#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_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_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
CHST3	9469	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	73767938	73767938	+	Silent	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr10:73767938C>T	ENST00000373115.4	+	3	1586	c.1149C>T	c.(1147-1149)cgC>cgT	p.R383R		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	383					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						AGAAGGCCCGCGAGATGTACC	0.701																																						.											0													8.0	9.0	9.0					10																	73767938		2054	4025	6079	SO:0001819	synonymous_variant	9469			AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"""Sulfotransferases, membrane-bound"""	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.1149C>T	10.37:g.73767938C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O75099|Q52M30	Silent	SNP	ENST00000373115.4	37	CCDS7312.1																																																																																				0.701	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273	
AMPD2	271	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	1	110168780	110168780	+	Splice_Site	SNP	A	A	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:110168780A>T	ENST00000256578.3	+	4	875		c.e4-1		RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000342115.4_Splice_Site|AMPD2_ENST00000528454.1_Splice_Site|AMPD2_ENST00000393688.3_Splice_Site|AMPD2_ENST00000358729.4_Splice_Site|AMPD2_ENST00000526301.1_Splice_Site|AMPD2_ENST00000528667.1_Splice_Site	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2						cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		TCTTGCCTCTAGGCTGGAGCC	0.607																																						.											0													73.0	56.0	62.0					1																	110168780		2203	4300	6503	SO:0001630	splice_region_variant	271			S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"""AMPD isoform L"""	102771	"""adenosine monophosphate deaminase 2 (isoform L)"""			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.516-1A>T	1.37:g.110168780A>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Splice_Site	SNP	ENST00000256578.3	37	CCDS805.1	.	.	.	.	.	.	.	.	.	.	A	16.57	3.160411	0.57368	.	.	ENSG00000116337	ENST00000531734;ENST00000342115;ENST00000528667;ENST00000531203;ENST00000256578;ENST00000358729;ENST00000369840;ENST00000527846;ENST00000528454;ENST00000393688	.	.	.	4.97	4.97	0.65823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.975	0.41777	0.9179:0.0:0.0821:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AMPD2	109970303	1.000000	0.71417	0.887000	0.34795	0.742000	0.42306	9.023000	0.93683	1.872000	0.54250	0.379000	0.24179	.		0.607	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1		Intron
RCN1	5954	broad.mit.edu;hgsc.bcm.edu	37	11	32118784	32118784	+	Frame_Shift_Del	DEL	T	T	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:32118784delT	ENST00000054950.3	+	2	642	c.349delT	c.(349-351)tttfs	p.F117fs	RCN1_ENST00000532942.1_Frame_Shift_Del_p.F66fs|RP1-65P5.3_ENST00000533009.1_RNA	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	117	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		F -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					AAGATACATCTTTGATAATGT	0.428																																						.											0													62.0	57.0	59.0					11																	32118784		2202	4296	6498	SO:0001589	frameshift_variant	5954			D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"""EF-hand domain containing"""	9934	protein-coding gene	gene with protein product	"""proliferation-inducing gene 20"""	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.349delT	11.37:g.32118784delT	ENSP00000054950:p.Phe117fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z1M1|D3DR00	Frame_Shift_Del	DEL	ENST00000054950.3	37	CCDS7876.1																																																																																				0.428	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901	
CHRDL2	25884	broad.mit.edu;hgsc.bcm.edu	37	11	74408313	74408316	+	Frame_Shift_Del	DEL	CTTT	CTTT	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	CTTT	CTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:74408313_74408316delCTTT	ENST00000376332.3	-	10	1643_1646	c.1147_1150delAAAG	c.(1147-1152)aaagtcfs	p.KV383fs	CHRDL2_ENST00000263671.5_Frame_Shift_Del_p.ES401fs	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	383					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					TGCTTCCTGACTTTCTTGATCTGA	0.544																																						.											0																																										SO:0001589	frameshift_variant	25884			AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.1147_1150delAAAG	11.37:g.74408313_74408316delCTTT	ENSP00000365510:p.Lys383fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Frame_Shift_Del	DEL	ENST00000376332.3	37																																																																																					0.544	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
CHIT1	1118	hgsc.bcm.edu;ucsc.edu	37	1	203188924	203188924	+	Silent	SNP	G	G	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:203188924G>T	ENST00000367229.1	-	8	817	c.783C>A	c.(781-783)atC>atA	p.I261I	CHIT1_ENST00000535569.1_Silent_p.I252I|CHIT1_ENST00000484834.1_5'UTR|CHIT1_ENST00000255427.3_Silent_p.I242I	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	261					chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						GCATGCCAAGGATCAGCTTGC	0.612																																						.											0													51.0	47.0	48.0					1																	203188924		2203	4300	6503	SO:0001819	synonymous_variant	1118			U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.783C>A	1.37:g.203188924G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Silent	SNP	ENST00000367229.1	37	CCDS1436.1																																																																																				0.612	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465	
RD3	343035	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	1	211654675	211654675	+	Missense_Mutation	SNP	G	G	A	rs61740157	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:211654675G>A	ENST00000367002.4	-	2	1246	c.83C>T	c.(82-84)aCg>aTg	p.T28M	RD3_ENST00000484910.1_Intron	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	28					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)					central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		CATCATAAGCGTCTCCAGCAC	0.627													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19913	0.0		0.0	False		,,,				2504	0.0					.											0								G	MET/THR,MET/THR	15,4391	22.3+/-47.3	0,15,2188	65.0	64.0	64.0		83,83	4.8	1.0	1	dbSNP_129	64	0,8600		0,0,4300	yes	missense,missense	RD3	NM_001164688.1,NM_183059.2	81,81	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	probably-damaging,probably-damaging	28/196,28/196	211654675	15,12991	2203	4300	6503	SO:0001583	missense	343035			AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"""chromosome 1 open reading frame 36"""	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.83C>T	1.37:g.211654675G>A	ENSP00000355969:p.Thr28Met	Somatic		WXS	Illumina HiSeq	Phase_I	A8K595	Missense_Mutation	SNP	ENST00000367002.4	37	CCDS1498.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	24.3	4.516183	0.85495	0.003404	0.0	ENSG00000198570	ENST00000367002	T	0.15834	2.39	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.43122	0.1233	M	0.70595	2.14	0.54753	D	0.999987	D	0.89917	1.0	D	0.91635	0.999	T	0.32079	-0.9920	10	0.49607	T	0.09	-44.5479	18.3198	0.90234	0.0:0.0:1.0:0.0	.	28	Q7Z3Z2	RD3_HUMAN	M	28	ENSP00000355969:T28M	ENSP00000355969:T28M	T	-	2	0	RD3	209721298	1.000000	0.71417	0.997000	0.53966	0.776000	0.43924	8.904000	0.92590	2.395000	0.81488	0.561000	0.74099	ACG		0.627	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059	
LRRC43	254050	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	12	122672370	122672370	+	Silent	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr12:122672370C>T	ENST00000339777.4	+	4	673	c.645C>T	c.(643-645)taC>taT	p.Y215Y	LRRC43_ENST00000425921.1_Silent_p.Y30Y	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	215										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		AAAGTCTCTACGTCACCGCTA	0.557																																						.											0													63.0	64.0	64.0					12																	122672370		1930	4135	6065	SO:0001819	synonymous_variant	254050			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.645C>T	12.37:g.122672370C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																				0.557	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
ADCY4	196883	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	14	24793320	24793320	+	Missense_Mutation	SNP	G	G	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr14:24793320G>C	ENST00000310677.4	-	17	2107	c.1994C>G	c.(1993-1995)gCc>gGc	p.A665G	ADCY4_ENST00000418030.2_Missense_Mutation_p.A665G|ADCY4_ENST00000554068.2_Missense_Mutation_p.A665G|ADCY4_ENST00000396747.3_Missense_Mutation_p.A358G	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	665					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		GGTGCCCAAGGCTATTCTCAG	0.612																																						.											0													75.0	67.0	70.0					14																	24793320		2203	4300	6503	SO:0001583	missense	196883			AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.1994C>G	14.37:g.24793320G>C	ENSP00000312126:p.Ala665Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909293	0.72868	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030;ENST00000396747	T;T;T;T	0.79940	-1.13;-1.13;-1.13;-1.32	4.93	4.93	0.64822	.	0.000000	0.46145	D	0.000319	T	0.77096	0.4080	L	0.56769	1.78	0.33050	D	0.532568	B	0.33841	0.428	B	0.33521	0.165	T	0.80372	-0.1410	10	0.25751	T	0.34	.	15.6732	0.77295	0.0:0.0:1.0:0.0	.	665	Q8NFM4	ADCY4_HUMAN	G	665;665;665;358	ENSP00000312126:A665G;ENSP00000452250:A665G;ENSP00000393177:A665G;ENSP00000379971:A358G	ENSP00000312126:A665G	A	-	2	0	ADCY4	23863160	0.979000	0.34478	0.996000	0.52242	0.912000	0.54170	1.769000	0.38522	2.569000	0.86673	0.563000	0.77884	GCC		0.612	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
RNF111	54778	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	15	59368246	59368246	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr15:59368246G>T	ENST00000557998.1	+	7	2067	c.1780G>T	c.(1780-1782)Gtt>Ttt	p.V594F	RNF111_ENST00000348370.4_Missense_Mutation_p.V594F|RNF111_ENST00000434298.1_Missense_Mutation_p.V594F|RNF111_ENST00000559209.1_Missense_Mutation_p.V594F|RNF111_ENST00000561186.1_Missense_Mutation_p.V594F	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	594					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CTGCTGCCCTGTTTCTTCCTC	0.512																																					NSCLC(72;983 1365 10746 34387 47081)	.											0													95.0	84.0	88.0					15																	59368246		2192	4291	6483	SO:0001583	missense	54778			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1780G>T	15.37:g.59368246G>T	ENSP00000452732:p.Val594Phe	Somatic		WXS	Illumina HiSeq	Phase_I	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	37	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059653	0.76074	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.15372	2.43;2.43	5.51	5.51	0.81932	.	0.233772	0.42172	D	0.000741	T	0.13970	0.0338	N	0.14661	0.345	0.48087	D	0.999583	B;B;B	0.27264	0.173;0.087;0.141	B;B;B	0.31686	0.134;0.046;0.1	T	0.15578	-1.0432	10	0.25751	T	0.34	-6.3302	19.7838	0.96428	0.0:0.0:1.0:0.0	.	594;594;594	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	F	594	ENSP00000288199:V594F;ENSP00000393641:V594F	ENSP00000288199:V594F	V	+	1	0	RNF111	57155538	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.146000	0.94640	2.755000	0.94549	0.650000	0.86243	GTT		0.512	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
C17orf53	78995	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	17	42225428	42225428	+	Missense_Mutation	SNP	C	C	A	rs563980398		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr17:42225428C>A	ENST00000319977.4	+	3	494	c.257C>A	c.(256-258)aCg>aAg	p.T86K	C17orf53_ENST00000245382.6_Missense_Mutation_p.T86K|C17orf53_ENST00000585683.1_Missense_Mutation_p.T86K	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	86										NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GCCTCCAGCACGCCCAGTGCT	0.602																																						.											0													84.0	73.0	76.0					17																	42225428		2203	4300	6503	SO:0001583	missense	78995			AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.257C>A	17.37:g.42225428C>A	ENSP00000313500:p.Thr86Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	.	.	.	.	.	.	.	.	.	.	C	1.476	-0.558590	0.03967	.	.	ENSG00000125319	ENST00000319977;ENST00000245382;ENST00000253405	T;T	0.43294	0.95;0.95	4.68	1.11	0.20524	.	1.059490	0.07253	N	0.866199	T	0.22126	0.0533	N	0.08118	0	0.09310	N	1	B;B;B	0.23937	0.006;0.094;0.006	B;B;B	0.22601	0.008;0.04;0.008	T	0.23833	-1.0177	10	0.42905	T	0.14	-0.1606	4.7069	0.12855	0.0:0.1771:0.1617:0.6612	.	86;86;86	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	K	86	ENSP00000313500:T86K;ENSP00000245382:T86K	ENSP00000245382:T86K	T	+	2	0	C17orf53	39580954	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.190000	0.09615	-0.009000	0.14296	-0.340000	0.08031	ACG		0.602	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	
LAMA1	284217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	18	6978199	6978199	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr18:6978199C>A	ENST00000389658.3	-	43	6279	c.6186G>T	c.(6184-6186)atG>atT	p.M2062I		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2062	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ACATACTGGCCATGGTGGAGT	0.562																																						.											0													212.0	189.0	197.0					18																	6978199		2203	4300	6503	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6186G>T	18.37:g.6978199C>A	ENSP00000374309:p.Met2062Ile	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	9.178	1.022806	0.19433	.	.	ENSG00000101680	ENST00000389658	T	0.44083	0.93	5.65	2.88	0.33553	Laminin II (1);	0.574082	0.19018	N	0.124884	T	0.34308	0.0893	L	0.51422	1.61	0.26194	N	0.979549	B	0.15141	0.012	B	0.15870	0.014	T	0.24297	-1.0164	10	0.44086	T	0.13	.	7.9278	0.29885	0.0:0.6485:0.0:0.3515	.	2062	P25391	LAMA1_HUMAN	I	2062	ENSP00000374309:M2062I	ENSP00000374309:M2062I	M	-	3	0	LAMA1	6968199	0.999000	0.42202	0.380000	0.26093	0.073000	0.16967	1.315000	0.33608	0.860000	0.35481	0.655000	0.94253	ATG		0.562	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
IL18RAP	8807	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	2	103068475	103068475	+	Missense_Mutation	SNP	T	T	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:103068475T>A	ENST00000264260.2	+	12	2223	c.1634T>A	c.(1633-1635)gTt>gAt	p.V545D	IL18RAP_ENST00000409369.1_Missense_Mutation_p.V403D	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	545	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						TTAAAATCAGTTCCTCCCAAT	0.453																																						.											0													129.0	139.0	135.0					2																	103068475		2203	4300	6503	SO:0001583	missense	8807			AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.1634T>A	2.37:g.103068475T>A	ENSP00000264260:p.Val545Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	37	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.743358	0.49151	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.07800	3.16;3.16	6.02	2.36	0.29203	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.409080	0.22957	N	0.053587	T	0.07369	0.0186	L	0.51422	1.61	0.19300	N	0.999979	P	0.42584	0.784	B	0.42522	0.39	T	0.18650	-1.0330	10	0.12430	T	0.62	.	3.9251	0.09261	0.0:0.3914:0.2101:0.3985	.	545	O95256	I18RA_HUMAN	D	545;403	ENSP00000264260:V545D;ENSP00000387201:V403D	ENSP00000264260:V545D	V	+	2	0	IL18RAP	102434907	0.000000	0.05858	0.038000	0.18304	0.871000	0.50021	0.579000	0.23788	0.516000	0.28340	0.528000	0.53228	GTT		0.453	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853	
HSPD1	3329	hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	2	198358117	198358117	+	Missense_Mutation	SNP	T	T	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:198358117T>A	ENST00000388968.3	-	7	1067	c.800A>T	c.(799-801)cAc>cTc	p.H267L	HSPD1_ENST00000345042.2_Missense_Mutation_p.H267L	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	267					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			AGGCTTACGGTGAGCATTGGC	0.388																																						.											0													112.0	112.0	112.0					2																	198358117		2203	4300	6503	SO:0001583	missense	3329			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.800A>T	2.37:g.198358117T>A	ENSP00000373620:p.His267Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B2R5M6|B7Z712|Q38L19|Q9UCR6	Missense_Mutation	SNP	ENST00000388968.3	37	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.651586	0.47362	.	.	ENSG00000144381	ENST00000388968;ENST00000345042;ENST00000536745	T;T	0.77098	-1.07;-1.07	5.33	5.33	0.75918	.	0.043715	0.85682	D	0.000000	T	0.68128	0.2967	N	0.17922	0.545	0.80722	D	1	B;B;B	0.27910	0.001;0.001;0.193	B;B;B	0.31390	0.005;0.003;0.129	T	0.68667	-0.5348	10	0.59425	D	0.04	-2.7515	15.5821	0.76452	0.0:0.0:0.0:1.0	.	258;267;267	B7Z597;B3GQS7;P10809	.;.;CH60_HUMAN	L	267;267;123	ENSP00000373620:H267L;ENSP00000340019:H267L	ENSP00000340019:H267L	H	-	2	0	HSPD1	198066362	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.941000	0.87700	2.139000	0.66308	0.477000	0.44152	CAC		0.388	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
NYAP2	57624	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	2	226273811	226273811	+	Missense_Mutation	SNP	T	T	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:226273811T>A	ENST00000272907.6	+	2	628	c.215T>A	c.(214-216)aTa>aAa	p.I72K	NYAP2_ENST00000409269.2_Missense_Mutation_p.I72K	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	72					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GAAGAAGCAATAAAGCGGtaa	0.373																																						.											0													39.0	33.0	35.0					2																	226273811		1831	4072	5903	SO:0001583	missense	57624			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.215T>A	2.37:g.226273811T>A	ENSP00000272907:p.Ile72Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.173537	0.78452	.	.	ENSG00000144460	ENST00000272907;ENST00000409269	T	0.39787	1.06	5.82	5.82	0.92795	.	0.055198	0.64402	D	0.000002	T	0.54983	0.1892	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.49818	-0.8899	10	0.06494	T	0.89	-26.1855	16.1986	0.82053	0.0:0.0:0.0:1.0	.	72;72	Q9P242-2;Q9P242	.;K1486_HUMAN	K	72	ENSP00000272907:I72K	ENSP00000272907:I72K	I	+	2	0	KIAA1486	225982055	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.160000	0.77495	2.227000	0.72691	0.455000	0.32223	ATA		0.373	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
UGT8	7368	hgsc.bcm.edu;ucsc.edu	37	4	115544546	115544546	+	Silent	SNP	T	T	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr4:115544546T>G	ENST00000310836.6	+	2	1032	c.510T>G	c.(508-510)gcT>gcG	p.A170A	UGT8_ENST00000394511.3_Silent_p.A170A	NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	170					axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		AAGTGGGTGCTCCTGCTCCAT	0.438																																						.											0													132.0	126.0	128.0					4																	115544546		2203	4300	6503	SO:0001819	synonymous_variant	7368			AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	2.4.1.45	"""UDP glucuronosyltransferases"""	12555	protein-coding gene	gene with protein product	"""2-hydroxyacylsphingosine 1-beta-galactosyltransferase"""	601291	"""UDP-galactose ceramide galactosyltransferase"""	CGT		8661025	Standard	NM_003360		Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.510T>G	4.37:g.115544546T>G		Somatic		WXS	Illumina HiSeq	Phase_I	B3KXU7|O00196	Silent	SNP	ENST00000310836.6	37	CCDS3705.1																																																																																				0.438	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256426.2	NM_003360	
DROSHA	29102	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	5	31521319	31521319	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr5:31521319C>A	ENST00000511367.2	-	5	1102	c.858G>T	c.(856-858)gaG>gaT	p.E286D	DROSHA_ENST00000442743.1_Missense_Mutation_p.E286D|DROSHA_ENST00000344624.3_Missense_Mutation_p.E286D|DROSHA_ENST00000513349.1_Missense_Mutation_p.E286D	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	286	Arg-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						CCCGTTCTCGCTCTCTTAAAG	0.403																																						.											0													210.0	193.0	199.0					5																	31521319		1884	4111	5995	SO:0001583	missense	29102			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.858G>T	5.37:g.31521319C>A	ENSP00000425979:p.Glu286Asp	Somatic		WXS	Illumina HiSeq	Phase_I	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411233	0.42817	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000382188	T;T;T;T	0.44482	1.49;1.49;0.92;0.92	5.95	4.08	0.47627	.	0.339654	0.31884	N	0.006907	T	0.20373	0.0490	N	0.08118	0	0.32783	N	0.502175	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.19844	-1.0293	10	0.18276	T	0.48	-20.681	9.2232	0.37390	0.0:0.6724:0.253:0.0746	.	286;286	E7EMP9;Q9NRR4	.;RNC_HUMAN	D	286;286;286;286;279	ENSP00000425979:E286D;ENSP00000339845:E286D;ENSP00000409335:E286D;ENSP00000424161:E286D	ENSP00000339845:E286D	E	-	3	2	DROSHA	31557076	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.805000	0.27112	1.527000	0.49086	0.655000	0.94253	GAG		0.403	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
CUL7	9820	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	6	43020113	43020113	+	Silent	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr6:43020113A>G	ENST00000265348.3	-	2	499	c.414T>C	c.(412-414)ctT>ctC	p.L138L	CUL7_ENST00000535468.1_Silent_p.L190L			Q14999	CUL7_HUMAN	cullin 7	138					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGACAGTGTGAAGTAGAGGAG	0.562																																						.											0													82.0	66.0	71.0					6																	43020113		2203	4300	6503	SO:0001819	synonymous_variant	9820			BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.414T>C	6.37:g.43020113A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																				0.562	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
PAX4	5078	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	7	127255519	127255519	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr7:127255519C>T	ENST00000341640.2	-	1	261	c.56G>A	c.(55-57)cGg>cAg	p.R19Q	PAX4_ENST00000463946.1_5'UTR|PAX4_ENST00000338516.3_Missense_Mutation_p.R27Q|PAX4_ENST00000378740.2_Missense_Mutation_p.R19Q	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	27	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						AATCTGCTGCCGGGTATCCAG	0.587																																					Ovarian(113;737 1605 7858 27720 34092)	.											0													84.0	87.0	86.0					7																	127255519		2203	4300	6503	SO:0001583	missense	5078				CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"""Paired boxes"", ""Homeoboxes / PRD class"""	8618	protein-coding gene	gene with protein product		167413	"""paired box gene 4"""				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.56G>A	7.37:g.127255519C>T	ENSP00000339906:p.Arg19Gln	Somatic		WXS	Illumina HiSeq	Phase_I	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	C	35	5.556378	0.96514	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740	D;D	0.99867	-7.31;-7.31	5.73	5.73	0.89815	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99864	0.9936	M	0.84846	2.72	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96679	0.9502	10	0.87932	D	0	.	17.4002	0.87458	0.0:1.0:0.0:0.0	.	19;27	O43316-4;O43316	.;PAX4_HUMAN	Q	19;27;27	ENSP00000339906:R19Q;ENSP00000344297:R27Q	ENSP00000344297:R27Q	R	-	2	0	PAX4	127042755	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.609000	0.82925	2.693000	0.91896	0.655000	0.94253	CGG		0.587	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1		
SSPO	23145	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	7	149486388	149486388	+	RNA	SNP	G	G	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr7:149486388G>T	ENST00000378016.2	+	0	4364							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGCCCCCAGGGCTTGCTGGCC	0.677																																						.											0													23.0	27.0	26.0					7																	149486388		2197	4295	6492			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149486388G>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MAL2	114569	hgsc.bcm.edu	37	8	120220776	120220776	+	Splice_Site	DEL	G	G	-	rs398009582|rs71302978		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr8:120220776delG	ENST00000276681.6	+	1	167	c.65delG	c.(64-66)cgg>cg	p.R22fs	MAL2_ENST00000521748.1_3'UTR	NM_052886.2	NP_443118.1	Q969L2	MAL2_HUMAN	mal, T-cell differentiation protein 2 (gene/pseudogene)	22						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)						all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			CCGCCGCCCCGGGGTCACCCT	0.771													GGG|GGGG|GGG|insertion	5008	1.0	1.0	1.0	5008	,	,		6681	1.0		1.0	False		,,,				2504	1.0					.											0										1571,11		785,1,5	1.0	1.0	1.0			0.7	0.8	8	dbSNP_130	1	4116,22		2057,2,10	no	frameshift	MAL2	NM_052886.2		2842,3,15	A1A1,A1R,RR		0.5317,0.6953,0.5769			120220776	5687,33	184	483	667	SO:0001630	splice_region_variant	114569			AL117612	CCDS75780.1	8q23	2011-01-26	2011-01-26			ENSG00000147676			13634	protein-coding gene	gene with protein product	"""MAL proteolipid protein 2"""	609684				11549320	Standard	NM_052886		Approved		uc003yop.3	Q969L2		ENST00000276681.6:c.66+1G>-	8.37:g.120220776delG		Somatic		WXS	Illumina HiSeq	Phase_I	B2R520|Q6ZMD9	Frame_Shift_Del	DEL	ENST00000276681.6	37																																																																																					0.771	MAL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052886	Frame_Shift_Del
TIGD5	84948	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	8	144680424	144680424	+	Silent	SNP	G	G	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr8:144680424G>T	ENST00000504548.2	+	1	351	c.351G>T	c.(349-351)cgG>cgT	p.R117R	EEF1D_ENST00000526838.1_5'Flank|EEF1D_ENST00000529272.1_5'Flank|EEF1D_ENST00000528610.1_5'Flank|RP11-661A12.14_ENST00000606452.1_lincRNA|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000317198.6_5'Flank|EEF1D_ENST00000442189.2_5'Flank|EEF1D_ENST00000419152.2_5'Flank|EEF1D_ENST00000524624.1_5'Flank|EEF1D_ENST00000423316.2_5'Flank|EEF1D_ENST00000531621.1_5'Flank|EEF1D_ENST00000395119.3_5'Flank|EEF1D_ENST00000532400.1_5'Flank|TIGD5_ENST00000321385.3_Silent_p.R68R	NM_032862.4	NP_116251.4	Q53EQ6	TIGD5_HUMAN	tigger transposable element derived 5	117	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	7	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			AGAAGATGCGGCTGGCCAACG	0.711																																						.											0													16.0	15.0	16.0					8																	144680424		2171	4274	6445	SO:0001819	synonymous_variant	84948			AK027832	CCDS6406.1, CCDS6406.2	8q24.3	2008-02-01				ENSG00000179886			18336	protein-coding gene	gene with protein product							Standard	NM_032862		Approved	FLJ14926	uc003yyx.2	Q53EQ6		ENST00000504548.2:c.351G>T	8.37:g.144680424G>T		Somatic		WXS	Illumina HiSeq	Phase_I	E7EWS2|Q6NT83|Q8N5A1|Q96JW8	Silent	SNP	ENST00000504548.2	37	CCDS6406.2																																																																																				0.711	TIGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368269.1	NM_032862	
DMD	1756	broad.mit.edu;hgsc.bcm.edu	37	X	31198540	31198550	+	Frame_Shift_Del	DEL	GACCAGAAAAA	GACCAGAAAAA	-	rs398123827		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	GACCAGAAAAA	GACCAGAAAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chrX:31198540_31198550delGACCAGAAAAA	ENST00000357033.4	-	69	10229_10239	c.10023_10033delTTTTTCTGGTC	c.(10021-10035)tttttttctggtcgafs	p.FFSGR3341fs	DMD_ENST00000361471.4_Frame_Shift_Del_p.FFSGR273fs|DMD_ENST00000343523.2_Frame_Shift_Del_p.FFSGR881fs|DMD_ENST00000541735.1_Frame_Shift_Del_p.FFSGR881fs|DMD_ENST00000474231.1_Frame_Shift_Del_p.FFSGR881fs|DMD_ENST00000378707.3_Frame_Shift_Del_p.FFSGR881fs|DMD_ENST00000359836.1_Frame_Shift_Del_p.FFSGR881fs|DMD_ENST00000378723.3_Frame_Shift_Del_p.FFSGR273fs|DMD_ENST00000378702.4_Frame_Shift_Del_p.FFSGR273fs|DMD_ENST00000378677.2_Frame_Shift_Del_p.FFSGR3337fs|DMD_ENST00000378680.2_Frame_Shift_Del_p.FFSGR273fs	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3341	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTTGCAACTCGACCAGAAAAAAAGCAGCTTT	0.412																																						.											0			GRCh37	CI040202|CM001666	DMD	I|M																																				SO:0001589	frameshift_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10023_10033delTTTTTCTGGTC	X.37:g.31198540_31198550delGACCAGAAAAA	ENSP00000354923:p.Phe3341fs	Somatic		WXS	Illumina HiSeq	Phase_I	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Del	DEL	ENST00000357033.4	37	CCDS14233.1																																																																																				0.412	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
ETNK1	55500	hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	12	22824236	22824236	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr12:22824236C>T	ENST00000266517.4	+	5	1087	c.998C>T	c.(997-999)tCt>tTt	p.S333F		NM_018638.4	NP_061108.2	Q9HBU6	EKI1_HUMAN	ethanolamine kinase 1	333					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TATGAATATTCTGGATACAAC	0.303																																					Esophageal Squamous(42;87 913 3224 6226 43339)	.											0													159.0	174.0	169.0					12																	22824236		2203	4299	6502	SO:0001583	missense	55500			BC006111	CCDS8698.1, CCDS41760.1	12p12.2	2004-07-09			ENSG00000139163	ENSG00000139163			24649	protein-coding gene	gene with protein product		609858				11912161, 11044454	Standard	XM_005253420		Approved	EKI1, EKI	uc001rft.3	Q9HBU6	OTTHUMG00000169008	ENST00000266517.4:c.998C>T	12.37:g.22824236C>T	ENSP00000266517:p.Ser333Phe	Somatic		WXS	Illumina HiSeq	Phase_I	G5E969	Missense_Mutation	SNP	ENST00000266517.4	37	CCDS8698.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919183	0.52546	.	.	ENSG00000139163	ENST00000266517;ENST00000381409	T	0.63096	-0.02	5.26	4.35	0.52113	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.282916	0.34555	N	0.003879	T	0.70937	0.3281	M	0.75777	2.31	0.80722	D	1	P;B	0.41498	0.752;0.411	P;B	0.49140	0.601;0.315	T	0.74833	-0.3530	10	0.87932	D	0	-2.5583	13.4388	0.61101	0.0:0.7:0.3:0.0	.	333;333	E9PD44;Q9HBU6	.;EKI1_HUMAN	F	333	ENSP00000266517:S333F	ENSP00000266517:S333F	S	+	2	0	ETNK1	22715503	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.224000	0.51238	1.184000	0.42957	0.460000	0.39030	TCT		0.303	ETNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401926.2	NM_018638	
DMD	1756	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	X	32382805	32382805	+	Missense_Mutation	SNP	G	G	C	rs146420425		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chrX:32382805G>C	ENST00000357033.4	-	36	5254	c.5048C>G	c.(5047-5049)aCt>aGt	p.T1683S	DMD_ENST00000378677.2_Missense_Mutation_p.T1679S	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1683	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CTGGTCAAAAGTTTCCATGTG	0.363																																						.											0								G	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	3,3830		0,3,1628,571	202.0	155.0	171.0		5024,5048,4679,5036,4679,1025,1016	2.5	1.0	X	dbSNP_134	171	0,6728		0,0,2428,1872	no	missense,missense,missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3	58,58,58,58,58,58,58	0,3,4056,2443	CC,CG,GG,G		0.0,0.0783,0.0284	benign,benign,benign,benign,benign,benign,benign	1675/3678,1683/3686,1560/3563,1679/3682,1560/3563,342/2345,339/2342	32382805	3,10558	2202	4300	6502	SO:0001583	missense	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5048C>G	X.37:g.32382805G>C	ENSP00000354923:p.Thr1683Ser	Somatic		WXS	Illumina HiSeq	Phase_I	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328845	0.24167	7.83E-4	0.0	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000420596;ENST00000448370	T;T	0.49432	0.78;0.78	5.38	2.49	0.30216	.	0.457777	0.15530	N	0.257580	T	0.30386	0.0763	N	0.19112	0.55	0.53005	D	0.999964	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.001;0.002;0.001;0.001	T	0.07028	-1.0794	10	0.09338	T	0.73	.	13.7945	0.63162	0.0:0.0:0.6002:0.3998	.	1675;1683;1679;342;339	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	S	1675;342;339;1679;1683;1683;1560;99;39	ENSP00000367948:T1679S;ENSP00000354923:T1683S	ENSP00000354923:T1683S	T	-	2	0	DMD	32292726	0.859000	0.29813	0.991000	0.47740	0.888000	0.51559	0.551000	0.23361	0.135000	0.18707	0.538000	0.68166	ACT		0.363	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
ZNF518A	9849	broad.mit.edu	37	10	97918856	97918856	+	RNA	DEL	A	A	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr10:97918856delA	ENST00000534948.1	+	0	3634							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		AATTCAGAACAAAAAAAAACT	0.348																																						.											0													43.0	42.0	42.0					10																	97918856		1795	4061	5856			9849			AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"""Zinc fingers, C2H2-type"""	29009	protein-coding gene	gene with protein product			"""zinc finger protein 518"""	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97918856delA		Somatic		WXS	Illumina HiSeq	Phase_I	A0PJI5|O15044|Q32MP4	Frame_Shift_Del	DEL	ENST00000534948.1	37																																																																																					0.348	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803	
NLRP6	171389	broad.mit.edu;mdanderson.org;bcgsc.ca	37	11	281811	281811	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:281811C>T	ENST00000312165.5	+	4	2077	c.2077C>T	c.(2077-2079)Cgg>Tgg	p.R693W	NLRP6_ENST00000534750.1_Missense_Mutation_p.R693W	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	693					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CCTGGGGAAGCGGCTCCAGGC	0.617																																						.											0													27.0	34.0	32.0					11																	281811		2200	4296	6496	SO:0001583	missense	171389			AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2077C>T	11.37:g.281811C>T	ENSP00000309767:p.Arg693Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	37	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.120457	0.37436	.	.	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.75050	-0.9;-0.86	3.22	-0.952	0.10366	.	5.443360	0.00881	U	0.002125	D	0.83115	0.5184	M	0.63428	1.95	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.967;0.99	T	0.64694	-0.6347	10	0.62326	D	0.03	.	6.2588	0.20889	0.0:0.4948:0.0:0.5052	.	693;693	E9PJZ8;P59044	.;NALP6_HUMAN	W	693	ENSP00000433617:R693W;ENSP00000309767:R693W	ENSP00000309767:R693W	R	+	1	2	NLRP6	271811	0.001000	0.12720	0.001000	0.08648	0.751000	0.42716	-0.508000	0.06344	-0.183000	0.10585	0.462000	0.41574	CGG		0.617	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
CTSD	1509	broad.mit.edu;mdanderson.org;bcgsc.ca	37	11	1774767	1774767	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:1774767T>C	ENST00000236671.2	-	9	1337	c.1205A>G	c.(1204-1206)aAc>aGc	p.N402S	IFITM10_ENST00000340134.4_5'Flank|RP11-295K3.1_ENST00000427721.1_Intron	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	402					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GCCCACCCTGTTGTTGTCACG	0.652																																						.											0													54.0	59.0	57.0					11																	1774767		2202	4298	6500	SO:0001583	missense	1509			M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"""Cathepsins"""	2529	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 10"""	116840	"""cathepsin D (lysosomal aspartyl protease)"""	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.1205A>G	11.37:g.1774767T>C	ENSP00000236671:p.Asn402Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	37	CCDS7725.1	.	.	.	.	.	.	.	.	.	.	t	15.40	2.823084	0.50739	.	.	ENSG00000117984	ENST00000236671;ENST00000429746	T;T	0.59224	0.28;0.33	3.75	3.75	0.43078	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.250635	0.43416	D	0.000580	T	0.56352	0.1979	M	0.64404	1.975	0.58432	D	0.999999	P	0.45531	0.86	B	0.43082	0.407	T	0.61217	-0.7107	10	0.45353	T	0.12	.	12.9513	0.58403	0.0:0.0:0.0:1.0	.	402	P07339	CATD_HUMAN	S	402;179	ENSP00000236671:N402S;ENSP00000402586:N179S	ENSP00000236671:N402S	N	-	2	0	CTSD	1731343	1.000000	0.71417	0.550000	0.28217	0.558000	0.35554	7.268000	0.78473	1.721000	0.51461	0.254000	0.18369	AAC		0.652	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909	
FOLH1B	219595	broad.mit.edu	37	11	89420569	89420569	+	RNA	DEL	A	A	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:89420569delA	ENST00000532352.1	+	0	1384							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						AAGTTGGACTAAAAAAAGTCC	0.343																																						.											0													57.0	59.0	58.0					11																	89420569		2201	4296	6497			219595			AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"""prostate specific membrane antigen like protein"", ""Cell growth-inhibiting gene 26 protein"", ""glutamate carboxypeptidase III"""	609020	"""folate hydrolase 2"""	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89420569delA		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000532352.1	37																																																																																					0.343	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696	
KRT77	374454	broad.mit.edu;bcgsc.ca	37	12	53084953	53084953	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr12:53084953T>C	ENST00000341809.3	-	9	1761	c.1733A>G	c.(1732-1734)gAg>gGg	p.E578G	KRT77_ENST00000537195.1_Missense_Mutation_p.E345G|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	578	Tail.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						AGGCCTCTACTCCAAGATCCG	0.637																																						.											0													51.0	43.0	46.0					12																	53084953		2199	4292	6491	SO:0001583	missense	374454			BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1733A>G	12.37:g.53084953T>C	ENSP00000342710:p.Glu578Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.619576	0.46736	.	.	ENSG00000189182	ENST00000341809;ENST00000537195	D;D	0.84298	-1.83;-1.54	3.63	1.21	0.21127	.	.	.	.	.	T	0.68430	0.3000	N	0.08118	0	0.25508	N	0.987483	B	0.14012	0.009	B	0.10450	0.005	T	0.58853	-0.7563	9	0.87932	D	0	.	5.486	0.16749	0.0:0.253:0.0:0.747	.	578	Q7Z794	K2C1B_HUMAN	G	578;345	ENSP00000342710:E578G;ENSP00000440803:E345G	ENSP00000342710:E578G	E	-	2	0	KRT77	51371220	1.000000	0.71417	0.840000	0.33206	0.122000	0.20287	1.758000	0.38410	0.125000	0.18397	0.454000	0.30748	GAG		0.637	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
BAG5	9529	broad.mit.edu	37	14	104026528	104026528	+	Frame_Shift_Del	DEL	T	T	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr14:104026528delT	ENST00000445922.2	-	2	1220	c.974delA	c.(973-975)aacfs	p.N325fs	APOPT1_ENST00000556253.2_5'Flank|BAG5_ENST00000299204.4_Frame_Shift_Del_p.N325fs|BAG5_ENST00000337322.4_Frame_Shift_Del_p.N366fs|RP11-73M18.2_ENST00000472726.2_5'Flank|APOPT1_ENST00000409074.2_5'Flank|APOPT1_ENST00000247618.4_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	325	BAG 4. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			GATGCAGGGGTTTTTTTCAAG	0.443																																					NSCLC(171;1832 2055 18950 31566 41632)	.											0													61.0	65.0	63.0					14																	104026528		2203	4300	6503	SO:0001589	frameshift_variant	9529			AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.974delA	14.37:g.104026528delT	ENSP00000391713:p.Asn325fs	Somatic		WXS	Illumina HiSeq	Phase_I	O94950|Q86W59	Frame_Shift_Del	DEL	ENST00000445922.2	37	CCDS9982.1																																																																																				0.443	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1		
INO80	54617	broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	41313154	41313154	+	Missense_Mutation	SNP	G	G	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr15:41313154G>C	ENST00000361937.3	-	26	3642	c.3218C>G	c.(3217-3219)gCt>gGt	p.A1073G	INO80_ENST00000401393.3_Missense_Mutation_p.A1073G|RP11-540O11.4_ENST00000558967.1_RNA			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1073	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CAGACCTCCAGCTGGCTCTGG	0.527																																						.											0													56.0	55.0	55.0					15																	41313154		2203	4300	6503	SO:0001583	missense	54617			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3218C>G	15.37:g.41313154G>C	ENSP00000355205:p.Ala1073Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941002	0.34283	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91124	-2.79;-2.79	5.35	2.35	0.29111	.	0.344090	0.34223	N	0.004142	T	0.80116	0.4564	N	0.20986	0.625	0.26586	N	0.973289	B	0.11235	0.004	B	0.13407	0.009	T	0.63778	-0.6560	10	0.22109	T	0.4	.	5.7046	0.17901	0.2319:0.0:0.6331:0.135	.	1073	Q9ULG1	INO80_HUMAN	G	1073	ENSP00000355205:A1073G;ENSP00000384686:A1073G	ENSP00000355205:A1073G	A	-	2	0	INO80	39100446	1.000000	0.71417	0.488000	0.27440	0.804000	0.45430	3.923000	0.56469	0.337000	0.23665	-0.345000	0.07892	GCT		0.527	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
RLTPR	146206	broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67679167	67679167	+	Missense_Mutation	SNP	C	C	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr16:67679167C>G	ENST00000334583.6	+	1	346	c.18C>G	c.(16-18)gaC>gaG	p.D6E	RLTPR_ENST00000545661.1_Missense_Mutation_p.D6E	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	6					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		AGACCCCCGACGGCATCTCCT	0.701																																						.											0													14.0	17.0	16.0					16																	67679167		1879	4091	5970	SO:0001583	missense	146206			AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.18C>G	16.37:g.67679167C>G	ENSP00000334958:p.Asp6Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	37	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	c	10.99	1.506105	0.26949	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.13538	2.6;2.58	4.19	0.764	0.18465	.	0.609572	0.14846	N	0.294975	T	0.04679	0.0127	N	0.08118	0	0.21950	N	0.999451	B;B	0.30763	0.294;0.149	B;B	0.24155	0.051;0.016	T	0.31916	-0.9926	10	0.35671	T	0.21	-11.9051	1.3041	0.02085	0.1712:0.4571:0.1671:0.2046	.	6;6	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	E	6	ENSP00000334958:D6E;ENSP00000441481:D6E	ENSP00000334958:D6E	D	+	3	2	RLTPR	66236668	0.156000	0.22821	0.998000	0.56505	0.966000	0.64601	-0.327000	0.07955	0.467000	0.27218	0.651000	0.88453	GAC		0.701	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
ALOX12B	242	broad.mit.edu	37	17	7980375	7980375	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr17:7980375T>C	ENST00000319144.4	-	9	1468	c.1208A>G	c.(1207-1209)cAc>cGc	p.H403R	AC129492.6_ENST00000399413.3_5'Flank|ALOX12B_ENST00000577351.1_5'UTR	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	403	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						AGCAATGAGGTGTGTCTCCAG	0.622										Multiple Myeloma(8;0.094)																												.											0													57.0	48.0	51.0					17																	7980375		2203	4300	6503	SO:0001583	missense	242			AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"""Arachidonate lipoxygenases"""	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.1208A>G	17.37:g.7980375T>C	ENSP00000315167:p.His403Arg	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.052970	0.55218	.	.	ENSG00000179477	ENST00000319144	D	0.96136	-3.92	4.82	4.82	0.62117	Lipoxygenase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.98002	0.9342	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98994	1.0809	10	0.87932	D	0	-37.0536	13.6567	0.62341	0.0:0.0:0.0:1.0	.	403	O75342	LX12B_HUMAN	R	403	ENSP00000315167:H403R	ENSP00000315167:H403R	H	-	2	0	ALOX12B	7921100	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	7.886000	0.87288	1.937000	0.56155	0.260000	0.18958	CAC		0.622	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3		
SHD	56961	broad.mit.edu	37	19	4280193	4280193	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr19:4280193C>A	ENST00000543264.2	+	1	1596	c.133C>A	c.(133-135)Ccc>Acc	p.P45T	SHD_ENST00000599689.1_Missense_Mutation_p.P45T	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	45										breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCGAGGACCCCTATGAGGA	0.687																																						.											0													24.0	29.0	27.0					19																	4280193		2203	4299	6502	SO:0001583	missense	56961			BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"""SH2 domain containing"""	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.133C>A	19.37:g.4280193C>A	ENSP00000446058:p.Pro45Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	37	CCDS12125.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.478308	0.84747	.	.	ENSG00000105251	ENST00000543264	T	0.64260	-0.09	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.78233	0.4251	M	0.75615	2.305	0.49483	D	0.999799	D	0.89917	1.0	D	0.79108	0.992	T	0.81549	-0.0882	10	0.87932	D	0	-0.5326	15.2492	0.73529	0.0:1.0:0.0:0.0	.	45	Q96IW2	SHD_HUMAN	T	45	ENSP00000446058:P45T	ENSP00000446058:P45T	P	+	1	0	SHD	4231193	1.000000	0.71417	1.000000	0.80357	0.504000	0.33889	6.467000	0.73547	2.267000	0.75376	0.484000	0.47621	CCC		0.687	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
CAPN12	147968	broad.mit.edu	37	19	39226063	39226063	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr19:39226063A>G	ENST00000328867.4	-	14	1941	c.1633T>C	c.(1633-1635)Tac>Cac	p.Y545H	CAPN12_ENST00000601953.1_Missense_Mutation_p.Y396H|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	545	Domain IV.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			AGGGGCAGGTAGGGGCCCTGC	0.677																																						.											0													41.0	40.0	40.0					19																	39226063		2185	4297	6482	SO:0001583	missense	147968			BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1633T>C	19.37:g.39226063A>G	ENSP00000331636:p.Tyr545His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.298308	0.23650	.	.	ENSG00000182472	ENST00000328867	D	0.86769	-2.17	4.0	2.97	0.34412	.	3.783630	0.00993	N	0.003551	D	0.83110	0.5183	L	0.40543	1.245	0.23984	N	0.99626	B	0.02656	0.0	B	0.01281	0.0	T	0.64253	-0.6451	10	0.41790	T	0.15	.	6.4766	0.22039	0.784:0.0:0.0:0.216	.	545	Q6ZSI9	CAN12_HUMAN	H	545	ENSP00000331636:Y545H	ENSP00000331636:Y545H	Y	-	1	0	CAPN12	43917903	0.160000	0.22878	0.595000	0.28798	0.013000	0.08279	0.553000	0.23391	0.562000	0.29204	0.397000	0.26171	TAC		0.677	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
SDC1	6382	broad.mit.edu	37	2	20402642	20402642	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:20402642A>G	ENST00000254351.4	-	5	1062	c.818T>C	c.(817-819)tTc>tCc	p.F273S	SDC1_ENST00000403076.1_Intron|SDC1_ENST00000482879.1_Intron|SDC1_ENST00000381150.1_Missense_Mutation_p.F273S	NM_002997.4	NP_002988	P18827	SDC1_HUMAN	syndecan 1	273					canonical Wnt signaling pathway (GO:0060070)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|myoblast development (GO:0048627)|odontogenesis (GO:0042476)|phototransduction, visible light (GO:0007603)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to toxic substance (GO:0009636)|retinoid metabolic process (GO:0001523)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|striated muscle cell development (GO:0055002)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|skin(2)	21	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		GTACAGCATGAAACCCACCAG	0.617																																						.											0													138.0	139.0	139.0					2																	20402642		2203	4300	6503	SO:0001583	missense	6382			AJ551176	CCDS1697.1	2p24.1	2008-02-05			ENSG00000115884	ENSG00000115884		"""CD molecules"", ""Proteoglycans / Cell Surface : Syndecans"""	10658	protein-coding gene	gene with protein product	"""syndecan proteoglycan 1"""	186355		SDC			Standard	XM_005262621		Approved	CD138, syndecan, SYND1	uc002rdo.1	P18827	OTTHUMG00000090751	ENST00000254351.4:c.818T>C	2.37:g.20402642A>G	ENSP00000254351:p.Phe273Ser	Somatic		WXS	Illumina HiSeq	Phase_I	D6W523|Q53QV0|Q546D3|Q96HB7	Missense_Mutation	SNP	ENST00000254351.4	37	CCDS1697.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398474	0.62177	.	.	ENSG00000115884	ENST00000254351;ENST00000381150	T;T	0.28666	1.6;1.6	4.63	4.63	0.57726	.	0.000000	0.51477	D	0.000095	T	0.55625	0.1932	M	0.80847	2.515	0.51767	D	0.99993	D	0.76494	0.999	D	0.72338	0.977	T	0.62011	-0.6944	10	0.87932	D	0	-19.074	12.2904	0.54815	1.0:0.0:0.0:0.0	.	273	P18827	SDC1_HUMAN	S	273	ENSP00000254351:F273S;ENSP00000370542:F273S	ENSP00000254351:F273S	F	-	2	0	SDC1	20266123	1.000000	0.71417	0.995000	0.50966	0.117000	0.20001	9.101000	0.94219	1.849000	0.53698	0.459000	0.35465	TTC		0.617	SDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207495.1	NM_001006946	
TRIM54	57159	broad.mit.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	2	27527838	27527838	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:27527838C>A	ENST00000380075.2	+	4	865	c.525C>A	c.(523-525)agC>agA	p.S175R	TRIM54_ENST00000296098.4_Missense_Mutation_p.S217R	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	175	Mediates microtubule-binding and homooligomerization. {ECO:0000250}.				cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|negative regulation of microtubule depolymerization (GO:0007026)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGAGCTCAGCGATGGCATCG	0.607																																						.											0													85.0	65.0	72.0					2																	27527838		2203	4300	6503	SO:0001583	missense	57159			AJ291714	CCDS1745.2, CCDS1746.2	2p23.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000138100	ENSG00000138100		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16008	protein-coding gene	gene with protein product		606474	"""ring finger protein 30"", ""tripartite motif-containing 54"""	RNF30		11243782	Standard	NM_032546		Approved	MURF, MURF-3	uc002rjn.3	Q9BYV2	OTTHUMG00000097078	ENST00000380075.2:c.525C>A	2.37:g.27527838C>A	ENSP00000369415:p.Ser175Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A5D8T7|Q53SY4|Q9BYV3	Missense_Mutation	SNP	ENST00000380075.2	37	CCDS1746.2	.	.	.	.	.	.	.	.	.	.	C	19.37	3.813742	0.70912	.	.	ENSG00000138100	ENST00000380075;ENST00000296098	T;T	0.56611	0.45;2.44	5.77	-8.68	0.00859	.	0.000000	0.85682	D	0.000000	T	0.46190	0.1380	L	0.51422	1.61	0.45087	D	0.998104	B;P	0.40534	0.058;0.72	B;P	0.44860	0.028;0.462	T	0.61237	-0.7103	10	0.33940	T	0.23	-19.0914	17.7535	0.88442	0.0:0.7584:0.0:0.2416	.	175;217	Q9BYV2;Q9BYV2-2	TRI54_HUMAN;.	R	175;217	ENSP00000369415:S175R;ENSP00000296098:S217R	ENSP00000296098:S217R	S	+	3	2	TRIM54	27381342	0.000000	0.05858	0.533000	0.28001	0.981000	0.71138	-1.638000	0.02013	-1.882000	0.01122	-0.291000	0.09656	AGC		0.607	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214199.2	NM_187841	
SAP130	79595	broad.mit.edu;bcgsc.ca	37	2	128747329	128747329	+	Missense_Mutation	SNP	C	C	A	rs199755359		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:128747329C>A	ENST00000259235.3	-	13	1796	c.1667G>T	c.(1666-1668)cGa>cTa	p.R556L	SAP130_ENST00000357702.5_Missense_Mutation_p.R556L|SAP130_ENST00000259234.6_Missense_Mutation_p.R530L	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	556					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		TTGAATATGTCGAGCATGCGA	0.577																																						.											0													116.0	98.0	104.0					2																	128747329		2203	4300	6503	SO:0001583	missense	79595			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.1667G>T	2.37:g.128747329C>A	ENSP00000259235:p.Arg556Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	37	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571602	0.65765	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234	.	.	.	5.56	4.68	0.58851	.	0.000000	0.64402	D	0.000007	T	0.62901	0.2466	L	0.27053	0.805	0.47778	D	0.999513	D;P;P;D;P	0.71674	0.998;0.901;0.761;0.997;0.901	D;B;B;D;B	0.80764	0.994;0.338;0.272;0.98;0.372	T	0.60276	-0.7295	9	0.27785	T	0.31	-10.0439	14.5671	0.68185	0.0:0.9295:0.0:0.0705	.	556;529;556;86;194	B7ZLM3;Q96DP1;Q9H0E3;Q9H0E3-2;B3KRT9	.;.;SP130_HUMAN;.;.	L	556;556;530	.	ENSP00000259234:R530L	R	-	2	0	SAP130	128463799	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.225000	0.65294	1.334000	0.45468	0.655000	0.94253	CGA		0.577	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
SEZ6L	23544	broad.mit.edu;mdanderson.org	37	22	26736527	26736527	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr22:26736527C>A	ENST00000248933.6	+	10	2236	c.2141C>A	c.(2140-2142)aCc>aAc	p.T714N	SEZ6L_ENST00000403121.1_Missense_Mutation_p.T487N|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T487N|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T714N|SEZ6L_ENST00000529632.2_Missense_Mutation_p.T714N|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T714N|SEZ6L_ENST00000404234.3_Missense_Mutation_p.T714N			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	714	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CCAGACTTAACCATCCAGTTC	0.507																																						.											0													97.0	85.0	89.0					22																	26736527		2203	4300	6503	SO:0001583	missense	23544			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2141C>A	22.37:g.26736527C>A	ENSP00000248933:p.Thr714Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.518095	0.64634	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.14	5.14	0.70334	CUB (5);	0.112900	0.39083	N	0.001478	T	0.47857	0.1468	M	0.91717	3.235	0.80722	D	1	B;B;B;B;B;B;B	0.29188	0.033;0.236;0.033;0.198;0.178;0.236;0.236	B;B;B;B;B;B;B	0.31686	0.03;0.133;0.033;0.081;0.134;0.133;0.133	T	0.56366	-0.7991	10	0.56958	D	0.05	.	17.7636	0.88470	0.0:1.0:0.0:0.0	.	714;714;487;714;714;714;714	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	N	714;714;714;714;714;487;487	ENSP00000384772:T714N;ENSP00000437037:T714N;ENSP00000354185:T714N;ENSP00000248933:T714N;ENSP00000342661:T714N;ENSP00000384838:T487N;ENSP00000384733:T487N	ENSP00000248933:T714N	T	+	2	0	SEZ6L	25066527	1.000000	0.71417	0.998000	0.56505	0.922000	0.55478	7.149000	0.77396	2.668000	0.90789	0.462000	0.41574	ACC		0.507	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
ROBO2	6092	broad.mit.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	3	77645803	77645803	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:77645803C>T	ENST00000461745.1	+	19	3656	c.2756C>T	c.(2755-2757)cCc>cTc	p.P919L	ROBO2_ENST00000487694.3_Missense_Mutation_p.P935L|ROBO2_ENST00000332191.8_Missense_Mutation_p.P919L	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	919					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GCTGGTGATCCCAGCTATCCA	0.458																																						.											0													144.0	140.0	141.0					3																	77645803		1863	4115	5978	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.2756C>T	3.37:g.77645803C>T	ENSP00000417164:p.Pro919Leu	Somatic		WXS	Illumina HiSeq	Phase_I	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.42|16.42	3.119351|3.119351	0.56505|0.56505	.|.	.|.	ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191|ENST00000490991	T;T;T|T	0.62498|0.66638	0.02;0.05;0.05|-0.22	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.148737|0.148737	0.30989|0.30989	N|N	0.008470|0.008470	T|T	0.77980|0.77980	0.4212|0.4212	L|L	0.58101|0.58101	1.795|1.795	.|.	.|.	.|.	P;D;B|.	0.54601|.	0.883;0.967;0.047|.	B;P;B|.	0.49252|.	0.4;0.604;0.017|.	T|T	0.73528|0.73528	-0.3954|-0.3954	9|7	0.66056|0.41790	D|T	0.02|0.15	.|.	20.8598|20.8598	0.99761|0.99761	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	935;919;919|.	Q19AB5;F8W703;Q9HCK4|.	.;.;ROBO2_HUMAN|.	L|S	935;935;939;919;919|76	ENSP00000417335:P935L;ENSP00000417164:P919L;ENSP00000327536:P919L|ENSP00000418344:P76S	ENSP00000327536:P919L|ENSP00000418344:P76S	P|P	+|+	2|1	0|0	ROBO2|ROBO2	77728493|77728493	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	7.270000|7.270000	0.78493|0.78493	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	CCC|CCA		0.458	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
ZBTB11	27107	broad.mit.edu	37	3	101395694	101395694	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:101395694G>A	ENST00000312938.4	-	1	645	c.65C>T	c.(64-66)gCg>gTg	p.A22V	ZBTB11_ENST00000461821.1_Missense_Mutation_p.A22V|ZBTB11-AS1_ENST00000536865.1_RNA|ZBTB11-AS1_ENST00000609682.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	22					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGTGCCCGGCGCATACGGCTC	0.657																																						.											0													27.0	26.0	26.0					3																	101395694		2191	4289	6480	SO:0001583	missense	27107			U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.65C>T	3.37:g.101395694G>A	ENSP00000326200:p.Ala22Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.066317|6.066317	0.97251|0.97251	.|.	.|.	ENSG00000066422|ENSG00000256628	ENST00000312938;ENST00000461821|ENST00000536865	T;T|.	0.62498|.	0.02;0.02|.	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.814523	.|0.09980	.|U	.|0.731163	T|T	0.71409|0.71409	0.3336|0.3336	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	D;D|D	0.89917|0.57257	1.0;0.992|0.979	D;P|P	0.68039|0.50049	0.955;0.609|0.629	T|T	0.71886|0.71886	-0.4457|-0.4457	9|9	0.87932|0.87932	D|D	0|0	-10.3773|-10.3773	19.8722|19.8722	0.96854|0.96854	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	22;22|69	C9J2L2;O95625|Q9BTX9	.;ZBT11_HUMAN|YC010_HUMAN	V|H	22|69	ENSP00000326200:A22V;ENSP00000417369:A22V|.	ENSP00000326200:A22V|ENSP00000444544:R69H	A|R	-|+	2|2	0|0	ZBTB11|AC084198.1	102878384|102878384	1.000000|1.000000	0.71417|0.71417	0.975000|0.975000	0.42487|0.42487	0.749000|0.749000	0.42624|0.42624	9.130000|9.130000	0.94437|0.94437	2.700000|2.700000	0.92200|0.92200	0.585000|0.585000	0.79938|0.79938	GCG|CGC		0.657	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
COL6A5	256076	broad.mit.edu	37	3	130114173	130114173	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:130114173G>T	ENST00000432398.2	+	8	3927	c.3433G>T	c.(3433-3435)Gtt>Ttt	p.V1145F	COL6A5_ENST00000265379.6_Missense_Mutation_p.V1145F	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1145	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CATAGGAGATGTTTATAAGGA	0.373																																						.											0													26.0	24.0	24.0					3																	130114173		692	1591	2283	SO:0001583	missense	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.3433G>T	3.37:g.130114173G>T	ENSP00000390895:p.Val1145Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	G	9.881	1.201710	0.22121	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.79653	-1.29;-1.29	5.31	3.38	0.38709	.	.	.	.	.	D	0.82388	0.5026	L	0.54323	1.7	0.09310	N	1	D	0.56287	0.975	P	0.59643	0.861	T	0.70615	-0.4823	9	0.59425	D	0.04	.	3.9523	0.09374	0.0876:0.1527:0.5773:0.1824	.	1145	A8TX70-2	.	F	1145	ENSP00000390895:V1145F;ENSP00000265379:V1145F	ENSP00000265379:V1145F	V	+	1	0	COL6A5	131596863	0.250000	0.23951	0.003000	0.11579	0.472000	0.32918	1.059000	0.30517	0.505000	0.28104	0.491000	0.48974	GTT		0.373	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
TOPBP1	11073	broad.mit.edu	37	3	133368474	133368474	+	Silent	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:133368474A>G	ENST00000260810.5	-	10	1388	c.1257T>C	c.(1255-1257)ccT>ccC	p.P419P	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	419	BRCT 3. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CCACTACATGAGGCCTACAAA	0.393								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)	.											0													72.0	66.0	68.0					3																	133368474		1875	4115	5990	SO:0001819	synonymous_variant	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.1257T>C	3.37:g.133368474A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																				0.393	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
OCIAD1	54940	broad.mit.edu	37	4	48859372	48859372	+	Frame_Shift_Del	DEL	A	A	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr4:48859372delA	ENST00000381473.3	+	8	1108	c.690delA	c.(688-690)ccafs	p.P230fs	OCIAD1_ENST00000264312.7_Frame_Shift_Del_p.P230fs|OCIAD1_ENST00000513391.2_Frame_Shift_Del_p.P230fs|OCIAD1_ENST00000396448.2_Intron|OCIAD1_ENST00000508293.1_Frame_Shift_Del_p.P230fs|OCIAD1_ENST00000425583.2_Intron|OCIAD1-AS1_ENST00000513576.1_RNA|OCIAD1_ENST00000444354.2_Intron|OCIAD1_ENST00000506801.1_Intron|OCIAD1_ENST00000509122.1_Frame_Shift_Del_p.P203fs	NM_001079839.2	NP_001073308.1	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1	230						endosome (GO:0005768)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(2)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	9						AAAGAGTGCCAAAAAAAGAAG	0.303																																						.											0													55.0	58.0	57.0					4																	48859372		2203	4297	6500	SO:0001589	frameshift_variant	54940			AF324350	CCDS3484.1, CCDS43228.1, CCDS47052.1	4p11	2010-03-19			ENSG00000109180	ENSG00000109180			16074	protein-coding gene	gene with protein product						11162530, 18328549	Standard	NM_017830		Approved	FLJ20455, TPA018, OCIA, Asrij	uc010igk.3	Q9NX40	OTTHUMG00000102095	ENST00000381473.3:c.690delA	4.37:g.48859372delA	ENSP00000370882:p.Pro230fs	Somatic		WXS	Illumina HiSeq	Phase_I	C9K030|G8JLN7|Q9BZE8	Frame_Shift_Del	DEL	ENST00000381473.3	37	CCDS3484.1																																																																																				0.303	OCIAD1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361812.3	NM_017830	
TKTL2	84076	broad.mit.edu;mdanderson.org;bcgsc.ca	37	4	164394497	164394497	+	Missense_Mutation	SNP	T	T	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr4:164394497T>A	ENST00000280605.3	-	1	550	c.390A>T	c.(388-390)ttA>ttT	p.L130F		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	130						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				ATGCAGTACCTAATCCCTGAC	0.537																																						.											0													112.0	106.0	108.0					4																	164394497		2203	4300	6503	SO:0001583	missense	84076			BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"""similar to transketolase"""					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.390A>T	4.37:g.164394497T>A	ENSP00000280605:p.Leu130Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	T	8.443	0.851355	0.17034	.	.	ENSG00000151005	ENST00000280605	T	0.38401	1.14	3.75	-4.32	0.03688	Transketolase, N-terminal (1);	0.000000	0.64402	D	0.000010	T	0.51890	0.1701	M	0.77313	2.365	0.42428	D	0.992665	D	0.89917	1.0	D	0.83275	0.996	T	0.54490	-0.8286	10	0.87932	D	0	-9.7836	9.1928	0.37209	0.0:0.7609:0.1078:0.1313	.	130	Q9H0I9	TKTL2_HUMAN	F	130	ENSP00000280605:L130F	ENSP00000280605:L130F	L	-	3	2	TKTL2	164613947	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-2.976000	0.00665	-1.026000	0.03330	-0.429000	0.05907	TTA		0.537	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136	
NIPBL	25836	broad.mit.edu	37	5	36985238	36985238	+	Silent	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr5:36985238A>G	ENST00000282516.8	+	10	2455	c.1956A>G	c.(1954-1956)aaA>aaG	p.K652K	NIPBL_ENST00000448238.2_Silent_p.K652K|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	652					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AAGAACTTAAACAGAATGAGA	0.353																																						.											0													92.0	94.0	93.0					5																	36985238		2203	4300	6503	SO:0001819	synonymous_variant	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1956A>G	5.37:g.36985238A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																				0.353	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
DAB2	1601	broad.mit.edu	37	5	39376947	39376947	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr5:39376947T>C	ENST00000320816.6	-	12	2409	c.1942A>G	c.(1942-1944)Atc>Gtc	p.I648V	DAB2_ENST00000339788.6_Missense_Mutation_p.I430V|DAB2_ENST00000509337.1_Missense_Mutation_p.I627V|DAB2_ENST00000545653.1_Missense_Mutation_p.I627V	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	648	Sufficient for interaction with GRB2. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			ACATCCTTGATCTCTTTATCC	0.552											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										.											0													56.0	60.0	58.0					5																	39376947		2203	4300	6503	SO:0001583	missense	1601			U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1942A>G	5.37:g.39376947T>C	ENSP00000313391:p.Ile648Val	Somatic	885	WXS	Illumina HiSeq	Phase_I	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	T	1.817	-0.473247	0.04445	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.09	3.0	0.34707	.	0.380726	0.29253	N	0.012700	T	0.12732	0.0309	N	0.08118	0	0.23132	N	0.998245	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.32025	-0.9922	10	0.02654	T	1	-7.1504	4.1642	0.10298	0.0:0.4387:0.0:0.5613	.	648;627	P98082;P98082-3	DAB2_HUMAN;.	V	648;430;627;627	ENSP00000313391:I648V;ENSP00000345508:I430V;ENSP00000439919:I627V;ENSP00000426245:I627V	ENSP00000313391:I648V	I	-	1	0	DAB2	39412704	1.000000	0.71417	0.991000	0.47740	0.838000	0.47535	4.637000	0.61346	1.116000	0.41820	-0.242000	0.12053	ATC		0.552	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
MSH3	4437	broad.mit.edu;mdanderson.org	37	5	79968625	79968625	+	Silent	SNP	C	C	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr5:79968625C>G	ENST00000265081.6	+	6	1055	c.975C>G	c.(973-975)ctC>ctG	p.L325L		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	325					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		GAAGTTCACTCTTTTCCCGGA	0.373								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	.											0													118.0	120.0	119.0					5																	79968625		2203	4300	6503	SO:0001819	synonymous_variant	4437			U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.975C>G	5.37:g.79968625C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																				0.373	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
ADGB	79747	broad.mit.edu	37	6	147105874	147105874	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr6:147105874G>A	ENST00000397944.3	+	31	4232	c.4156G>A	c.(4156-4158)Gaa>Aaa	p.E1386K	ADGB_ENST00000367493.3_Intron|ADGB_ENST00000523560.1_Intron|ADGB_ENST00000367488.1_Missense_Mutation_p.E109K	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	1386					oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						AAGGGCAGATGAAATCCGAGC	0.413																																						.											0													72.0	68.0	69.0					6																	147105874		692	1591	2283	SO:0001583	missense	79747			AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.4156G>A	6.37:g.147105874G>A	ENSP00000381036:p.Glu1386Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		.	.	.	.	.	.	.	.	.	.	G	27.8	4.863268	0.91511	.	.	ENSG00000118492	ENST00000397944;ENST00000367490;ENST00000326916;ENST00000367488	T;T	0.55234	1.15;0.53	5.68	5.68	0.88126	.	.	.	.	.	T	0.59702	0.2213	L	0.39147	1.195	0.41678	D	0.98927	D;D	0.89917	1.0;1.0	D;D	0.87578	0.99;0.998	T	0.59392	-0.7463	9	0.51188	T	0.08	.	18.5639	0.91111	0.0:0.0:1.0:0.0	.	1386;331	Q8N7X0;Q8N7X0-2	CAN7L_HUMAN;.	K	1386;344;109;109	ENSP00000381036:E1386K;ENSP00000356460:E344K	ENSP00000323839:E109K	E	+	1	0	C6orf103	147147567	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.771000	0.68881	2.681000	0.91329	0.650000	0.86243	GAA		0.413	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
ZFHX4	79776	broad.mit.edu;mdanderson.org	37	8	77763344	77763344	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr8:77763344A>G	ENST00000521891.2	+	10	4635	c.4187A>G	c.(4186-4188)aAg>aGg	p.K1396R	ZFHX4_ENST00000518282.1_Missense_Mutation_p.K1370R|ZFHX4_ENST00000455469.2_Missense_Mutation_p.K1351R|ZFHX4_ENST00000050961.6_Missense_Mutation_p.K1351R	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CATGTCTACAAGTATCGCTGT	0.428										HNSCC(33;0.089)																												.											0													93.0	88.0	90.0					8																	77763344		1895	4117	6012	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4187A>G	8.37:g.77763344A>G	ENSP00000430497:p.Lys1396Arg	Somatic		WXS	Illumina HiSeq	Phase_I	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	15.26	2.781160	0.49891	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55413	0.52;0.6;0.56;0.55	4.65	4.65	0.58169	.	0.000000	0.46758	U	0.000279	T	0.71316	0.3325	M	0.76002	2.32	0.58432	D	0.999996	D;D;D	0.67145	0.993;0.996;0.996	D;D;D	0.77557	0.978;0.99;0.99	T	0.75425	-0.3322	10	0.66056	D	0.02	.	14.5713	0.68213	1.0:0.0:0.0:0.0	.	1351;1351;1396	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	R	1396;1396;1351;1351;1370	ENSP00000430497:K1396R;ENSP00000399605:K1351R;ENSP00000050961:K1351R;ENSP00000430848:K1370R	ENSP00000050961:K1351R	K	+	2	0	ZFHX4	77925899	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.087000	0.94110	2.096000	0.63516	0.454000	0.30748	AAG		0.428	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
MAGEB2	4113	broad.mit.edu;mdanderson.org;bcgsc.ca	37	X	30237265	30237265	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chrX:30237265G>A	ENST00000378988.4	+	2	669	c.568G>A	c.(568-570)Gaa>Aaa	p.E190K		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	190	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						CACTGATGAGGAATCCCTGCT	0.502																																						.											0													61.0	47.0	52.0					X																	30237265		2202	4300	6502	SO:0001583	missense	4113			AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 6"", ""melanoma-associated antigen B2"", ""cancer/testis antigen family 3, member 2"""	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.568G>A	X.37:g.30237265G>A	ENSP00000368273:p.Glu190Lys	Somatic		WXS	Illumina HiSeq	Phase_I	O75860	Missense_Mutation	SNP	ENST00000378988.4	37	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.391388	0.25118	.	.	ENSG00000099399	ENST00000378988	T	0.05025	3.51	3.13	2.26	0.28386	.	1.425730	0.05041	N	0.476377	T	0.12135	0.0295	M	0.82193	2.58	0.09310	N	1	B	0.33637	0.42	B	0.32022	0.139	T	0.34601	-0.9822	10	0.66056	D	0.02	.	5.6343	0.17528	0.156:0.0:0.844:0.0	.	190	O15479	MAGB2_HUMAN	K	190	ENSP00000368273:E190K	ENSP00000368273:E190K	E	+	1	0	MAGEB2	30147186	0.011000	0.17503	0.001000	0.08648	0.001000	0.01503	1.681000	0.37618	0.723000	0.32274	0.436000	0.28706	GAA		0.502	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364	
PRG4	10216	broad.mit.edu	37	1	186276256	186276257	+	In_Frame_Ins	INS	-	-	CCA	rs149342058	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:186276256_186276257insCCA	ENST00000445192.2	+	7	1450_1451	c.1405_1406insCCA	c.(1405-1407)ccc>cCCAcc	p.471_472insT	PRG4_ENST00000367486.3_In_Frame_Ins_p.428_429insT|PRG4_ENST00000367485.4_In_Frame_Ins_p.378_379insT|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_In_Frame_Ins_p.430_431insT	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	471	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GGAGCCTGCACCCACCACCAAG	0.653																																						.											0																																										SO:0001652	inframe_insertion	10216			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1412_1414dupCCA	1.37:g.186276263_186276265dupCCA	ENSP00000399679:p.Thr471_Thr471dup	Somatic		WXS	Illumina HiSeq	Phase_I	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	In_Frame_Ins	INS	ENST00000445192.2	37	CCDS1369.1																																																																																				0.653	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
DEAF1	10522	broad.mit.edu	37	11	694933	694934	+	Frame_Shift_Ins	INS	-	-	AG			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:694933_694934insAG	ENST00000382409.3	-	1	598_599	c.114_115insCT	c.(112-117)gaggagfs	p.E39fs	DEAF1_ENST00000338675.6_Frame_Shift_Ins_p.E39fs|TMEM80_ENST00000397510.3_5'Flank|TMEM80_ENST00000397512.3_5'Flank|TMEM80_ENST00000608174.1_5'Flank	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	39	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		AGCACCGGCTCCTCCGCCTCGC	0.782																																						.											0																																										SO:0001589	frameshift_variant	10522			AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.114_115insCT	11.37:g.694933_694934insAG	ENSP00000371846:p.Glu39fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Frame_Shift_Ins	INS	ENST00000382409.3	37	CCDS31327.1																																																																																				0.782	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
MICALCL	84953	broad.mit.edu	37	11	12315174	12315175	+	Frame_Shift_Ins	INS	-	-	G	rs148792670	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:12315174_12315175insG	ENST00000256186.2	+	3	487_488	c.196_197insG	c.(196-198)cggfs	p.R66fs		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	66	Interaction with MAPK1. {ECO:0000250}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)	p.R66W(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		CCCAAACTTTCGGAGGCGAGCC	0.55																																						.											1	Substitution - Missense(1)	endometrium(1)																																								SO:0001589	frameshift_variant	84953			BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.198dupG	11.37:g.12315176_12315176dupG	ENSP00000256186:p.Arg66fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q7RTP7|Q96JU6	Frame_Shift_Ins	INS	ENST00000256186.2	37	CCDS41620.1																																																																																				0.550	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
MUC4	4585	broad.mit.edu	37	3	195512280	195512281	+	Frame_Shift_Ins	INS	-	-	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:195512280_195512281insG	ENST00000463781.3	-	2	6629_6630	c.6170_6171insC	c.(6169-6171)gtafs	p.V2057fs	MUC4_ENST00000475231.1_Frame_Shift_Ins_p.V2057fs|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CACCTGTGGATACTGAGGAAAG	0.564																																						.											0																																										SO:0001589	frameshift_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6170_6171insC	3.37:g.195512280_195512281insG	ENSP00000417498:p.Val2057fs	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Frame_Shift_Ins	INS	ENST00000463781.3	37	CCDS54700.1																																																																																				0.564	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FLT4	2324	broad.mit.edu	37	5	180048849	180048850	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr5:180048849_180048850insGC	ENST00000261937.6	-	13	1790_1791	c.1712_1713insGC	c.(1711-1713)ggcfs	p.G571fs	FLT4_ENST00000393347.3_Frame_Shift_Ins_p.G571fs|FLT4_ENST00000502649.1_Frame_Shift_Ins_p.G571fs|FLT4_ENST00000424276.2_5'UTR	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	571	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCACCGGCTGGCCCTCTAGTAG	0.629																																					Colon(97;1075 1466 27033 27547 35871)	.											0																																										SO:0001589	frameshift_variant	2324			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.1712_1713insGC	5.37:g.180048849_180048850insGC	ENSP00000261937:p.Gly571fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Frame_Shift_Ins	INS	ENST00000261937.6	37	CCDS4457.1																																																																																				0.629	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
FGD3	89846	ucsc.edu	37	9	95792199	95792199	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr9:95792199A>G	ENST00000375482.3	+	15	2097	c.1601A>G	c.(1600-1602)gAg>gGg	p.E534G	FGD3_ENST00000337352.6_Missense_Mutation_p.E534G|FGD3_ENST00000538555.1_Missense_Mutation_p.E137G|FGD3_ENST00000416701.2_Missense_Mutation_p.E534G	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	534					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						CGTGACAAGGAGAAGCAGAGC	0.537																																						.											0													111.0	115.0	114.0					9																	95792199		2094	4227	6321	SO:0001583	missense	89846			AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1601A>G	9.37:g.95792199A>G	ENSP00000364631:p.Glu534Gly	Somatic		WXS	Illumina HiSeq	Phase_I	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	37	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.171529	0.78452	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352;ENST00000538555	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	4.64	4.64	0.57946	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.33057	N	0.005326	D	0.83151	0.5192	M	0.64630	1.985	0.52501	D	0.999958	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.995	D	0.84793	0.0780	10	0.72032	D	0.01	.	12.3041	0.54891	1.0:0.0:0.0:0.0	.	534;534	F8W7P2;Q5JSP0	.;FGD3_HUMAN	G	534;534;534;137	ENSP00000364631:E534G;ENSP00000413833:E534G;ENSP00000336914:E534G;ENSP00000442560:E137G	ENSP00000336914:E534G	E	+	2	0	FGD3	94832020	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.006000	0.76329	1.875000	0.54330	0.459000	0.35465	GAG		0.537	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
KIF11	3832	ucsc.edu	37	10	94399586	94399586	+	Silent	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr10:94399586A>G	ENST00000260731.3	+	17	2286	c.2196A>G	c.(2194-2196)agA>agG	p.R732R		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	732					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGACAGAGAGATTCTGTGCTT	0.333																																					Colon(47;212 1003 2764 4062 8431)	.											0													109.0	117.0	114.0					10																	94399586		2203	4297	6500	SO:0001819	synonymous_variant	3832			X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"""Kinesins"""	6388	protein-coding gene	gene with protein product		148760	"""kinesin-like 1"""	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.2196A>G	10.37:g.94399586A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A0AV49|B2RMV3|Q15716|Q5VWX0	Silent	SNP	ENST00000260731.3	37	CCDS7422.1																																																																																				0.333	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523	
LYST	1130	ucsc.edu	37	1	235964396	235964396	+	Splice_Site	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:235964396C>T	ENST00000389794.3	-	9	3888	c.3714G>A	c.(3712-3714)ggG>ggA	p.G1238G	LYST_ENST00000389793.2_Splice_Site_p.G1238G|LYST_ENST00000536965.1_Splice_Site_p.G1238G			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1238					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TTAAGTCTACCCCTGAAAAGA	0.333																																						.											0													70.0	73.0	72.0					1																	235964396		2202	4299	6501	SO:0001630	splice_region_variant	1130			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.3713-1G>A	1.37:g.235964396C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																				0.333	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		Silent
MYCBP2	23077	ucsc.edu;mdanderson.org	37	13	77799637	77799637	+	Silent	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr13:77799637A>G	ENST00000544440.2	-	19	2693	c.2676T>C	c.(2674-2676)ccT>ccC	p.P892P	MYCBP2_ENST00000407578.2_Silent_p.P930P|MYCBP2_ENST00000357337.6_Silent_p.P892P|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CAGAGCCTGGAGGGTATGTTG	0.443																																						.											0													197.0	166.0	176.0					13																	77799637		2203	4300	6503	SO:0001819	synonymous_variant	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.2676T>C	13.37:g.77799637A>G		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000544440.2	37																																																																																					0.443	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
PFKFB3	5209	ucsc.edu	37	10	6261653	6261653	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr10:6261653A>G	ENST00000379775.4	+	7	950	c.620A>G	c.(619-621)gAc>gGc	p.D207G	PFKFB3_ENST00000379782.3_Missense_Mutation_p.D207G|PFKFB3_ENST00000540253.1_Missense_Mutation_p.D221G|PFKFB3_ENST00000360521.2_Missense_Mutation_p.D207G|PFKFB3_ENST00000379785.1_Missense_Mutation_p.D207G|PFKFB3_ENST00000536985.1_3'UTR|PFKFB3_ENST00000379789.4_Missense_Mutation_p.D187G|PFKFB3_ENST00000317350.4_Missense_Mutation_p.D207G	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	207	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						GACAAATGCGACAGGTGATTC	0.507																																						.											0													69.0	68.0	69.0					10																	6261653		2203	4300	6503	SO:0001583	missense	5209				CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.620A>G	10.37:g.6261653A>G	ENSP00000369100:p.Asp207Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	37	CCDS7078.1	.	.	.	.	.	.	.	.	.	.	A	19.07	3.755617	0.69648	.	.	ENSG00000170525	ENST00000379789;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.	.	.	5.56	5.56	0.83823	6-phosphofructo-2-kinase (1);	0.000000	0.85682	D	0.000000	D	0.84061	0.5389	M	0.86805	2.84	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.997;0.999	D;D;D;D	0.97110	1.0;0.999;0.973;0.999	D	0.87133	0.2198	9	0.87932	D	0	-4.2194	15.7063	0.77583	1.0:0.0:0.0:0.0	.	221;207;207;187	B7Z955;Q16875-2;Q16875;Q5VX15	.;.;F263_HUMAN;.	G	187;221;207;207;207;207;207;207	.	ENSP00000369105:D207G	D	+	2	0	PFKFB3	6301659	1.000000	0.71417	0.982000	0.44146	0.229000	0.25112	9.097000	0.94193	2.111000	0.64477	0.482000	0.46254	GAC		0.507	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1		
RING1	6015	ucsc.edu	37	6	33179664	33179664	+	Missense_Mutation	SNP	A	A	G	rs73741545		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr6:33179664A>G	ENST00000374656.4	+	6	1212	c.1004A>G	c.(1003-1005)gAg>gGg	p.E335G	RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	335	Gly-rich.|Necessary for interaction with CBX2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						TGTGGCGGGGAGGGTGGGGGT	0.667																																						.											0													17.0	21.0	19.0					6																	33179664		2199	4288	6487	SO:0001583	missense	6015				CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"""RING-type (C3HC4) zinc fingers"""	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.1004A>G	6.37:g.33179664A>G	ENSP00000363787:p.Glu335Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Missense_Mutation	SNP	ENST00000374656.4	37	CCDS34424.1	.	.	.	.	.	.	.	.	.	.	A	13.99	2.400621	0.42613	.	.	ENSG00000204227	ENST00000374656	D	0.84660	-1.88	4.04	4.04	0.47022	.	0.268117	0.27126	N	0.020812	T	0.51143	0.1657	N	0.08118	0	0.35818	D	0.824394	B	0.10296	0.003	B	0.06405	0.002	T	0.49826	-0.8898	10	0.33141	T	0.24	-38.3332	5.9934	0.19480	0.8842:0.0:0.1158:0.0	.	335	Q06587	RING1_HUMAN	G	335	ENSP00000363787:E335G	ENSP00000363787:E335G	E	+	2	0	RING1	33287642	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	3.206000	0.51098	1.674000	0.50907	0.368000	0.22195	GAG		0.667	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2		
SBNO2	22904	ucsc.edu	37	19	1132115	1132115	+	Intron	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr19:1132115A>G	ENST00000361757.3	-	5	517				SBNO2_ENST00000587024.1_Intron|SBNO2_ENST00000438103.2_Missense_Mutation_p.W28R	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)						bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AACTGCAGCCACAGCTGCAGC	0.716																																						.											0													7.0	8.0	8.0					19																	1132115		1763	4004	5767	SO:0001627	intron_variant	22904			AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.280-4351T>C	19.37:g.1132115A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	37	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518610	0.64634	.	.	ENSG00000064932	ENST00000438103;ENST00000250872	.	.	.	4.09	2.98	0.34508	.	.	.	.	.	T	0.32010	0.0815	L	0.44542	1.39	0.22127	N	0.999344	B;B	0.32573	0.107;0.376	B;B	0.28709	0.043;0.093	T	0.27536	-1.0071	8	0.87932	D	0	-23.9825	7.103	0.25348	0.7995:0.0:0.0:0.2005	.	28;28	B4DL53;Q9Y2G9-3	.;.	R	28;7	.	ENSP00000250872:W7R	W	-	1	0	SBNO2	1083115	1.000000	0.71417	0.957000	0.39632	0.843000	0.47879	3.547000	0.53663	1.510000	0.48803	0.459000	0.35465	TGG		0.716	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
SPDYE4	388333	ucsc.edu	37	17	8661681	8661681	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr17:8661681C>T	ENST00000328794.6	-	1	196	c.20G>A	c.(19-21)cGc>cAc	p.R7H		NM_001128076.1	NP_001121548.1	A6NLX3	SPDE4_HUMAN	speedy/RINGO cell cycle regulator family member E4	7										breast(1)|endometrium(2)|kidney(1)	4						AAACGGGGGGCGCGCTTGACC	0.562																																						.											0													22.0	25.0	24.0					17																	8661681		692	1591	2283	SO:0001583	missense	388333			BC146949	CCDS45609.1	17p13.1	2013-05-08	2013-05-08			ENSG00000183318		"""Speedy homologs"""	35463	protein-coding gene	gene with protein product			"""speedy homolog E4 (Xenopus laevis)"""				Standard	NM_001128076		Approved		uc010cnz.1	A6NLX3		ENST00000328794.6:c.20G>A	17.37:g.8661681C>T	ENSP00000329522:p.Arg7His	Somatic		WXS	Illumina HiSeq	Phase_I	B2RUZ6	Missense_Mutation	SNP	ENST00000328794.6	37	CCDS45609.1	.	.	.	.	.	.	.	.	.	.	C	0.952	-0.706226	0.03255	.	.	ENSG00000183318	ENST00000328794	.	.	.	2.38	-4.77	0.03219	.	7.820830	0.00424	N	0.000061	T	0.07007	0.0178	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23297	-1.0192	9	0.21540	T	0.41	.	1.1614	0.01806	0.2396:0.3748:0.1786:0.207	.	7	A6NLX3	SPDE4_HUMAN	H	7	.	ENSP00000329522:R7H	R	-	2	0	SPDYE4	8602406	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.285000	0.02791	-3.424000	0.00166	-1.501000	0.00957	CGC		0.562	SPDYE4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442494.1	NM_001128076	
AEBP1	165	mdanderson.org	37	7	44147485	44147485	+	Missense_Mutation	SNP	C	C	A	rs2537188	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr7:44147485C>A	ENST00000223357.3	+	5	1122	c.817C>A	c.(817-819)Ccc>Acc	p.P273T	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_5'Flank	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	273	Pro-rich.		P -> T (in dbSNP:rs2537188).		cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						CTGGCCAGAGCCCCCTGAGGA	0.697													C|||	1790	0.357428	0.3684	0.2695	5008	,	,		13134	0.2738		0.3519	False		,,,				2504	0.4969					.											0								C	THR/PRO	1512,2824		285,942,941	10.0	13.0	12.0		817	1.4	0.1	7	dbSNP_100	12	3187,5327		639,1909,1709	no	missense	AEBP1	NM_001129.3	38	924,2851,2650	AA,AC,CC		37.4325,34.8708,36.5681	possibly-damaging	273/1159	44147485	4699,8151	2168	4257	6425	SO:0001583	missense	165			D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.817C>A	7.37:g.44147485C>A	ENSP00000223357:p.Pro273Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	697	0.3191391941391941	148	0.3008130081300813	113	0.31215469613259667	155	0.270979020979021	281	0.370712401055409	C	8.109	0.778353	0.16120	0.348708	0.374325	ENSG00000106624	ENST00000223357	T	0.39997	1.05	4.54	1.41	0.22369	.	7.491200	0.00166	N	0.000008	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	9.000000000036756E-6	B	0.19817	0.039	B	0.14023	0.01	T	0.34950	-0.9808	9	0.48119	T	0.1	-0.4184	7.7789	0.29054	0.1715:0.4951:0.3335:0.0	rs2537188;rs60349212	273	Q8IUX7	AEBP1_HUMAN	T	273	ENSP00000223357:P273T	ENSP00000223357:P273T	P	+	1	0	AEBP1	44114010	0.001000	0.12720	0.074000	0.20217	0.361000	0.29550	0.387000	0.20718	0.318000	0.23185	0.491000	0.48974	CCC		0.697	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
ANKLE1	126549	mdanderson.org	37	19	17393530	17393530	+	Missense_Mutation	SNP	T	T	A	rs8108174	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr19:17393530T>A	ENST00000394458.3	+	3	557	c.281T>A	c.(280-282)cTg>cAg	p.L94Q	ANKLE1_ENST00000404085.1_Missense_Mutation_p.L116Q|CTD-2278I10.6_ENST00000596542.1_3'UTR|ANKLE1_ENST00000433424.2_Missense_Mutation_p.L148Q|ANKLE1_ENST00000598347.1_Missense_Mutation_p.L94Q|ANKLE1_ENST00000594072.1_Missense_Mutation_p.L83Q	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	94			L -> Q (in dbSNP:rs8108174). {ECO:0000269|Ref.1}.							large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GGCCTGGAGCTGCTGCTGAGC	0.706											OREG0025341	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2307	0.460663	0.5053	0.3905	5008	,	,		14289	0.3115		0.5726	False		,,,				2504	0.4888					.											0								T	GLN/LEU	2060,1610		662,736,437	2.0	3.0	3.0		281	4.3	1.0	19	dbSNP_116	3	4143,3109		1303,1537,786	no	missense	ANKLE1	NM_152363.4	113	1965,2273,1223	AA,AT,TT		42.8709,43.8692,43.2064	probably-damaging	94/616	17393530	6203,4719	1835	3626	5461	SO:0001583	missense	126549			AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.281T>A	19.37:g.17393530T>A	ENSP00000377971:p.Leu94Gln	Somatic	717	WXS	Illumina HiSeq	Phase_I	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	37	CCDS12354.2	1011	0.46291208791208793	245	0.49796747967479676	160	0.4419889502762431	164	0.2867132867132867	442	0.58311345646438	T	17.43	3.387803	0.61956	0.561308	0.571291	ENSG00000160117	ENST00000404261;ENST00000433424;ENST00000404085;ENST00000394458;ENST00000438921	T;T;T	0.69926	-0.44;-0.44;-0.44	4.27	4.27	0.50696	Ankyrin repeat-containing domain (4);	0.097299	0.42964	D	0.000624	T	0.00012	0.0000	M	0.64080	1.96	0.23515	P	0.99751696	P;D;D	0.89917	0.793;1.0;1.0	B;D;D	0.91635	0.426;0.999;0.999	T	0.51702	-0.8672	9	0.56958	D	0.05	-2.4128	11.4078	0.49908	0.0:0.0:0.0:1.0	rs8108174	94;80;94	E7ETZ9;Q8NAG6-1;Q8NAG6	.;.;ANKL1_HUMAN	Q	94;148;116;83;94	ENSP00000384753:L94Q;ENSP00000394460:L148Q;ENSP00000384008:L116Q	ENSP00000377971:L83Q	L	+	2	0	ANKLE1	17254530	1.000000	0.71417	0.997000	0.53966	0.070000	0.16714	4.664000	0.61540	1.800000	0.52685	0.459000	0.35465	CTG		0.706	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
BCAP29	55973	mdanderson.org	37	7	107253813	107253813	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr7:107253813A>G	ENST00000005259.4	+	7	965	c.626A>G	c.(625-627)aAg>aGg	p.K209R	BCAP29_ENST00000494086.1_3'UTR|BCAP29_ENST00000379117.2_Missense_Mutation_p.K209R|BCAP29_ENST00000465919.1_Missense_Mutation_p.K115R|BCAP29_ENST00000379121.2_Missense_Mutation_p.K115R|BCAP29_ENST00000379119.2_Missense_Mutation_p.K209R|BCAP29_ENST00000445771.2_Missense_Mutation_p.K209R	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	209					apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						ATGGAAATGAAGATGCAGTCA	0.328																																						.											0													84.0	82.0	83.0					7																	107253813		2203	4300	6503	SO:0001583	missense	55973				CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.626A>G	7.37:g.107253813A>G	ENSP00000005259:p.Lys209Arg	Somatic		WXS	Illumina HiSeq	Phase_I	G5E9L4|O95003	Missense_Mutation	SNP	ENST00000005259.4	37	CCDS34731.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.589608	0.28357	.	.	ENSG00000075790	ENST00000005259;ENST00000465919;ENST00000445771;ENST00000457837;ENST00000379117;ENST00000379119;ENST00000491150;ENST00000379121	T	0.44881	0.91	5.08	3.93	0.45458	.	0.183317	0.56097	D	0.000024	T	0.34948	0.0915	L	0.54908	1.71	0.58432	D	0.999997	B;B;B	0.23442	0.047;0.035;0.085	B;B;B	0.26094	0.033;0.066;0.066	T	0.10613	-1.0622	10	0.25106	T	0.35	0.119	7.3851	0.26878	0.903:0.0:0.097:0.0	.	209;209;209	G5E9L4;C9JTE9;Q9UHQ4	.;.;BAP29_HUMAN	R	209;115;209;209;209;209;166;115	ENSP00000368416:K115R	ENSP00000005259:K209R	K	+	2	0	BCAP29	107041049	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	2.274000	0.43390	0.969000	0.38237	0.454000	0.30748	AAG		0.328	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844	
CELSR2	1952	mdanderson.org	37	1	109801121	109801121	+	Silent	SNP	C	C	T	rs684138	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:109801121C>T	ENST00000271332.3	+	2	3439	c.3378C>T	c.(3376-3378)acC>acT	p.T1126T		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1126	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		AGATGCTCACCCACAGCATCA	0.652													C|||	583	0.116414	0.3033	0.0893	5008	,	,		19037	0.0		0.1044	False		,,,				2504	0.0153				NSCLC(158;1285 2011 34800 34852 42084)	.											0								C		1202,3202		164,874,1164	42.0	34.0	36.0		3378	-1.5	1.0	1	dbSNP_83	36	817,7779		44,729,3525	yes	coding-synonymous	CELSR2	NM_001408.2		208,1603,4689	TT,TC,CC		9.5044,27.2934,15.5308		1126/2924	109801121	2019,10981	2202	4298	6500	SO:0001819	synonymous_variant	1952			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.3378C>T	1.37:g.109801121C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																				0.652	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
CHIA	27159	mdanderson.org;bcgsc.ca	37	1	111863044	111863044	+	Missense_Mutation	SNP	G	G	A	rs142653250	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:111863044G>A	ENST00000369740.1	+	12	1490	c.1387G>A	c.(1387-1389)Ggg>Agg	p.G463R	CHIA_ENST00000451398.2_Missense_Mutation_p.G302R|CHIA_ENST00000343320.6_Missense_Mutation_p.G463R|CHIA_ENST00000483391.1_Missense_Mutation_p.G302R|CHIA_ENST00000430615.1_Missense_Mutation_p.G355R|CHIA_ENST00000353665.6_Missense_Mutation_p.G302R|RP5-1125M8.2_ENST00000426321.1_RNA	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	463	Chitin-binding type-2. {ECO:0000255|PROSITE-ProRule:PRU00144}.				apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CTGCCAGGCCGGGCTTGTCTT	0.527													G|||	3	0.000599042	0.0	0.0014	5008	,	,		21604	0.001		0.001	False		,,,				2504	0.0					.											0								G	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	62.0	61.0	62.0		1063,1387	1.8	0.0	1	dbSNP_134	62	14,8586	9.8+/-36.6	0,14,4286	yes	missense,missense	CHIA	NM_021797.2,NM_201653.2	125,125	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	possibly-damaging,possibly-damaging	355/369,463/477	111863044	15,12991	2203	4300	6503	SO:0001583	missense	27159			AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.1387G>A	1.37:g.111863044G>A	ENSP00000358755:p.Gly463Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	G	12.12	1.841326	0.32513	2.27E-4	0.001628	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000430615	T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85	4.77	1.8	0.24995	Chitin binding domain (5);	0.000000	0.56097	U	0.000034	T	0.45196	0.1330	H	0.98594	4.275	0.09310	N	1	P	0.39847	0.691	B	0.38880	0.284	T	0.52253	-0.8600	10	0.62326	D	0.03	-1.4299	5.9113	0.19029	0.1698:0.0:0.6772:0.153	.	463	Q9BZP6	CHIA_HUMAN	R	407;302;463;463;302;302;355	ENSP00000387671:G407R;ENSP00000436946:G302R;ENSP00000358755:G463R;ENSP00000341828:G463R;ENSP00000390476:G302R;ENSP00000338970:G302R;ENSP00000391132:G355R	ENSP00000341828:G463R	G	+	1	0	CHIA	111664567	0.399000	0.25287	0.000000	0.03702	0.668000	0.39293	1.995000	0.40767	0.298000	0.22638	0.655000	0.94253	GGG		0.527	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
CNTNAP3B	728577	mdanderson.org	37	9	43828112	43828112	+	Silent	SNP	A	A	G	rs555608997	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr9:43828112A>G	ENST00000377564.3	+	9	1761	c.1368A>G	c.(1366-1368)gtA>gtG	p.V456V		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	456	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						GGCACTCTGTATCCTTCTCTG	0.458													N|||	1273	0.254193	0.2209	0.2378	5008	,	,		7147	0.4355		0.2455	False		,,,				2504	0.1329					.											0																																										SO:0001819	synonymous_variant	728577			BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.1368A>G	9.37:g.43828112A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Silent	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	N	5.461	0.270213	0.10349	.	.	ENSG00000154529	ENST00000377561	.	.	.	2.6	-5.2	0.02823	.	.	.	.	.	T	0.15782	0.0380	.	.	.	0.51767	P	6.499999999998174E-5	.	.	.	.	.	.	T	0.22034	-1.0228	3	.	.	.	.	0.8201	0.01109	0.4314:0.1307:0.1593:0.2786	.	.	.	.	C	505	.	.	Y	+	2	0	CNTNAP3B	43768108	0.072000	0.21174	0.010000	0.14722	0.245000	0.25701	-0.184000	0.09698	-1.395000	0.02074	-1.123000	0.02005	TAT		0.458	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
EIF2B4	8890	mdanderson.org	37	2	27592316	27592316	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:27592316T>C	ENST00000347454.4	-	3	347	c.176A>G	c.(175-177)gAg>gGg	p.E59G	EIF2B4_ENST00000451130.2_Missense_Mutation_p.E80G|EIF2B4_ENST00000445933.2_Missense_Mutation_p.E59G|EIF2B4_ENST00000493344.2_Missense_Mutation_p.E80G|SNX17_ENST00000542478.1_5'Flank|SNX17_ENST00000537606.1_5'Flank|AC074117.10_ENST00000412749.1_RNA|SNX17_ENST00000543024.1_5'Flank|SNX17_ENST00000233575.2_5'Flank	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	59					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation (GO:0045947)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translation (GO:0006417)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(5)|skin(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGCCAGTCTCTGGTTCTGC	0.522																																						.											0													233.0	194.0	207.0					2																	27592316		2203	4300	6503	SO:0001583	missense	8890			AJ011306	CCDS33164.1, CCDS46244.1, CCDS46245.1	2p23.3	2008-02-05	2002-08-29		ENSG00000115211	ENSG00000115211			3260	protein-coding gene	gene with protein product		606687	"""eukaryotic translation initiation factor 2B, subunit 4 (delta, 67kD)"""			8929216, 7982969	Standard	NM_172195		Approved	EIF2Bdelta, EIF-2B, DKFZP586J0119, EIF2B	uc002rjz.3	Q9UI10	OTTHUMG00000151927	ENST00000347454.4:c.176A>G	2.37:g.27592316T>C	ENSP00000233552:p.Glu59Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Missense_Mutation	SNP	ENST00000347454.4	37	CCDS33164.1	.	.	.	.	.	.	.	.	.	.	T	19.52	3.843101	0.71488	.	.	ENSG00000115211	ENST00000347454;ENST00000414437;ENST00000445933;ENST00000451130;ENST00000493344	D;D;D;D	0.94828	-3.53;-3.53;-3.53;-3.53	4.87	3.65	0.41850	.	0.570797	0.19966	N	0.102106	D	0.91583	0.7341	L	0.46157	1.445	0.47441	D	0.999425	P;B;B;B;B	0.44139	0.827;0.277;0.277;0.181;0.277	B;B;B;B;B	0.44133	0.442;0.053;0.053;0.024;0.053	D	0.90164	0.4230	10	0.45353	T	0.12	-3.4995	8.6998	0.34318	0.0:0.0:0.191:0.809	.	53;57;59;59;80	Q59FC8;F5H6W1;Q9UI10-3;Q9UI10;Q9UI10-2	.;.;.;EI2BD_HUMAN;.	G	59;57;59;80;80	ENSP00000233552:E59G;ENSP00000394397:E59G;ENSP00000394869:E80G;ENSP00000429323:E80G	ENSP00000233552:E59G	E	-	2	0	EIF2B4	27445820	0.006000	0.16342	0.169000	0.22859	0.969000	0.65631	0.807000	0.27140	2.049000	0.60858	0.459000	0.35465	GAG		0.522	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1		
FOXJ1	2302	mdanderson.org	37	17	74133974	74133974	+	Silent	SNP	C	C	T	rs894542	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr17:74133974C>T	ENST00000322957.6	-	3	1080	c.726G>A	c.(724-726)acG>acA	p.T242T	RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	242					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			CGGTATTCACCGTCAGCGGCC	0.716													C|||	385	0.076877	0.0431	0.134	5008	,	,		12954	0.0347		0.1103	False		,,,				2504	0.091					.											0								C		156,3988		3,150,1919	4.0	6.0	5.0		726	1.5	1.0	17	dbSNP_86	5	700,7392		28,644,3374	no	coding-synonymous	FOXJ1	NM_001454.3		31,794,5293	TT,TC,CC		8.6505,3.7645,6.9958		242/422	74133974	856,11380	2072	4046	6118	SO:0001819	synonymous_variant	2302			X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"""Forkhead boxes"""	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.726G>A	17.37:g.74133974C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O00630	Silent	SNP	ENST00000322957.6	37	CCDS32739.1																																																																																				0.716	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454	
HSP90AB1	3326	mdanderson.org	37	6	44221265	44221265	+	Missense_Mutation	SNP	C	C	A	rs200104342	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr6:44221265C>A	ENST00000371554.1	+	12	2319	c.2105C>A	c.(2104-2106)gCt>gAt	p.A702D	SLC35B2_ENST00000495706.1_5'Flank|HSP90AB1_ENST00000371646.5_Missense_Mutation_p.A702D|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.A702D|MIR4647_ENST00000583964.1_RNA			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	702					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GAACCCAATGCTGCAGTTCCT	0.458											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										.											0													75.0	76.0	76.0					6																	44221265		2203	4300	6503	SO:0001583	missense	3326			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2105C>A	6.37:g.44221265C>A	ENSP00000360609:p.Ala702Asp	Somatic	922	WXS	Illumina HiSeq	Phase_I	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920870	0.52653	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.09350	2.99;2.99;2.99	3.9	3.9	0.45041	.	0.750751	0.11539	U	0.553976	T	0.07188	0.0182	M	0.68593	2.085	0.51767	D	0.999931	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.20577	0.03;0.013;0.005	T	0.05354	-1.0890	10	0.33940	T	0.23	-11.1759	12.1165	0.53868	0.0:0.9118:0.0:0.0882	.	664;692;702	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	D	702	ENSP00000360709:A702D;ENSP00000325875:A702D;ENSP00000360609:A702D	ENSP00000325875:A702D	A	+	2	0	HSP90AB1	44329243	0.999000	0.42202	1.000000	0.80357	0.877000	0.50540	3.853000	0.55941	2.183000	0.69458	0.603000	0.83216	GCT		0.458	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
MUC4	4585	mdanderson.org	37	3	195505772	195505772	+	Missense_Mutation	SNP	C	C	G	rs556354486		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:195505772C>G	ENST00000463781.3	-	2	13138	c.12679G>C	c.(12679-12681)Gtc>Ctc	p.V4227L	MUC4_ENST00000475231.1_Missense_Mutation_p.V4227L|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	984					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V4227L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGCTGGTGACAGGAAGAGGG	0.582													.|||	1	0.000199681	0.0	0.0	5008	,	,		15508	0.0		0.001	False		,,,				2504	0.0					.											1	Substitution - Missense(1)	lung(1)																																								SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12679G>C	3.37:g.195505772C>G	ENSP00000417498:p.Val4227Leu	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	5.247	0.230981	0.09969	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.6	1.57	0.566	0.17317	.	.	.	.	.	T	0.14227	0.0344	N	0.14661	0.345	0.19300	N	0.999978	B	0.27765	0.188	B	0.22601	0.04	T	0.27640	-1.0068	8	.	.	.	.	5.595	0.17321	0.0:0.6491:0.3509:0.0	.	4099	E7ESK3	.	L	4227	ENSP00000417498:V4227L;ENSP00000420243:V4227L	.	V	-	1	0	MUC4	196990551	0.000000	0.05858	0.020000	0.16555	0.011000	0.07611	-0.070000	0.11523	0.201000	0.20466	0.484000	0.47621	GTC		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NAMPT	10135	mdanderson.org	37	7	105903965	105903965	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr7:105903965T>C	ENST00000222553.3	-	7	1149	c.842A>G	c.(841-843)tAt>tGt	p.Y281C	NAMPT_ENST00000354289.4_Missense_Mutation_p.Y281C	NM_005746.2	NP_005737.1	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	281					cell-cell signaling (GO:0007267)|circadian regulation of gene expression (GO:0032922)|NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|nicotinamide metabolic process (GO:0006769)|positive regulation of cell proliferation (GO:0008284)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|nicotinamide phosphoribosyltransferase activity (GO:0047280)|nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						ATAAATGTCATAGCTATCGCT	0.378																																						.											0													126.0	118.0	120.0					7																	105903965		2203	4300	6503	SO:0001583	missense	10135			U02020	CCDS5737.1	7q22.3	2012-10-02	2008-03-27	2008-03-27	ENSG00000105835	ENSG00000105835			30092	protein-coding gene	gene with protein product	"""visfatin"""	608764	"""pre-B-cell colony enhancing factor 1"""	PBEF1		8289818	Standard	NM_005746		Approved	PBEF	uc003vdq.3	P43490	OTTHUMG00000140388	ENST00000222553.3:c.842A>G	7.37:g.105903965T>C	ENSP00000222553:p.Tyr281Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A4D0Q9|A4D0R0|Q3KQV0|Q8WW95	Missense_Mutation	SNP	ENST00000222553.3	37	CCDS5737.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402609	0.83230	.	.	ENSG00000105835	ENST00000222553;ENST00000354289	.	.	.	5.54	5.54	0.83059	Quinolinate phosphoribosyl transferase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87200	0.6118	H	0.95539	3.685	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	D	0.91052	0.4879	9	0.87932	D	0	-0.9235	15.9649	0.79961	0.0:0.0:0.0:1.0	.	194;262;281	B7Z8W6;Q5SYT8;P43490	.;.;NAMPT_HUMAN	C	281	.	ENSP00000222553:Y281C	Y	-	2	0	NAMPT	105691201	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.655000	0.83696	2.232000	0.73038	0.533000	0.62120	TAT		0.378	NAMPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277146.1	NM_182790	
NBPF10	100132406	mdanderson.org	37	1	145299805	145299805	+	Missense_Mutation	SNP	A	A	C	rs61814629	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:145299805A>C	ENST00000369338.1	+	2	231	c.41A>C	c.(40-42)gAg>gCg	p.E14A	NBPF10_ENST00000342960.5_Missense_Mutation_p.E285A|NBPF10_ENST00000369339.3_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	285						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.E285A(1)|p.E14A(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAGAAGGCAGAGATGAACATT	0.493													.|||	179	0.0357428	0.0015	0.0231	5008	,	,		43597	0.0635		0.0487	False		,,,				2504	0.0491					.											2	Substitution - Missense(2)	skin(2)											9.0	8.0	8.0					1																	145299805		690	1570	2260	SO:0001583	missense	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.41A>C	1.37:g.145299805A>C	ENSP00000358344:p.Glu14Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	11.71	1.719994	0.30503	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.03663	3.85;3.85	1.05	1.05	0.20165	.	.	.	.	.	T	0.03095	0.0091	M	0.74647	2.275	0.09310	N	1	P	0.37398	0.593	P	0.45577	0.486	T	0.39941	-0.9589	9	0.66056	D	0.02	.	4.3442	0.11124	1.0:0.0:0.0:0.0	rs61814629	14	Q86T75-2	.	A	210;14;14;285	ENSP00000358344:E14A;ENSP00000345684:E285A	ENSP00000345684:E285A	E	+	2	0	NBPF10	144011162	0.002000	0.14202	0.003000	0.11579	0.032000	0.12392	-0.314000	0.08092	0.731000	0.32448	0.234000	0.17832	GAG		0.493	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
PABPC1	26986	mdanderson.org	37	8	101730065	101730065	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr8:101730065T>C	ENST00000318607.5	-	3	1567	c.439A>G	c.(439-441)Acg>Gcg	p.T147A	PABPC1_ENST00000519004.1_Missense_Mutation_p.T102A|PABPC1_ENST00000522387.1_Missense_Mutation_p.T115A|PABPC1_ENST00000519596.1_5'Flank	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	147	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GCTTCCTGCGTCTCAAAGTGT	0.333																																						.											0													92.0	87.0	89.0					8																	101730065		2203	4300	6503	SO:0001583	missense	26986			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.439A>G	8.37:g.101730065T>C	ENSP00000313007:p.Thr147Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.3|20.3	3.960720|3.960720	0.74016|0.74016	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000523555|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000518196	.|D;D;T;T	.|0.87256	.|-2.23;-2.23;2.25;2.25	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.64402	.|D	.|0.000003	D|D	0.85775|0.85775	0.5775|0.5775	L|L	0.31804|0.31804	0.96|0.96	0.58432|0.58432	D|D	0.999999|0.999999	.|P;B;P	.|0.46020	.|0.535;0.309;0.871	.|P;B;P	.|0.49451	.|0.611;0.135;0.513	D|D	0.87858|0.87858	0.2662|0.2662	5|10	.|0.87932	.|D	.|0	.|.	15.6618|15.6618	0.77193|0.77193	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|115;147;147	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	G|A	93|147;147;102;115;102	.|ENSP00000313007:T147A;ENSP00000429594:T102A;ENSP00000429395:T115A;ENSP00000430159:T102A	.|ENSP00000313007:T147A	D|T	-|-	2|1	0|0	PABPC1|PABPC1	101799241|101799241	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	8.010000|8.010000	0.88615|0.88615	2.167000|2.167000	0.68274|0.68274	0.528000|0.528000	0.53228|0.53228	GAC|ACG		0.333	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
PI4KAP2	375133	mdanderson.org	37	22	21829555	21829555	+	RNA	SNP	T	T	G	rs377578228		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr22:21829555T>G	ENST00000450651.1	-	0	1783							A4QPH2	PI4P2_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha pseudogene 2						phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.I530L(4)		endometrium(3)|urinary_tract(1)	4						TCCAACATGATAGTGACCAGG	0.607																																						.											4	Substitution - Missense(4)	endometrium(3)|urinary_tract(1)											26.0	21.0	23.0					22																	21829555		692	1582	2274			375133					22q11.21	2014-03-20	2007-08-14		ENSG00000183506	ENSG00000183506			33577	pseudogene	pseudogene							Standard	NR_003700		Approved		uc011aie.1	A4QPH2	OTTHUMG00000150827		22.37:g.21829555T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	SNP	ENST00000450651.1	37																																																																																					0.607	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
PLEKHM1	9842	mdanderson.org	37	17	43531297	43531297	+	Missense_Mutation	SNP	G	G	A	rs2684501		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr17:43531297G>A	ENST00000430334.3	-	7	2054	c.1921C>T	c.(1921-1923)Cca>Tca	p.P641S	AC091132.1_ENST00000433601.1_RNA|PLEKHM1_ENST00000421073.2_Missense_Mutation_p.P552S	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	641					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GGCTGGTCTGGGTACTGCACG	0.682																																						.											0													34.0	40.0	38.0					17																	43531297		2202	4299	6501	SO:0001583	missense	9842			X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.1921C>T	17.37:g.43531297G>A	ENSP00000389913:p.Pro641Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	37	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	G	7.679	0.688696	0.14973	.	.	ENSG00000225190	ENST00000430334;ENST00000446609;ENST00000421073	T;T	0.64991	-0.13;-0.13	4.8	3.84	0.44239	.	0.460522	0.24649	N	0.036725	T	0.50735	0.1633	L	0.46157	1.445	0.27650	N	0.947413	P;P;P	0.48503	0.831;0.911;0.741	B;B;B	0.39840	0.209;0.311;0.104	T	0.44081	-0.9351	10	0.21014	T	0.42	.	11.4789	0.50314	0.0876:0.0:0.9124:0.0	rs2684501	552;590;641	F8W648;B4DRX1;Q9Y4G2	.;.;PKHM1_HUMAN	S	641;590;552	ENSP00000389913:P641S;ENSP00000414352:P552S	ENSP00000414352:P552S	P	-	1	0	PLEKHM1	40887080	0.611000	0.26992	0.608000	0.28969	0.466000	0.32739	1.220000	0.32491	1.262000	0.44165	0.586000	0.80456	CCA		0.682	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
RBMXL1	494115	mdanderson.org	37	1	89448940	89448940	+	Silent	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:89448940A>G	ENST00000321792.5	-	2	997	c.570T>C	c.(568-570)taT>taC	p.Y190Y	RBMXL1_ENST00000399794.2_Silent_p.Y190Y|RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370485.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	190					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										GTGGACCTCCATAACTATCTC	0.502																																						.											0													175.0	174.0	174.0					1																	89448940		2203	4300	6503	SO:0001819	synonymous_variant	494115			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.570T>C	1.37:g.89448940A>G		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000321792.5	37	CCDS716.1																																																																																				0.502	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
SLC25A45	283130	mdanderson.org;bcgsc.ca	37	11	65144406	65144406	+	Missense_Mutation	SNP	G	G	A	rs34377244	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:65144406G>A	ENST00000527174.1	-	5	536	c.481C>T	c.(481-483)Cgg>Tgg	p.R161W	SLC25A45_ENST00000360662.3_Missense_Mutation_p.R137W|SLC25A45_ENST00000526432.1_Missense_Mutation_p.R99W|SLC25A45_ENST00000417511.2_Missense_Mutation_p.R119W|SLC25A45_ENST00000294187.6_Missense_Mutation_p.R119W|RP11-867O8.5_ENST00000533886.1_RNA|SLC25A45_ENST00000534028.1_Missense_Mutation_p.R137W|SLC25A45_ENST00000377152.2_Missense_Mutation_p.R57W|SLC25A45_ENST00000398802.1_Missense_Mutation_p.R161W			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	161					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						AACAGCCCCCGGGGCCCCTCC	0.672													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		14885	0.0		0.0	False		,,,				2504	0.0					.											0								G	TRP/ARG,TRP/ARG	39,3711		0,39,1836	38.0	42.0	40.0		355,481	1.0	0.2	11	dbSNP_126	40	0,8204		0,0,4102	no	missense,missense	SLC25A45	NM_001077241.1,NM_182556.2	101,101	0,39,5938	AA,AG,GG		0.0,1.04,0.3263	benign,benign	119/247,161/289	65144406	39,11915	1875	4102	5977	SO:0001583	missense	283130			BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"""Solute carriers"""	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.481C>T	11.37:g.65144406G>A	ENSP00000435489:p.Arg161Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	14	0.00641025641025641	9	0.018292682926829267	5	0.013812154696132596	0	0.0	0	0.0	G	11.01	1.514063	0.27123	0.0104	0.0	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	T;T;T;T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	5.23	1.02	0.19986	Mitochondrial carrier domain (2);	0.754501	0.12173	N	0.492860	T	0.64789	0.2630	M	0.83118	2.625	0.09310	N	1	B;B;B	0.22800	0.027;0.027;0.075	B;B;B	0.21546	0.029;0.013;0.035	T	0.63229	-0.6684	10	0.40728	T	0.16	-1.2411	3.8445	0.08928	0.2378:0.0:0.4608:0.3015	rs34377244	99;137;161	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	W	161;137;161;137;57;119;119;99	ENSP00000435489:R161W;ENSP00000431769:R137W;ENSP00000381782:R161W;ENSP00000353879:R137W;ENSP00000366357:R57W;ENSP00000294187:R119W;ENSP00000407530:R119W;ENSP00000435547:R99W	ENSP00000294187:R119W	R	-	1	2	SLC25A45	64900982	0.000000	0.05858	0.177000	0.23020	0.632000	0.37999	0.441000	0.21611	0.267000	0.21916	0.561000	0.74099	CGG		0.672	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556	
TRIM49	57093	mdanderson.org	37	11	89537461	89537461	+	Silent	SNP	G	G	T	rs368472876		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:89537461G>T	ENST00000329758.1	-	3	505	c.177C>A	c.(175-177)acC>acA	p.T59T	TRIM49_ENST00000532501.2_Silent_p.T59T	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	59						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				TTATCTGCTCGGTTGACTTTG	0.458																																						.											0													140.0	125.0	130.0					11																	89537461		2191	4297	6488	SO:0001819	synonymous_variant	57093			AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13431	protein-coding gene	gene with protein product		606124	"""ring finger protein 18"", ""tripartite motif-containing 49"""	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.177C>A	11.37:g.89537461G>T		Somatic		WXS	Illumina HiSeq	Phase_I	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Silent	SNP	ENST00000329758.1	37	CCDS8287.1																																																																																				0.458	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358	
ZFHX4	79776	mdanderson.org;bcgsc.ca	37	8	77763346	77763346	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr8:77763346T>C	ENST00000521891.2	+	10	4637	c.4189T>C	c.(4189-4191)Tat>Cat	p.Y1397H	ZFHX4_ENST00000518282.1_Missense_Mutation_p.Y1371H|ZFHX4_ENST00000455469.2_Missense_Mutation_p.Y1352H|ZFHX4_ENST00000050961.6_Missense_Mutation_p.Y1352H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1352					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGTCTACAAGTATCGCTGTAA	0.433										HNSCC(33;0.089)																												.											0													94.0	89.0	90.0					8																	77763346		1894	4118	6012	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4189T>C	8.37:g.77763346T>C	ENSP00000430497:p.Tyr1397His	Somatic		WXS	Illumina HiSeq	Phase_I	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	T	12.95	2.091083	0.36855	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.40469	U	0.001088	T	0.44787	0.1310	M	0.83953	2.67	0.49582	D	0.999804	B;B;B	0.14438	0.006;0.01;0.01	B;B;B	0.17722	0.005;0.019;0.019	T	0.51004	-0.8760	10	0.72032	D	0.01	.	14.5713	0.68213	0.0:0.0:0.0:1.0	.	1352;1352;1397	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	H	1397;1397;1352;1352;1371	ENSP00000430497:Y1397H;ENSP00000399605:Y1352H;ENSP00000050961:Y1352H;ENSP00000430848:Y1371H	ENSP00000050961:Y1352H	Y	+	1	0	ZFHX4	77925901	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.086000	0.71352	2.096000	0.63516	0.454000	0.30748	TAT		0.433	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
TPR	7175	bcgsc.ca	37	1	186283126	186283126	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr1:186283126T>C	ENST00000367478.4	-	51	7365	c.7069A>G	c.(7069-7071)Ata>Gta	p.I2357V	PRG4_ENST00000445192.2_3'UTR|PRG4_ENST00000367486.3_3'UTR|PRG4_ENST00000367485.4_3'UTR|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367484.3_3'UTR|PRG4_ENST00000367483.4_3'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2357					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CCTCTGTTTATTCCTCCTCTC	0.294			T	NTRK1	papillary thyroid																																	.		Dom	yes		1	1q25	7175	translocated promoter region		E	0													102.0	101.0	102.0					1																	186283126		1816	4073	5889	SO:0001583	missense	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.7069A>G	1.37:g.186283126T>C	ENSP00000356448:p.Ile2357Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.694038	0.30052	.	.	ENSG00000047410	ENST00000367478	T	0.23147	1.92	5.79	3.47	0.39725	.	0.407546	0.27816	N	0.017721	T	0.19644	0.0472	L	0.36672	1.1	0.28273	N	0.924309	B	0.13594	0.008	B	0.12156	0.007	T	0.13150	-1.0520	10	0.21014	T	0.42	.	12.5726	0.56344	0.0:0.0:0.3977:0.6023	.	2357	P12270	TPR_HUMAN	V	2357	ENSP00000356448:I2357V	ENSP00000356448:I2357V	I	-	1	0	TPR	184549749	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.572000	0.36461	0.981000	0.38548	0.528000	0.53228	ATA		0.294	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
RCN1	5954	bcgsc.ca	37	11	32118785	32118785	+	Frame_Shift_Del	DEL	T	T	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:32118785delT	ENST00000054950.3	+	2	643	c.350delT	c.(349-351)tttfs	p.F117fs	RCN1_ENST00000532942.1_Frame_Shift_Del_p.F66fs|RP1-65P5.3_ENST00000533009.1_RNA	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	117	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		F -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					AGATACATCTTTGATAATGTC	0.423																																						.											0													63.0	57.0	59.0					11																	32118785		2202	4296	6498	SO:0001589	frameshift_variant	5954			D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"""EF-hand domain containing"""	9934	protein-coding gene	gene with protein product	"""proliferation-inducing gene 20"""	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.350delT	11.37:g.32118785delT	ENSP00000054950:p.Phe117fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z1M1|D3DR00	Frame_Shift_Del	DEL	ENST00000054950.3	37	CCDS7876.1																																																																																				0.423	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901	
CHRDL2	25884	bcgsc.ca	37	11	74408314	74408317	+	Frame_Shift_Del	DEL	CTTT	CTTT	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	CTTT	CTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr11:74408314_74408317delCTTT	ENST00000376332.3	-	10	1642_1645	c.1146_1149delAAAG	c.(1144-1149)aaaaagfs	p.KK382fs	CHRDL2_ENST00000263671.5_Frame_Shift_Del_p.KG401fs	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	382					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					GCTTCCTGACTTTCTTGATCTGAG	0.544																																						.											0																																										SO:0001589	frameshift_variant	25884			AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.1146_1149delAAAG	11.37:g.74408314_74408317delCTTT	ENSP00000365510:p.Lys382fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Frame_Shift_Del	DEL	ENST00000376332.3	37																																																																																					0.544	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
TMC5	79838	bcgsc.ca	37	16	19509242	19509242	+	Splice_Site	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr16:19509242A>G	ENST00000396229.2	+	22	3724	c.2975A>G	c.(2974-2976)gAc>gGc	p.D992G	TMC5_ENST00000542583.2_Splice_Site_p.D992G|TMC5_ENST00000564959.1_Splice_Site_p.D675G|TMC5_ENST00000219821.5_Splice_Site_p.D746G|TMC5_ENST00000561503.1_Splice_Site_p.D633G|RNU4-46P_ENST00000410818.1_RNA|TMC5_ENST00000381414.4_Splice_Site_p.D934G|TMC5_ENST00000541464.1_Splice_Site_p.D940G	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	992					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TCAAACCTAGACTTGCGATCT	0.458																																						.											0													302.0	266.0	278.0					16																	19509242		2197	4300	6497	SO:0001630	splice_region_variant	79838			AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2975-1A>G	16.37:g.19509242A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.27|12.27	1.888056|1.888056	0.33348|0.33348	.|.	.|.	ENSG00000103534|ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821|ENST00000440743	T;T;T;T;T|.	0.69561|.	-0.2;-0.34;-0.31;-0.31;-0.41|.	4.44|4.44	3.35|3.35	0.38373|0.38373	.|.	911.436000|.	0.00913|.	N|.	0.002494|.	T|T	0.48003|0.48003	0.1476|0.1476	L|L	0.44542|0.44542	1.39|1.39	0.34702|0.34702	D|D	0.72684|0.72684	D;D;D;D|.	0.89917|.	1.0;0.998;1.0;1.0|.	D;D;D;D|.	0.87578|.	0.998;0.937;0.996;0.998|.	T|T	0.55573|0.55573	-0.8120|-0.8120	9|5	.|.	.|.	.|.	.|.	6.9366|6.9366	0.24470|0.24470	0.8973:0.0:0.1027:0.0|0.8973:0.0:0.1027:0.0	.|.	940;746;992;934|.	F5GYU8;Q6UXY8-3;Q6UXY8;Q6UXY8-2|.	.;.;TMC5_HUMAN;.|.	G|A	940;934;992;992;746|675	ENSP00000441227:D940G;ENSP00000370822:D934G;ENSP00000379531:D992G;ENSP00000446274:D992G;ENSP00000219821:D746G|.	.|.	D|T	+|+	2|1	0|0	TMC5|TMC5	19416743|19416743	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.032000|0.032000	0.12392|0.12392	3.612000|3.612000	0.54142|0.54142	1.022000|1.022000	0.39626|0.39626	-0.290000|-0.290000	0.09829|0.09829	GAC|ACT		0.458	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	Missense_Mutation
IMMT	10989	bcgsc.ca	37	2	86408441	86408441	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr2:86408441A>G	ENST00000410111.3	-	2	487	c.100T>C	c.(100-102)Tct>Cct	p.S34P	IMMT_ENST00000442664.2_Missense_Mutation_p.S34P|IMMT_ENST00000449247.2_Missense_Mutation_p.S34P|IMMT_ENST00000254636.5_5'UTR|IMMT_ENST00000409051.2_Missense_Mutation_p.S34P	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	34					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCTGAAGTAGAGTATCTGCGG	0.443																																						.											0													73.0	71.0	72.0					2																	86408441		1931	4130	6061	SO:0001583	missense	10989			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.100T>C	2.37:g.86408441A>G	ENSP00000387262:p.Ser34Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	A	14.42	2.529243	0.44969	.	.	ENSG00000132305	ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	T;T;T;T	0.37058	1.22;1.24;1.24;1.3	5.55	5.55	0.83447	.	0.178411	0.50627	D	0.000117	T	0.34454	0.0898	L	0.27053	0.805	0.35412	D	0.792516	B;B;B;D;B;B;B;B;B	0.53462	0.003;0.001;0.002;0.96;0.02;0.005;0.003;0.005;0.002	B;B;B;P;B;B;B;B;B	0.49451	0.018;0.003;0.008;0.611;0.026;0.03;0.018;0.03;0.008	T	0.49409	-0.8943	10	0.59425	D	0.04	-12.2889	12.1652	0.54125	0.8575:0.1425:0.0:0.0	.	34;34;34;34;34;34;34;34;34	F5GZ32;B9A067;B4DKR1;Q05DN3;B4E2B5;F8W9I1;Q16891-2;Q16891-3;Q16891	.;.;.;.;.;.;.;.;IMMT_HUMAN	P	34	ENSP00000396899:S34P;ENSP00000387262:S34P;ENSP00000407788:S34P;ENSP00000387227:S34P	ENSP00000366526:S34P	S	-	1	0	IMMT	86261952	1.000000	0.71417	0.997000	0.53966	0.887000	0.51463	3.512000	0.53407	2.118000	0.64928	0.533000	0.62120	TCT		0.443	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
ZNF133	7692	bcgsc.ca	37	20	18295937	18295951	+	In_Frame_Del	DEL	GGGAGAAGGTGCCAT	GGGAGAAGGTGCCAT	-	rs139158783		TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	GGGAGAAGGTGCCAT	GGGAGAAGGTGCCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr20:18295937_18295951delGGGAGAAGGTGCCAT	ENST00000316358.4	+	4	539_553	c.442_456delGGGAGAAGGTGCCAT	c.(442-456)gggagaaggtgccatdel	p.GRRCH148del	ZNF133_ENST00000535822.1_In_Frame_Del_p.GRRCH53del|ZNF133_ENST00000396026.3_In_Frame_Del_p.GRRCH151del|ZNF133_ENST00000377671.3_In_Frame_Del_p.GRRCH147del|ZNF133_ENST00000538547.1_In_Frame_Del_p.GRRCH53del|ZNF133_ENST00000401790.1_In_Frame_Del_p.GRRCH148del|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000402618.2_In_Frame_Del_p.GRRCH85del|RP4-568F9.3_ENST00000436848.1_RNA	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	148					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						AGGTCCTGAGGGAGAAGGTGCCATGCCTTTGTTTG	0.6																																						.											0																																										SO:0001651	inframe_deletion	7692			AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.442_456delGGGAGAAGGTGCCAT	20.37:g.18295937_18295951delGGGAGAAGGTGCCAT	ENSP00000346090:p.Gly148_His152del	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	In_Frame_Del	DEL	ENST00000316358.4	37																																																																																					0.600	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
POU1F1	5449	bcgsc.ca	37	3	87311219	87311219	+	Splice_Site	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr3:87311219A>G	ENST00000350375.2	-	4	729		c.e4+1		POU1F1_ENST00000560656.1_Intron|POU1F1_ENST00000344265.3_Splice_Site	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1						B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		ACAATTTAGTACCTCCTACTT	0.388																																						.											0													119.0	112.0	115.0					3																	87311219		2203	4300	6503	SO:0001630	splice_region_variant	5449			D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"""Homeoboxes / POU class"""	9210	protein-coding gene	gene with protein product	"""growth hormone factor 1"""	173110	"""POU domain class 1, transcription factor 1"""	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.604+1T>C	3.37:g.87311219A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Splice_Site	SNP	ENST00000350375.2	37	CCDS2919.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560317	0.45590	.	.	ENSG00000064835	ENST00000350375;ENST00000344265	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3807	0.60766	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	POU1F1	87393909	1.000000	0.71417	0.996000	0.52242	0.541000	0.35023	7.146000	0.77373	2.257000	0.74773	0.528000	0.53228	.		0.388	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306	Intron
CRIPAK	285464	bcgsc.ca	37	4	1388697	1388697	+	Missense_Mutation	SNP	C	C	T	rs113316888	byFrequency	TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr4:1388697C>T	ENST00000324803.4	+	1	3358	c.398C>T	c.(397-399)gCg>gTg	p.A133V		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	133					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGCGGAGTGCCCG	0.701													N|||	623	0.124401	0.1399	0.1527	5008	,	,		12463	0.2083		0.0736	False		,,,				2504	0.0491					.											0													57.0	58.0	58.0					4																	1388697		2192	4288	6480	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.398C>T	4.37:g.1388697C>T	ENSP00000323978:p.Ala133Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	11.32	1.604146	0.28534	.	.	ENSG00000179979	ENST00000324803	T	0.18810	2.19	0.948	-1.08	0.09936	.	.	.	.	.	T	0.06645	0.0170	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	9	0.02654	T	1	.	2.1758	0.03862	0.2485:0.1979:0.0:0.5536	.	133	Q8N1N5	CRPAK_HUMAN	V	133	ENSP00000323978:A133V	ENSP00000323978:A133V	A	+	2	0	CRIPAK	1378697	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-2.200000	0.01237	-1.804000	0.01241	-1.950000	0.00486	GCG		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CD109	135228	bcgsc.ca	37	6	74468723	74468723	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chr6:74468723A>G	ENST00000287097.5	+	7	842	c.730A>G	c.(730-732)Aag>Gag	p.K244E	CD109_ENST00000437994.2_Missense_Mutation_p.K244E|CD109_ENST00000422508.2_Missense_Mutation_p.K167E			Q6YHK3	CD109_HUMAN	CD109 molecule	244					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TATGAATTCTAAGCATTTAAA	0.313																																						.											0													84.0	81.0	82.0					6																	74468723		2203	4297	6500	SO:0001583	missense	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.730A>G	6.37:g.74468723A>G	ENSP00000287097:p.Lys244Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	A	2.464	-0.323558	0.05350	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.19938	2.11;2.28;2.11	5.16	3.99	0.46301	.	1.797440	0.02279	N	0.069181	T	0.04092	0.0114	N	0.21282	0.65	0.09310	N	1	B;B;B;B	0.15141	0.012;0.003;0.0;0.004	B;B;B;B	0.15052	0.005;0.012;0.005;0.003	T	0.32107	-0.9919	10	0.07990	T	0.79	.	6.4719	0.22013	0.7626:0.1561:0.0813:0.0	.	167;244;244;244	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	E	244;167;244	ENSP00000388062:K244E;ENSP00000404475:K167E;ENSP00000287097:K244E	ENSP00000287097:K244E	K	+	1	0	CD109	74525444	0.418000	0.25440	0.297000	0.24988	0.653000	0.38743	1.828000	0.39111	0.984000	0.38629	0.379000	0.24179	AAG		0.313	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
MT-ND5	4540	bcgsc.ca	37	M	12631	12631	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chrM:12631T>C	ENST00000361567.2	+	1	295	c.295T>C	c.(295-297)Tcc>Ccc	p.S99P	MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	99			S -> P. {ECO:0000269|PubMed:1757091}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCGTTACATGGTCCATCATAG	0.373																																						.											0																																										SO:0001583	missense	0					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.295T>C	M.37:g.12631T>C	ENSP00000354813:p.Ser99Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																					0.373	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
DMD	1756	bcgsc.ca	37	X	31198541	31198551	+	Frame_Shift_Del	DEL	GACCAGAAAAA	GACCAGAAAAA	-			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	GACCAGAAAAA	GACCAGAAAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chrX:31198541_31198551delGACCAGAAAAA	ENST00000357033.4	-	69	10228_10238	c.10022_10032delTTTTTCTGGTC	c.(10021-10032)ttttttctggtcfs	p.FFLV3341fs	DMD_ENST00000361471.4_Frame_Shift_Del_p.FFLV273fs|DMD_ENST00000343523.2_Frame_Shift_Del_p.FFLV881fs|DMD_ENST00000541735.1_Frame_Shift_Del_p.FFLV881fs|DMD_ENST00000474231.1_Frame_Shift_Del_p.FFLV881fs|DMD_ENST00000378707.3_Frame_Shift_Del_p.FFLV881fs|DMD_ENST00000359836.1_Frame_Shift_Del_p.FFLV881fs|DMD_ENST00000378723.3_Frame_Shift_Del_p.FFLV273fs|DMD_ENST00000378702.4_Frame_Shift_Del_p.FFLV273fs|DMD_ENST00000378677.2_Frame_Shift_Del_p.FFLV3337fs|DMD_ENST00000378680.2_Frame_Shift_Del_p.FFLV273fs	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3341	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTGCAACTCGACCAGAAAAAAAGCAGCTTTG	0.412																																						.											0			GRCh37	CI040202	DMD	I																																				SO:0001589	frameshift_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10022_10032delTTTTTCTGGTC	X.37:g.31198541_31198551delGACCAGAAAAA	ENSP00000354923:p.Phe3341fs	Somatic		WXS	Illumina HiSeq	Phase_I	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Del	DEL	ENST00000357033.4	37	CCDS14233.1																																																																																				0.412	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
MT-ND1	4535	bcgsc.ca	37	M	3566	3567	+	Frame_Shift_Ins	INS	-	-	C			TCGA-KL-8343-01A-11D-2310-10	TCGA-KL-8343-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	34739bd6-b3be-441d-8cdb-e4233bf14080	25275f7f-a079-4c74-bec8-33b107316d1b	g.chrM:3566_3567insC	ENST00000361390.2	+	1	260_261	c.260_261insC	c.(259-264)acccccfs	p.TP87fs	MT-RNR1_ENST00000389680.2_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TV_ENST00000387342.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	87			T -> A. {ECO:0000269|PubMed:7530363}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TCTACTATGAACCCCCCTCCCC	0.53																																						.											0																																										SO:0001589	frameshift_variant	10625					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.265dupC	M.37:g.3572_3572dupC	ENSP00000354687:p.Thr87fs	Somatic		WXS	Illumina HiSeq	Phase_I	C0JKH6|Q37523	Frame_Shift_Ins	INS	ENST00000361390.2	37																																																																																					0.530	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
