAB24	19	.	0			c.G211C						PASS	.						98.0	93.0	95.0					5																	176729807		2203	4300	6503	SO:0001583	missense	53917	exon3			TGGCCTCATAGCG	AF087904	CCDS34300.1	5q35.3	2009-10-06			ENSG00000169228	ENSG00000169228		"""RAB, member RAS oncogene"""	9765	protein-coding gene	gene with protein product		612415					Standard	NM_001031677		Approved		uc003mfw.3	Q969Q5	OTTHUMG00000130849	ENST00000303251.6:c.211G>C	chr5.hg19:g.176729807C>G	ENSP00000304376:p.Glu71Gln	109.0	0.0	.		97.0	4.0	.	NM_001031677	Q7Z4Z7	Missense_Mutation	SNP	ENST00000303251.6	hg19	CCDS34300.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064810	0.76187	.	.	ENSG00000169228	ENST00000393611;ENST00000303251;ENST00000303270	T;T;T	0.76968	-1.06;-1.06;-1.06	5.49	5.49	0.81192	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	T	0.60637	0.2284	N	0.02765	-0.5	0.80722	D	1	P;P	0.39181	0.536;0.663	B;B	0.37833	0.223;0.259	T	0.70019	-0.4987	10	0.59425	D	0.04	1.7456	18.9659	0.92695	0.0:1.0:0.0:0.0	.	71;42	Q969Q5;F8W8H5	RAB24_HUMAN;.	Q	71;71;42	ENSP00000377235:E71Q;ENSP00000304376:E71Q;ENSP00000302085:E42Q	ENSP00000304376:E71Q	E	-	1	0	RAB24	176662413	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	7.185000	0.77714	2.576000	0.86940	0.555000	0.69702	GAG	.	.	.	none		0.537	RAB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253416.1	NM_130781	
KIAA0319	9856	hgsc.bcm.edu	37	6	24578370	24578370	+	Missense_Mutation	SNP	C	C	G			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr6:24578370C>G	ENST00000378214.3	-	9	1997	c.1473G>C	c.(1471-1473)ttG>ttC	p.L491F	KIAA0319_ENST00000543707.1_Missense_Mutation_p.L491F|KIAA0319_ENST00000537886.1_Missense_Mutation_p.L491F|KIAA0319_ENST00000430948.2_Missense_Mutation_p.L446F|KIAA0319_ENST00000535378.1_Missense_Mutation_p.L482F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	491	PKD 2. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CAAGGTTAGACAAGCGTAAGA	0.408																																					p.L491F		Atlas-SNP	.											.	KIAA0319	117	.	0			c.G1473C						PASS	.						144.0	138.0	140.0					6																	24578370		2203	4300	6503	SO:0001583	missense	9856	exon9			GTTAGACAAGCGT	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1473G>C	chr6.hg19:g.24578370C>G	ENSP00000367459:p.Leu491Phe	116.0	0.0	.		131.0	44.0	.	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	hg19	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.558223	0.45590	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53	4.12	3.14	0.36123	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD/REJ-like protein (1);PKD domain (2);	0.101129	0.41396	D	0.000885	T	0.20981	0.0505	M	0.64080	1.96	0.43628	D	0.99601	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.00518	-1.1693	10	0.72032	D	0.01	-0.9176	8.9471	0.35764	0.0:0.8102:0.0:0.1898	.	491;482;491	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	F	491;482;446;491;491	ENSP00000439700:L491F;ENSP00000442403:L482F;ENSP00000401086:L446F;ENSP00000367459:L491F;ENSP00000437656:L491F	ENSP00000367459:L491F	L	-	3	2	KIAA0319	24686349	1.000000	0.71417	0.460000	0.27093	0.015000	0.08874	0.975000	0.29449	2.105000	0.64084	0.555000	0.69702	TTG	.	.	.	none		0.408	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
SVIL	6840	hgsc.bcm.edu	37	10	29811367	29811367	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:29811367G>C	ENST00000355867.4	-	16	4113	c.3361C>G	c.(3361-3363)Ccc>Gcc	p.P1121A	SVIL_ENST00000535393.1_Missense_Mutation_p.P19A|SVIL_ENST00000375400.3_Missense_Mutation_p.P695A|SVIL_ENST00000375398.2_Missense_Mutation_p.P1121A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1121					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GTTTTGCTGGGTGAGTCAAGA	0.468																																					p.P1121A		Atlas-SNP	.											.	SVIL	226	.	0			c.C3361G						PASS	.						70.0	70.0	70.0					10																	29811367		2203	4300	6503	SO:0001583	missense	6840	exon16			TGCTGGGTGAGTC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3361C>G	chr10.hg19:g.29811367G>C	ENSP00000348128:p.Pro1121Ala	101.0	0.0	.		86.0	29.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	9.477	1.097117	0.20552	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994	T;T;T;T	0.12255	2.79;2.83;2.83;2.7	5.82	2.6	0.31112	.	0.415737	0.28482	N	0.015187	T	0.07863	0.0197	L	0.32530	0.975	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.21827	-1.0234	10	0.12430	T	0.62	-11.1568	4.4588	0.11656	0.2785:0.2093:0.5123:0.0	.	19;695;1121	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	A	695;1121;1121;19;75	ENSP00000364549:P695A;ENSP00000364547:P1121A;ENSP00000348128:P1121A;ENSP00000445472:P19A	ENSP00000348128:P1121A	P	-	1	0	SVIL	29851373	0.955000	0.32602	0.678000	0.29963	0.512000	0.34134	1.769000	0.38522	0.798000	0.33994	0.563000	0.77884	CCC	.	.	.	none		0.468	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
PARD3	56288	hgsc.bcm.edu	37	10	34648076	34648076	+	Splice_Site	SNP	T	T	C			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:34648076T>C	ENST00000374789.3	-	14	2391	c.2066A>G	c.(2065-2067)gAg>gGg	p.E689G	PARD3_ENST00000374794.3_Splice_Site_p.E632G|PARD3_ENST00000374773.1_Splice_Site_p.E689G|PARD3_ENST00000374768.1_Splice_Site_p.E127G|PARD3_ENST00000544292.1_Splice_Site_p.E406G|PARD3_ENST00000374776.1_Splice_Site_p.E676G|PARD3_ENST00000545693.1_Splice_Site_p.E676G|PARD3_ENST00000340077.5_Splice_Site_p.E689G|PARD3_ENST00000374790.3_Splice_Site_p.E632G|PARD3_ENST00000374788.3_Splice_Site_p.E689G|PARD3_ENST00000346874.4_Splice_Site_p.E689G|PARD3_ENST00000350537.4_Splice_Site_p.E676G|PARD3_ENST00000545260.1_Splice_Site_p.E632G	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	689					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				ATTTCTTACCTCATTGCACTT	0.378																																					p.E689G		Atlas-SNP	.											.	PARD3	131	.	0			c.A2066G						PASS	.						167.0	156.0	160.0					10																	34648076		2203	4300	6503	SO:0001630	splice_region_variant	56288	exon14			CTTACCTCATTGC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2067+1A>G	chr10.hg19:g.34648076T>C		171.0	0.0	.		161.0	47.0	.	NM_001184792	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328750	0.41197	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292;ENST00000374768	T;T;T;T;T;T;T;T;T;T;T;T;T	0.20332	2.43;2.43;2.49;2.49;2.52;2.45;2.42;2.43;2.1;2.08;2.16;2.12;2.25	5.56	5.56	0.83823	PDZ/DHR/GLGF (1);	0.414096	0.28706	N	0.014403	T	0.30916	0.0780	L	0.50333	1.59	0.80722	D	1	P;P;B;P;B;P;P;B;B;P;P;B;B;P;B	0.46512	0.719;0.879;0.391;0.719;0.391;0.82;0.719;0.236;0.023;0.597;0.825;0.069;0.076;0.506;0.085	B;B;B;B;B;P;B;B;B;B;P;B;B;P;B	0.49502	0.377;0.409;0.304;0.377;0.304;0.613;0.377;0.076;0.013;0.209;0.533;0.113;0.078;0.502;0.113	T	0.01508	-1.1337	10	0.45353	T	0.12	.	15.7055	0.77577	0.0:0.0:0.0:1.0	.	632;632;676;676;676;689;689;689;632;676;689;689;676;689;406	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;.	G	676;632;689;689;689;632;676;632;676;689;689;406;127	ENSP00000443147:E676G;ENSP00000440857:E632G;ENSP00000363921:E689G;ENSP00000363920:E689G;ENSP00000340591:E689G;ENSP00000363926:E632G;ENSP00000311986:E676G;ENSP00000363922:E632G;ENSP00000363908:E676G;ENSP00000341844:E689G;ENSP00000363905:E689G;ENSP00000444429:E406G;ENSP00000363900:E127G	ENSP00000341844:E689G	E	-	2	0	PARD3	34688082	1.000000	0.71417	0.990000	0.47175	0.190000	0.23558	6.186000	0.72026	2.114000	0.64651	0.533000	0.62120	GAG	.	.	.	none		0.378	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	Missense_Mutation
TMEM26	219623	hgsc.bcm.edu	37	10	63212836	63212836	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:63212836C>T	ENST00000399298.3	-	1	372	c.4G>A	c.(4-6)Gag>Aag	p.E2K	TMEM26_ENST00000399293.1_Missense_Mutation_p.E2K|RP11-809M12.1_ENST00000389640.4_RNA	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	2						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					ACCAGTCCCTCCATGCTGGCC	0.667																																					p.E2K		Atlas-SNP	.											.	TMEM26	47	.	0			c.G4A						PASS	.						45.0	54.0	51.0					10																	63212836		2126	4227	6353	SO:0001583	missense	219623	exon1			GTCCCTCCATGCT	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.4G>A	chr10.hg19:g.63212836C>T	ENSP00000382237:p.Glu2Lys	71.0	0.0	.		75.0	28.0	.	NM_178505	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	hg19	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755604	0.49362	.	.	ENSG00000196932	ENST00000399298;ENST00000399293	.	.	.	5.01	4.1	0.47936	.	0.902018	0.09509	N	0.792586	T	0.46132	0.1377	L	0.50333	1.59	0.34559	D	0.71215	P	0.43392	0.805	B	0.34722	0.188	T	0.53373	-0.8448	9	0.24483	T	0.36	-18.3363	14.8814	0.70537	0.1446:0.8554:0.0:0.0	.	2	Q6ZUK4	TMM26_HUMAN	K	2	.	ENSP00000382232:E2K	E	-	1	0	TMEM26	62882842	1.000000	0.71417	1.000000	0.80357	0.204000	0.24138	4.777000	0.62361	1.315000	0.45114	-0.182000	0.12963	GAG	.	.	.	none		0.667	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505	
DNAJB12	54788	hgsc.bcm.edu	37	10	74100871	74100871	+	Missense_Mutation	SNP	T	T	A			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:74100871T>A	ENST00000444643.2	-	4	847	c.515A>T	c.(514-516)cAg>cTg	p.Q172L	DNAJB12_ENST00000394903.2_Missense_Mutation_p.Q206L|DNAJB12_ENST00000338820.3_Missense_Mutation_p.Q206L|DNAJB12_ENST00000461919.1_5'UTR			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	172	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						ATCGCCGAACTGGTCATACTG	0.602																																					p.Q206L		Atlas-SNP	.											.	DNAJB12	22	.	0			c.A617T						PASS	.						75.0	67.0	69.0					10																	74100871		2203	4300	6503	SO:0001583	missense	54788	exon4			CCGAACTGGTCAT	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"""Heat shock proteins / DNAJ (HSP40)"""	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.515A>T	chr10.hg19:g.74100871T>A	ENSP00000403313:p.Gln172Leu	79.0	0.0	.		69.0	24.0	.	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.916	0.959878	0.18507	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.73258	-0.73;-0.73;-0.73	5.48	5.48	0.80851	Heat shock protein DnaJ, N-terminal (3);	0.122950	0.64402	D	0.000020	T	0.59528	0.2200	N	0.17474	0.49	0.58432	D	0.999999	D;P	0.54207	0.965;0.879	P;B	0.49887	0.625;0.227	T	0.59721	-0.7401	10	0.02654	T	1	-6.3488	15.622	0.76813	0.0:0.0:0.0:1.0	.	172;172	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	L	206;206;172	ENSP00000345575:Q206L;ENSP00000378363:Q206L;ENSP00000403313:Q172L	ENSP00000345575:Q206L	Q	-	2	0	DNAJB12	73770877	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	5.015000	0.64035	2.086000	0.62901	0.529000	0.55759	CAG	.	.	.	none		0.602	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2		
EML3	256364	hgsc.bcm.edu	37	11	62376458	62376458	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:62376458C>A	ENST00000394773.2	-	7	1212	c.905G>T	c.(904-906)cGg>cTg	p.R302L	EML3_ENST00000278845.4_Missense_Mutation_p.R303L|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.R274L|EML3_ENST00000531557.1_Missense_Mutation_p.R85L|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000529309.1_Missense_Mutation_p.R302L|ROM1_ENST00000534093.1_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	302						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TGTGTGCCCCCGGTAATGTCT	0.637																																					p.R302L		Atlas-SNP	.											.	EML3	61	.	0			c.G905T						PASS	.						134.0	149.0	144.0					11																	62376458		2202	4299	6501	SO:0001583	missense	256364	exon7			TGCCCCCGGTAAT	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.905G>T	chr11.hg19:g.62376458C>A	ENSP00000378254:p.Arg302Leu	286.0	0.0	.		325.0	16.0	.	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	C	3.507	-0.100684	0.06967	.	.	ENSG00000149499	ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15	5.69	4.69	0.59074	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.290099	0.31199	N	0.008070	T	0.27241	0.0668	N	0.02403	-0.565	0.39947	D	0.974484	B;B;B;B;B	0.11235	0.003;0.001;0.0;0.004;0.002	B;B;B;B;B	0.12156	0.006;0.007;0.0;0.006;0.003	T	0.28776	-1.0033	10	0.02654	T	1	-16.8234	12.6609	0.56813	0.2364:0.7636:0.0:0.0	.	302;302;85;303;274	Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0	.;EMAL3_HUMAN;.;.;.	L	302;303;85;274;302	ENSP00000378254:R302L;ENSP00000278845:R303L;ENSP00000433417:R85L;ENSP00000435064:R274L;ENSP00000434513:R302L	ENSP00000278845:R303L	R	-	2	0	EML3	62133034	0.991000	0.36638	1.000000	0.80357	0.981000	0.71138	1.076000	0.30729	2.676000	0.91093	0.655000	0.94253	CGG	.	.	.	none		0.637	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
NRXN2	9379	hgsc.bcm.edu	37	11	64453122	64453122	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:64453122C>T	ENST00000377551.1	-	5	1359	c.1148G>A	c.(1147-1149)cGc>cAc	p.R383H	NRXN2_ENST00000409571.1_Missense_Mutation_p.R383H|NRXN2_ENST00000265459.6_Missense_Mutation_p.R383H|NRXN2_ENST00000377559.3_Missense_Mutation_p.R359H			Q9P2S2	NRX2A_HUMAN	neurexin 2	383	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TCCTACCTGGCGCAGGTTTCG	0.602																																					p.R383H		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1148A						PASS	.						86.0	87.0	86.0					11																	64453122		2201	4297	6498	SO:0001583	missense	9379	exon6			ACCTGGCGCAGGT		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1148G>A	chr11.hg19:g.64453122C>T	ENSP00000366774:p.Arg383His	112.0	0.0	.		124.0	40.0	.	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.9|25.9	4.684359|4.684359	0.88639|0.88639	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000417749|ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300	.|T;T;T;T;T	.|0.78481	.|-1.18;-1.18;-1.18;-1.18;-1.18	4.0|4.0	4.0|4.0	0.46444|0.46444	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.|0.000000	.|0.44097	.|U	.|0.000496	D|D	0.84969|0.84969	0.5590|0.5590	M|M	0.62088|0.62088	1.915|1.915	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.987;0.998	D|D	0.86396|0.86396	0.1739|0.1739	5|10	.|0.87932	.|D	.|0	.|.	11.9853|11.9853	0.53145|0.53145	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|359;383;136	.|Q9P2S2-2;Q9P2S2;E7EV67	.|.;NRX2A_HUMAN;.	T|H	144|383;359;383;359;383;154	.|ENSP00000366774:R383H;ENSP00000366782:R359H;ENSP00000265459:R383H;ENSP00000386416:R383H;ENSP00000388971:R154H	.|ENSP00000265459:R383H	A|R	-|-	1|2	0|0	NRXN2|NRXN2	64209698|64209698	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.814000|7.814000	0.86154|0.86154	1.951000|1.951000	0.56629|0.56629	0.467000|0.467000	0.42956|0.42956	GCC|CGC	.	.	.	none		0.602	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
ROBO4	54538	hgsc.bcm.edu	37	11	124765531	124765531	+	Silent	SNP	G	G	A			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:124765531G>A	ENST00000306534.3	-	6	1343	c.858C>T	c.(856-858)acC>acT	p.T286T	ROBO4_ENST00000533054.1_Silent_p.T141T|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	286	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGCAGTCTGGGTCCTGAACA	0.672																																					p.T286T		Atlas-SNP	.											.	ROBO4	130	.	0			c.C858T						PASS	.						36.0	44.0	41.0					11																	124765531		2193	4283	6476	SO:0001819	synonymous_variant	54538	exon6			AGTCTGGGTCCTG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.858C>T	chr11.hg19:g.124765531G>A		89.0	0.0	.		117.0	36.0	.	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	hg19	CCDS8455.1																																																																																			.	.	.	none		0.672	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
CAND1	55832	hgsc.bcm.edu	37	12	67691215	67691215	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr12:67691215C>A	ENST00000545606.1	+	5	957	c.520C>A	c.(520-522)Cct>Act	p.P174T		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	174					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAATTTCCATCCTTCAATTCT	0.408																																					p.P174T		Atlas-SNP	.											.	CAND1	100	.	0			c.C520A						PASS	.						119.0	122.0	121.0					12																	67691215		2203	4300	6503	SO:0001583	missense	55832	exon5			TTCCATCCTTCAA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.520C>A	chr12.hg19:g.67691215C>A	ENSP00000442318:p.Pro174Thr	141.0	0.0	.		154.0	35.0	.	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.751582	0.49257	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.66099	-0.19	5.34	5.34	0.76211	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63546	0.2520	M	0.65498	2.005	0.80722	D	1	B	0.25521	0.128	B	0.27380	0.079	T	0.59968	-0.7354	9	.	.	.	-15.7741	19.057	0.93069	0.0:1.0:0.0:0.0	.	174	Q86VP6	CAND1_HUMAN	T	174;174;16	ENSP00000442318:P174T	.	P	+	1	0	CAND1	65977482	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.879000	0.69690	2.508000	0.84585	0.655000	0.94253	CCT	.	.	.	none		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448	
NR2F2	7026	hgsc.bcm.edu	37	15	96875635	96875635	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr15:96875635A>G	ENST00000394166.3	+	1	1690	c.301A>G	c.(301-303)Agc>Ggc	p.S101G	NR2F2_ENST00000421109.2_Intron|NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000394171.2_5'Flank|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	101					anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			GGGCTGCAAGAGCTTCTTCAA	0.612																																					p.S101G		Atlas-SNP	.											.	NR2F2	35	.	0			c.A301G						PASS	.						66.0	53.0	57.0					15																	96875635		2197	4298	6495	SO:0001583	missense	7026	exon1			TGCAAGAGCTTCT	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"""Nuclear hormone receptors"""	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.301A>G	chr15.hg19:g.96875635A>G	ENSP00000377721:p.Ser101Gly	29.0	0.0	.		35.0	14.0	.	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.468861	0.63625	.	.	ENSG00000185551	ENST00000394166	D	0.96745	-4.11	4.61	4.61	0.57282	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.187668	0.42821	N	0.000656	D	0.91784	0.7401	N	0.01235	-0.94	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.88109	0.2824	10	0.02654	T	1	.	12.8472	0.57837	1.0:0.0:0.0:0.0	.	101	P24468	COT2_HUMAN	G	101	ENSP00000377721:S101G	ENSP00000377721:S101G	S	+	1	0	NR2F2	94676639	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.257000	0.72480	1.705000	0.51264	0.379000	0.24179	AGC	.	.	.	none		0.612	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1		
CAMKK1	84254	hgsc.bcm.edu	37	17	3788981	3788981	+	Start_Codon_SNP	SNP	T	T	C			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:3788981T>C	ENST00000348335.2	-	2	149	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	CAMKK1_ENST00000381769.2_Missense_Mutation_p.M28V|CAMKK1_ENST00000158166.5_Start_Codon_SNP_p.M1V|CAMKK1_ENST00000381771.2_Start_Codon_SNP_p.M1V	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	1					synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		CCCCCCTCCATTGCTTCAGTC	0.582																																					p.M1V		Atlas-SNP	.											.	CAMKK1	70	.	0			c.A1G						PASS	.						39.0	38.0	39.0					17																	3788981		2203	4300	6503	SO:0001582	initiator_codon_variant	84254	exon2			CCTCCATTGCTTC	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.1A>G	chr17.hg19:g.3788981T>C	ENSP00000323118:p.Met1Val	56.0	0.0	.		99.0	17.0	.	NM_032294	Q9BQH3	Missense_Mutation	SNP	ENST00000348335.2	hg19	CCDS11038.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.496111	0.44352	.	.	ENSG00000004660	ENST00000381769;ENST00000348335;ENST00000381771;ENST00000158166	T;T;T;T	0.74421	-0.47;-0.37;-0.84;-0.81	4.6	4.6	0.57074	.	0.057619	0.64402	D	0.000004	D	0.83806	0.5334	.	.	.	0.80722	D	1	P;P	0.43578	0.811;0.713	P;P	0.60789	0.879;0.678	D	0.85601	0.1252	9	0.87932	D	0	-40.8262	11.9824	0.53127	0.0:0.0:0.0:1.0	.	1;1	F8W9H1;Q8N5S9	.;KKCC1_HUMAN	V	28;1;1;1	ENSP00000371188:M28V;ENSP00000323118:M1V;ENSP00000371190:M1V;ENSP00000158166:M1V	ENSP00000158166:M1V	M	-	1	0	CAMKK1	3735730	0.992000	0.36948	0.978000	0.43139	0.923000	0.55619	2.528000	0.45624	1.953000	0.56701	0.459000	0.35465	ATG	.	.	.	none		0.582	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	Missense_Mutation
MYBBP1A	10514	hgsc.bcm.edu	37	17	4451584	4451584	+	Silent	SNP	C	C	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:4451584C>T	ENST00000254718.4	-	12	1884	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	MYBBP1A_ENST00000381556.2_Silent_p.T526T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	526	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GCTTGAACTGCGTGCTGAGGG	0.637																																					p.T526T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G1578A						PASS	.						64.0	64.0	64.0					17																	4451584		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon12			GAACTGCGTGCTG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.1578G>A	chr17.hg19:g.4451584C>T		136.0	0.0	.		198.0	111.0	.	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.	.	none		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
GPRC5C	55890	hgsc.bcm.edu	37	17	72436053	72436053	+	Silent	SNP	T	T	A			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:72436053T>A	ENST00000481232.1	+	2	784	c.273T>A	c.(271-273)tcT>tcA	p.S91S	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Silent_p.S58S|GPRC5C_ENST00000392627.1_Silent_p.S91S			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	46					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						GTGACCGCTCTGGGGCGTGGG	0.662																																					p.S91S		Atlas-SNP	.											.	GPRC5C	92	.	0			c.T273A						PASS	.						62.0	59.0	60.0					17																	72436053		2203	4299	6502	SO:0001819	synonymous_variant	55890	exon2			CCGCTCTGGGGCG	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000481232.1:c.273T>A	chr17.hg19:g.72436053T>A		95.0	0.0	.		178.0	98.0	.	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Silent	SNP	ENST00000481232.1	hg19																																																																																				.	.	.	none		0.662	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000145095.2		
APMAP	57136	hgsc.bcm.edu	37	20	24944513	24944513	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr20:24944513C>T	ENST00000217456.2	-	9	1477	c.1187G>A	c.(1186-1188)gGg>gAg	p.G396E	APMAP_ENST00000447138.1_3'UTR	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	396					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										GTACAGGTGCCCATCGTGTTC	0.627																																					p.G396E		Atlas-SNP	.											.	APMAP	3	.	0			c.G1187A						PASS	.						103.0	94.0	97.0					20																	24944513		2203	4300	6503	SO:0001583	missense	57136	exon9			AGGTGCCCATCGT	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.1187G>A	chr20.hg19:g.24944513C>T	ENSP00000217456:p.Gly396Glu	109.0	0.0	.		139.0	24.0	.	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	hg19	CCDS13166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.06|17.06	3.291373|3.291373	0.59976|0.59976	.|.	.|.	ENSG00000101474|ENSG00000101474	ENST00000217456|ENST00000451442	T|T	0.36520|0.35605	1.25|1.3	4.86|4.86	4.86|4.86	0.63082|0.63082	Six-bladed beta-propeller, TolB-like (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.58708|0.58708	0.2141|0.2141	M|M	0.82132|0.82132	2.575|2.575	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.973|.	D;P|.	0.68192|.	0.956;0.685|.	T|T	0.64643|0.64643	-0.6359|-0.6359	10|8	0.44086|0.62326	T|D	0.13|0.03	-18.3321|-18.3321	15.4972|15.4972	0.75662|0.75662	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	388;396|.	A2A2F9;Q9HDC9|.	.;APMAP_HUMAN|.	E|S	396|389	ENSP00000217456:G396E|ENSP00000395874:G389S	ENSP00000217456:G396E|ENSP00000395874:G389S	G|G	-|-	2|1	0|0	C20orf3|C20orf3	24892513|24892513	1.000000|1.000000	0.71417|0.71417	0.502000|0.502000	0.27614|0.27614	0.164000|0.164000	0.22412|0.22412	7.726000|7.726000	0.84824|0.84824	2.216000|2.216000	0.71823|0.71823	0.561000|0.561000	0.74099|0.74099	GGG|GGC	.	.	.	none		0.627	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
DSCAM	1826	hgsc.bcm.edu	37	21	41459172	41459172	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr21:41459172G>A	ENST00000400454.1	-	22	4370	c.3893C>T	c.(3892-3894)cCa>cTa	p.P1298L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1298	Ig-like C2-type 10.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTTCATCCATGGAGTAGTCAC	0.488																																					p.P1298L	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C3893T						PASS	.						152.0	147.0	149.0					21																	41459172		1995	4169	6164	SO:0001583	missense	1826	exon22			ATCCATGGAGTAG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.3893C>T	chr21.hg19:g.41459172G>A	ENSP00000383303:p.Pro1298Leu	165.0	0.0	.		137.0	14.0	.	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.670051	0.88348	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.25912	1.77;1.77	4.71	4.71	0.59529	Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41488	0.1161	L	0.33339	1.005	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.35226	-0.9797	10	0.59425	D	0.04	.	18.0505	0.89347	0.0:0.0:1.0:0.0	.	1298	O60469	DSCAM_HUMAN	L	1298;1050	ENSP00000383303:P1298L;ENSP00000385342:P1050L	ENSP00000383303:P1298L	P	-	2	0	DSCAM	40381042	1.000000	0.71417	0.262000	0.24481	0.988000	0.76386	9.633000	0.98432	2.316000	0.78162	0.563000	0.77884	CCA	.	.	.	none		0.488	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
SNAP29	9342	hgsc.bcm.edu	37	22	21237785	21237785	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr22:21237785G>C	ENST00000215730.7	+	4	675	c.547G>C	c.(547-549)Gcc>Ccc	p.A183P		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	183					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			GGCTGGTTCTGCCATGAGTAC	0.498																																					p.A183P		Atlas-SNP	.											SNAP29,right_lower_lobe,carcinoma,0,1	SNAP29	22	.	0			c.G547C						PASS	.						218.0	198.0	205.0					22																	21237785		2203	4300	6503	SO:0001583	missense	9342	exon4			GGTTCTGCCATGA	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.547G>C	chr22.hg19:g.21237785G>C	ENSP00000215730:p.Ala183Pro	385.0	1.0	.		327.0	100.0	.	NM_004782		Missense_Mutation	SNP	ENST00000215730.7	hg19	CCDS13784.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.944634	0.34283	.	.	ENSG00000099940	ENST00000215730;ENST00000439214	.	.	.	4.17	-2.31	0.06765	SNAP-25 (1);	0.598056	0.18243	N	0.147169	T	0.17408	0.0418	N	0.22421	0.69	0.09310	N	1	P	0.41524	0.753	P	0.44921	0.464	T	0.12319	-1.0552	9	0.33141	T	0.24	-0.0293	2.763	0.05312	0.3197:0.0:0.3417:0.3386	.	183	O95721	SNP29_HUMAN	P	183;90	.	ENSP00000215730:A183P	A	+	1	0	SNAP29	19567785	0.014000	0.17966	0.001000	0.08648	0.009000	0.06853	0.143000	0.16115	-0.176000	0.10707	-0.218000	0.12543	GCC	.	.	.	none		0.498	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
KAT6A	7994	hgsc.bcm.edu	37	8	41836161	41836161	+	Splice_Site	DEL	C	C	-			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr8:41836161delC	ENST00000396930.3	-	7	1585	c.1042delG	c.(1042-1044)gta>ta	p.V348fs	KAT6A_ENST00000265713.2_Splice_Site_p.V348fs|KAT6A_ENST00000406337.1_Splice_Site_p.V348fs|KAT6A_ENST00000485568.1_Splice_Site_p.V348fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	348	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ACAACTTACACCGTGTTTTGT	0.383																																					p.V348fs		Atlas-INDEL	.											.	.	.	.	0			c.1043delT						PASS	.						338.0	340.0	340.0					8																	41836161		2203	4300	6503	SO:0001630	splice_region_variant	7994	exon7			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1043+1G>-	chr8.hg19:g.41836161delC		420.0	0.0	0		379.0	105.0	0.277045	NM_001099412	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.	.	none		0.383	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	Frame_Shift_Del
FGL2	10875	hgsc.bcm.edu	37	7	76828725	76828726	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr7:76828725_76828726insT	ENST00000248598.5	-	1	417_418	c.385_386insA	c.(385-387)agafs	p.R129fs	CCDC146_ENST00000285871.4_Intron|RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	129						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						TTCTCTAACTCTGTTATCACCA	0.495																																					p.R129fs		Atlas-INDEL	.											.	FGL2	40	.	0			c.386_387insA						PASS	.																																			SO:0001589	frameshift_variant	10875	exon1			.	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"""Fibrinogen C domain containing"""	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.386dupA	chr7.hg19:g.76828726_76828726dupT	ENSP00000248598:p.Arg129fs	129.0	0.0	0		164.0	33.0	0.20122	NM_006682		Frame_Shift_Ins	INS	ENST00000248598.5	hg19	CCDS5591.1																																																																																			.	.	.	none		0.495	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682	
CNTLN	54875	hgsc.bcm.edu	37	9	17462949	17462949	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr9:17462949delT	ENST00000380647.3	+	20	3426	c.3342delT	c.(3340-3342)aatfs	p.N1114fs	CNTLN_ENST00000262360.5_Frame_Shift_Del_p.N1114fs|CNTLN_ENST00000425824.1_Frame_Shift_Del_p.N1114fs			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	1114					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGTCATCAAATGTGAAGACTT	0.299																																					p.N1114fs		Atlas-INDEL	.											.	CNTLN	128	.	0			c.3341delA						PASS	.						83.0	81.0	81.0					9																	17462949		1809	4069	5878	SO:0001589	frameshift_variant	54875	exon20			.	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.3342delT	chr9.hg19:g.17462949delT	ENSP00000370021:p.Asn1114fs	114.0	0.0	0		97.0	29.0	0.298969	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Frame_Shift_Del	DEL	ENST00000380647.3	hg19	CCDS43789.1																																																																																			.	.	.	none		0.299	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
RSPRY1	89970	hgsc.bcm.edu	37	16	57261323	57261323	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr16:57261323delA	ENST00000537866.1	+	11	2104	c.1231delA	c.(1231-1233)aatfs	p.N411fs	RSPRY1_ENST00000394420.4_Frame_Shift_Del_p.N411fs|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	411	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						GATTTGGTACAATGCCAGAAG	0.453																																					p.Y410X		Atlas-INDEL	.											.	RSPRY1	49	.	0			c.1230delC						PASS	.						122.0	104.0	110.0					16																	57261323		2198	4300	6498	SO:0001589	frameshift_variant	89970	exon11			.	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"""RING-type (C3HC4) zinc fingers"""	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1231delA	chr16.hg19:g.57261323delA	ENSP00000443176:p.Asn411fs	85.0	0.0	0		99.0	54.0	0.545455	NM_133368	Q6UX21|Q8ND53	Frame_Shift_Del	DEL	ENST00000537866.1	hg19	CCDS10775.1																																																																																			.	.	.	none		0.453	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368	
BACH1	571	hgsc.bcm.edu	37	21	30698866	30698866	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr21:30698866delA	ENST00000399921.1	+	3	964	c.721delA	c.(721-723)actfs	p.T241fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.T241fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						CAGAGTCCGTACTGGGGAATC	0.453																																					p.R240fs		Atlas-INDEL	.											.	BACH1	66	.	0			c.720delT						PASS	.						57.0	59.0	58.0					21																	30698866		2203	4300	6503	SO:0001589	frameshift_variant	571	exon3			.	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.721delA	chr21.hg19:g.30698866delA	ENSP00000382805:p.Thr241fs	92.0	0.0	0		113.0	38.0	0.336283	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.	.	none		0.453	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866	
