#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_ORegAnno_bin	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
ATAD3B	83858	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	1	1425803	1425803	+	Splice_Site	SNP	C	C	T	rs371526893		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:1425803C>T	ENST00000308647.7	+	14	1620	c.1504C>T	c.(1504-1506)Cgg>Tgg	p.R502W		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	502						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		AGAAGGAAAACGGTGAGTGTC	0.617																																						.											0								C	TRP/ARG	0,4406		0,0,2203	63.0	53.0	56.0		1504	2.0	1.0	1		56	1,8597		0,1,4298	no	missense-near-splice	ATAD3B	NM_031921.4	101	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	502/649	1425803	1,13003	2203	4299	6502	SO:0001630	splice_region_variant	83858			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1505+1C>T	1.37:g.1425803C>T			A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.89|12.89	2.072670|2.072670	0.36566|0.36566	0.0|0.0	1.16E-4|1.16E-4	ENSG00000160072|ENSG00000160072	ENST00000378737|ENST00000308647	.|T	.|0.20738	.|2.05	2.03|2.03	2.03|2.03	0.26663|0.26663	.|.	0.059036|0.059036	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.28699|0.28699	0.0711|0.0711	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	.|D;P	.|0.69078	.|0.997;0.952	.|P;P	.|0.54924	.|0.764;0.453	T|T	0.08006|0.08006	-1.0743|-1.0743	7|10	0.66056|0.66056	D|D	0.02|0.02	.|.	11.3705|11.3705	0.49697|0.49697	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|456;502	.|Q5T9A4-3;Q5T9A4	.|.;ATD3B_HUMAN	C|W	305|502	.|ENSP00000311766:R502W	ENSP00000368011:R305C|ENSP00000311766:R502W	R|R	+|+	1|1	0|2	ATAD3B|ATAD3B	1415666|1415666	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.013000|0.013000	0.08279|0.08279	7.417000|7.417000	0.80156|0.80156	1.135000|1.135000	0.42183|0.42183	0.194000|0.194000	0.17425|0.17425	CGC|CGG		0.617	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	Missense_Mutation
ZBTB40	9923	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	1	22839532	22839532	+	Silent	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:22839532C>T	ENST00000375647.4	+	12	2784	c.2577C>T	c.(2575-2577)acC>acT	p.T859T	ZBTB40_ENST00000374651.4_Silent_p.T747T|ZBTB40_ENST00000404138.1_Silent_p.T859T	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	859					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		GCCTTCACACCGGGGACCGCC	0.572																																						.											0													85.0	69.0	74.0					1																	22839532		2203	4300	6503	SO:0001819	synonymous_variant	9923			AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.2577C>T	1.37:g.22839532C>T			O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	37	CCDS224.1																																																																																				0.572	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
SPATA5L1	79029	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	15	45707899	45707899	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr15:45707899C>A	ENST00000305560.6	+	5	1858	c.1759C>A	c.(1759-1761)Ctt>Att	p.L587I	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.L587I	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	587						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		AGAACGAGTTCTTTCTGTTCT	0.398																																						.											0													69.0	65.0	66.0					15																	45707899		2198	4298	6496	SO:0001583	missense	79029			AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1759C>A	15.37:g.45707899C>A	ENSP00000305494:p.Leu587Ile		C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	37	CCDS10123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.0|23.0	4.363412|4.363412	0.82353|0.82353	.|.	.|.	ENSG00000171763|ENSG00000171763	ENST00000531624|ENST00000305560	.|D	.|0.93076	.|-3.16	5.54|5.54	4.61|4.61	0.57282|0.57282	.|ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.93815|0.93815	0.8022|0.8022	L|L	0.42529|0.42529	1.33|1.33	0.41337|0.41337	D|D	0.987271|0.987271	.|D	.|0.54397	.|0.966	.|P	.|0.61397	.|0.888	D|D	0.92006|0.92006	0.5614|0.5614	5|10	.|0.21014	.|T	.|0.42	-18.5177|-18.5177	14.7514|14.7514	0.69528|0.69528	0.1461:0.8539:0.0:0.0|0.1461:0.8539:0.0:0.0	.|.	.|587	.|Q9BVQ7	.|SPA5L_HUMAN	L|I	91|587	.|ENSP00000305494:L587I	.|ENSP00000305494:L587I	F|L	+|+	3|1	2|0	SPATA5L1|SPATA5L1	43495191|43495191	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.522000|6.522000	0.73783|0.73783	1.450000|1.450000	0.47717|0.47717	-0.181000|-0.181000	0.13052|0.13052	TTC|CTT		0.398	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
ZNF609	23060	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	15	64966530	64966530	+	Missense_Mutation	SNP	G	G	A	rs200890644		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr15:64966530G>A	ENST00000326648.3	+	4	1605	c.1477G>A	c.(1477-1479)Gtc>Atc	p.V493I	ZNF609_ENST00000559364.1_3'UTR|RNU6-549P_ENST00000384433.1_RNA	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	493						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCCCTCCCCCGTCCTAATTGA	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		18089	0.0		0.0	False		,,,				2504	0.001					.											0								G	ILE/VAL	0,4406		0,0,2203	85.0	70.0	75.0		1477	5.6	1.0	15		75	6,8592	5.0+/-18.6	0,6,4293	yes	missense	ZNF609	NM_015042.1	29	0,6,6496	AA,AG,GG		0.0698,0.0,0.0461	benign	493/1412	64966530	6,12998	2203	4299	6502	SO:0001583	missense	23060			BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"""Zinc fingers, C2H2-type"""	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.1477G>A	15.37:g.64966530G>A	ENSP00000316527:p.Val493Ile		Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	37	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.775434	0.31411	0.0	6.98E-4	ENSG00000180357	ENST00000326648	T	0.53857	0.6	5.61	5.61	0.85477	.	0.108019	0.64402	D	0.000006	T	0.38558	0.1045	L	0.33093	0.98	0.46849	D	0.999221	B	0.10296	0.003	B	0.13407	0.009	T	0.25676	-1.0125	10	0.33940	T	0.23	-11.9829	7.3316	0.26586	0.2008:0.0:0.7992:0.0	.	493	O15014	ZN609_HUMAN	I	493	ENSP00000316527:V493I	ENSP00000316527:V493I	V	+	1	0	ZNF609	62753583	1.000000	0.71417	0.987000	0.45799	0.989000	0.77384	4.442000	0.59988	2.638000	0.89438	0.650000	0.86243	GTC		0.522	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833	
ZFHX3	463	hgsc.bcm.edu	37	16	72991713	72991715	+	In_Frame_Del	DEL	CCA	CCA	-	rs4788682	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr16:72991713_72991715delCCA	ENST00000268489.5	-	2	3002_3004	c.2330_2332delTGG	c.(2329-2334)gtggct>gct	p.V777del	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	777	Poly-Ala.		V -> A (in dbSNP:rs4788682). {ECO:0000269|PubMed:7592926}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V777V(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				gccgccgcagccaccgccgccgc	0.635																																						.											1	Substitution - coding silent(1)	lung(1)							,	1706,1886		582,542,672					,	5.5	0.1			17	4240,2792		1606,1028,882	no	coding,intron	ZFHX3	NM_006885.3,NM_001164766.1	,	2188,1570,1554	A1A1,A1R,RR		39.7042,47.4944,44.0324	,	,		5946,4678				SO:0001651	inframe_deletion	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2330_2332delTGG	16.37:g.72991713_72991715delCCA	ENSP00000268489:p.Val777del		D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	CCDS10908.1																																																																																				0.635	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
TP53	7157	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	17	7577114	7577114	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr17:7577114C>T	ENST00000269305.4	-	8	1013	c.824G>A	c.(823-825)tGt>tAt	p.C275Y	TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.C275Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.C275Y|TP53_ENST00000455263.2_Missense_Mutation_p.C275Y|TP53_ENST00000359597.4_Missense_Mutation_p.C275Y	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	275	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7887414}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|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 core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C275Y(53)|p.C275F(37)|p.0?(8)|p.C275fs*70(3)|p.?(2)|p.C275S(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGACAGGCACAAACACGCAC	0.552		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	115	Substitution - Missense(92)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	lung(14)|large_intestine(13)|breast(13)|upper_aerodigestive_tract(12)|central_nervous_system(10)|haematopoietic_and_lymphoid_tissue(10)|ovary(7)|urinary_tract(6)|stomach(5)|oesophagus(5)|bone(5)|liver(5)|skin(3)|pancreas(2)|NS(2)|prostate(2)|biliary_tract(1)	GRCh37	CM076568|CM951234	TP53	M							71.0	61.0	64.0					17																	7577114		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.824G>A	17.37:g.7577114C>T	ENSP00000269305:p.Cys275Tyr		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.605675	0.87157	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99874	-7.39;-7.39;-7.39;-7.39;-7.39;-7.39	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.997;0.997	D	0.96317	0.9233	10	0.87932	D	0	-17.2181	15.662	0.77193	0.0:1.0:0.0:0.0	.	275;275;275;275	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	Y	275;275;275;275;275;264;143	ENSP00000352610:C275Y;ENSP00000269305:C275Y;ENSP00000398846:C275Y;ENSP00000391127:C275Y;ENSP00000391478:C275Y;ENSP00000425104:C143Y	ENSP00000269305:C275Y	C	-	2	0	TP53	7517839	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	TGT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
CACNA1G	8913	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	17	48653145	48653145	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr17:48653145G>A	ENST00000359106.5	+	8	1382	c.1382G>A	c.(1381-1383)cGg>cAg	p.R461Q	CACNA1G_ENST00000515411.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000502264.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R461Q|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R461Q|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R461Q|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R461Q|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000510366.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R461Q|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R461Q|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R461Q|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R461Q|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R461Q|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R461Q|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R461Q	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	461					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GCAGGTGTGCGGGTTGGGCTG	0.677																																						.											0													10.0	13.0	12.0					17																	48653145		1905	4073	5978	SO:0001583	missense	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1382G>A	17.37:g.48653145G>A	ENSP00000352011:p.Arg461Gln		D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	15.01	2.705026	0.48412	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97114	-4.12;-4.12;-4.25;-4.06;-4.12;-4.11;-4.15;-4.18;-4.15;-4.16;-4.17;-4.07;-4.07;-4.12;-4.11;-4.05;-4.15;-4.1;-4.07;-4.15;-4.12;-4.08;-4.14;-4.07;-4.14;-4.14	5.15	4.18	0.49190	.	0.317948	0.29783	N	0.011202	D	0.97433	0.9160	L	0.61036	1.89	0.37399	D	0.912769	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;B;D	0.76494	0.998;0.983;0.997;0.997;0.992;0.998;0.999;0.985;0.999;0.963;0.992;0.99;0.983;0.985;0.999;0.926;0.998;0.959;0.992;0.996;0.998;0.983;0.992;0.983;0.024;0.999	D;B;P;D;P;P;D;P;D;P;P;P;P;P;D;P;P;B;P;P;D;P;P;P;B;P	0.73380	0.96;0.389;0.895;0.98;0.656;0.895;0.974;0.573;0.974;0.474;0.59;0.69;0.493;0.59;0.974;0.474;0.791;0.305;0.573;0.781;0.945;0.493;0.504;0.474;0.003;0.897	D	0.98025	1.0373	10	0.62326	D	0.03	.	8.3868	0.32505	0.2364:0.0:0.7636:0.0	.	461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	Q	461	ENSP00000353990:R461Q;ENSP00000339302:R461Q;ENSP00000392390:R461Q;ENSP00000347078:R461Q;ENSP00000409759:R461Q;ENSP00000425522:R461Q;ENSP00000426261:R461Q;ENSP00000425451:R461Q;ENSP00000422407:R461Q;ENSP00000426814:R461Q;ENSP00000427238:R461Q;ENSP00000423112:R461Q;ENSP00000420918:R461Q;ENSP00000426172:R461Q;ENSP00000423045:R461Q;ENSP00000427173:R461Q;ENSP00000426098:R461Q;ENSP00000425698:R461Q;ENSP00000426232:R461Q;ENSP00000423317:R461Q;ENSP00000350979:R461Q;ENSP00000352011:R461Q;ENSP00000414388:R461Q;ENSP00000423155:R461Q;ENSP00000422268:R461Q;ENSP00000421518:R461Q	ENSP00000339302:R461Q	R	+	2	0	CACNA1G	46008144	1.000000	0.71417	0.995000	0.50966	0.130000	0.20726	2.164000	0.42387	1.163000	0.42636	0.655000	0.94253	CGG		0.677	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
C19orf70	125988	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	19	5679701	5679701	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr19:5679701C>A	ENST00000309324.4	-	2	512	c.103G>T	c.(103-105)Gac>Tac	p.D35Y	HSD11B1L_ENST00000422535.2_5'Flank|RPL36_ENST00000579649.1_Intron|HSD11B1L_ENST00000342970.2_5'Flank|HSD11B1L_ENST00000301382.4_5'Flank|RPL36_ENST00000577222.1_5'Flank|C19orf70_ENST00000585605.1_5'UTR|HSD11B1L_ENST00000339423.2_5'Flank|HSD11B1L_ENST00000581773.1_5'Flank|C19orf70_ENST00000590389.1_Missense_Mutation_p.D57Y|HSD11B1L_ENST00000411793.2_5'Flank|HSD11B1L_ENST00000583928.1_5'Flank|HSD11B1L_ENST00000423665.2_5'Flank|C19orf70_ENST00000587950.1_Missense_Mutation_p.D57Y|HSD11B1L_ENST00000577917.1_5'Flank|HSD11B1L_ENST00000581521.1_5'Flank|HSD11B1L_ENST00000581893.1_5'Flank|C19orf70_ENST00000587589.1_Missense_Mutation_p.D35Y	NM_205767.1	NP_991330.1	Q5XKP0	QIL1_HUMAN	chromosome 19 open reading frame 70	35						mitochondrion (GO:0005739)				endometrium(1)|lung(1)	2						TGGCTCTTGTCGCTGGGCCCC	0.647																																						.											0													31.0	28.0	29.0					19																	5679701		2203	4299	6502	SO:0001583	missense	125988			BC009557	CCDS12143.1	19p13.3	2012-10-26			ENSG00000174917	ENSG00000174917			33702	protein-coding gene	gene with protein product						14702039, 17353931	Standard	NM_205767		Approved	QIL1, P117	uc002mch.1	Q5XKP0		ENST00000309324.4:c.103G>T	19.37:g.5679701C>A	ENSP00000309561:p.Asp35Tyr		Q86YE5	Missense_Mutation	SNP	ENST00000309324.4	37	CCDS12143.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.267720	0.40095	.	.	ENSG00000174917	ENST00000309324	T	0.27720	1.65	4.74	2.45	0.29901	.	0.608391	0.14659	N	0.306042	T	0.37404	0.1002	L	0.51422	1.61	0.36444	D	0.865693	D	0.56035	0.974	P	0.52823	0.71	T	0.49606	-0.8922	10	0.72032	D	0.01	-38.7297	9.7456	0.40444	0.1521:0.6992:0.1487:0.0	.	35	Q5XKP0	QIL1_HUMAN	Y	35	ENSP00000309561:D35Y	ENSP00000309561:D35Y	D	-	1	0	C19orf70	5630701	0.004000	0.15560	0.998000	0.56505	0.976000	0.68499	0.225000	0.17757	2.187000	0.69744	0.462000	0.41574	GAC		0.647	C19orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451656.1	NM_205767	
TMEM150B	284417	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	19	55824239	55824239	+	Silent	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr19:55824239C>T	ENST00000326652.4	-	8	872	c.690G>A	c.(688-690)ccG>ccA	p.P230P	TMEM150B_ENST00000438693.1_Silent_p.P230P|CTD-2105E13.14_ENST00000596786.1_RNA	NM_001282011.1	NP_001268940.1	A6NC51	T150B_HUMAN	transmembrane protein 150B	230						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3						ACAGCTGGACCGGCAGGGAGA	0.667																																						.											0													6.0	8.0	8.0					19																	55824239		1959	4082	6041	SO:0001819	synonymous_variant	284417			BC020862	CCDS42629.1	19q13.42	2009-06-12	2009-06-12	2009-06-12		ENSG00000180061			34415	protein-coding gene	gene with protein product			"""transmembrane protein 224"""	TMEM224			Standard	XM_005258812		Approved		uc010esw.1	A6NC51		ENST00000326652.4:c.690G>A	19.37:g.55824239C>T			B7ZW71	Silent	SNP	ENST00000326652.4	37	CCDS42629.1																																																																																				0.667	TMEM150B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452685.1	NM_001085488	
RNF103	7844	hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	2	86831681	86831681	+	Missense_Mutation	SNP	T	T	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr2:86831681T>A	ENST00000237455.4	-	4	2311	c.1343A>T	c.(1342-1344)aAt>aTt	p.N448I	CHMP3_ENST00000439940.2_Intron|RNF103_ENST00000477307.1_5'Flank|AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000426549.1_RNA|AC015971.2_ENST00000439077.1_RNA|RNF103-CHMP3_ENST00000604011.1_Intron	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	448					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N448I(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						GTTATTGGCATTGACTTCATC	0.418																																						.											1	Substitution - Missense(1)	kidney(1)											125.0	124.0	125.0					2																	86831681		2203	4300	6503	SO:0001583	missense	7844			D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"""RING-type (C3HC4) zinc fingers"""	12859	protein-coding gene	gene with protein product		602507	"""zinc finger protein 103 homolog (mouse)"""	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.1343A>T	2.37:g.86831681T>A	ENSP00000237455:p.Asn448Ile		A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Missense_Mutation	SNP	ENST00000237455.4	37	CCDS33237.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.722675	0.48728	.	.	ENSG00000239305	ENST00000237455	T	0.46451	0.87	5.59	5.59	0.84812	.	0.044753	0.85682	D	0.000000	T	0.61476	0.2350	L	0.60455	1.87	0.54753	D	0.999988	D	0.76494	0.999	D	0.80764	0.994	T	0.64002	-0.6509	10	0.66056	D	0.02	-16.2147	15.7662	0.78128	0.0:0.0:0.0:1.0	.	448	O00237	RN103_HUMAN	I	448	ENSP00000237455:N448I	ENSP00000237455:N448I	N	-	2	0	RNF103	86685192	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	3.609000	0.54117	2.133000	0.65898	0.377000	0.23210	AAT		0.418	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667	
DHX36	170506	hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	3	154033067	154033067	+	Missense_Mutation	SNP	T	T	A	rs138481688		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:154033067T>A	ENST00000496811.1	-	3	451	c.371A>T	c.(370-372)tAc>tTc	p.Y124F	DHX36_ENST00000329463.5_Missense_Mutation_p.Y124F|DHX36_ENST00000544526.1_Missense_Mutation_p.Y124F|DHX36_ENST00000308361.6_Missense_Mutation_p.Y124F	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	124					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTCAGTACCGTATCTGTTTTG	0.333																																						.											0													68.0	67.0	67.0					3																	154033067		2203	4297	6500	SO:0001583	missense	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.371A>T	3.37:g.154033067T>A	ENSP00000417078:p.Tyr124Phe		B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.884336	0.33255	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.09350	2.99;2.99;2.99;2.99;2.99	5.52	5.52	0.82312	.	0.389150	0.28476	N	0.015219	T	0.07413	0.0187	N	0.24115	0.695	0.35513	D	0.800764	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.08055	0.002;0.003;0.001	T	0.24621	-1.0155	10	0.10902	T	0.67	.	12.0359	0.53425	0.0:0.0:0.0:1.0	.	124;124;124	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	F	124;124;124;124;38	ENSP00000417078:Y124F;ENSP00000309296:Y124F;ENSP00000444247:Y124F;ENSP00000330113:Y124F;ENSP00000419862:Y38F	ENSP00000309296:Y124F	Y	-	2	0	DHX36	155515761	0.623000	0.27094	1.000000	0.80357	0.454000	0.32378	1.778000	0.38614	2.100000	0.63781	0.467000	0.42956	TAC		0.333	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
MAGI1	9223	hgsc.bcm.edu	37	3	65425594	65425594	+	Silent	SNP	C	C	T	rs552500635	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:65425594C>T	ENST00000497477.2	-	9	1229	c.1230G>A	c.(1228-1230)caG>caA	p.Q410Q	MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000483466.1_Silent_p.Q410Q|MAGI1_ENST00000402939.2_Silent_p.Q410Q|MAGI1_ENST00000330909.8_Silent_p.Q410Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	410	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		gctgctgttgctgctgctgtt	0.542											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	722	0.144169	0.0893	0.1282	5008	,	,		14940	0.2024		0.0825	False		,,,				2504	0.2331					.											0													65.0	61.0	62.0					3																	65425594		2199	4283	6482	SO:0001819	synonymous_variant	9223			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1230G>A	3.37:g.65425594C>T		1084	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	1.063	-0.672234	0.03403	.	.	ENSG00000151276	ENST00000460329	.	.	.	3.3	-0.172	0.13327	.	.	.	.	.	T	0.20292	0.0488	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.22556	-1.0213	4	.	.	.	0.8958	1.6281	0.02727	0.1431:0.3787:0.1264:0.3517	.	.	.	.	N	291	.	.	S	-	2	0	MAGI1	65400634	0.371000	0.25056	0.001000	0.08648	0.001000	0.01503	-1.015000	0.03637	-0.726000	0.04895	-0.813000	0.03139	AGC		0.542	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
NDUFB5	4711	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	3	179336311	179336311	+	Splice_Site	SNP	T	T	C			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:179336311T>C	ENST00000259037.3	+	5	563		c.e5+2		NDUFB5_ENST00000472629.1_Splice_Site|NDUFB5_ENST00000493866.1_Splice_Site|NDUFB5_ENST00000473500.1_Splice_Site	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa						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)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			TGAATTACGGTAGGAAAAACG	0.373																																						.											0													52.0	53.0	52.0					3																	179336311		2203	4300	6503	SO:0001630	splice_region_variant	4711			AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"""Mitochondrial respiratory chain complex / Complex I"""	7700	protein-coding gene	gene with protein product	"""complex I SGDH subunit"""	603841	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"""			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.449+2T>C	3.37:g.179336311T>C			Q561V6	Splice_Site	SNP	ENST00000259037.3	37	CCDS3234.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.418381	0.62622	.	.	ENSG00000136521	ENST00000259037;ENST00000493866;ENST00000472629;ENST00000482604	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4432	0.75204	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NDUFB5	180819005	1.000000	0.71417	0.999000	0.59377	0.769000	0.43574	5.492000	0.66893	2.284000	0.76573	0.523000	0.50628	.		0.373	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492	Intron
ANKRD17	26057	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	4	73959889	73959889	+	Missense_Mutation	SNP	C	C	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr4:73959889C>A	ENST00000358602.4	-	28	5350	c.5234G>T	c.(5233-5235)gGc>gTc	p.G1745V	ANKRD17_ENST00000509867.2_Missense_Mutation_p.G1632V|ANKRD17_ENST00000330838.6_Missense_Mutation_p.G1494V	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1745	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATATTACAGCCTCCTCTTCC	0.348																																						.											0													162.0	151.0	155.0					4																	73959889		2203	4300	6503	SO:0001583	missense	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.5234G>T	4.37:g.73959889C>A	ENSP00000351416:p.Gly1745Val		E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.775657	0.90195	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000426917	D;D;D	0.94184	-3.37;-3.37;-3.37	5.52	5.52	0.82312	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.64402	D	0.000006	D	0.98375	0.9460	H	0.99058	4.415	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;1.0	D	0.99616	1.0982	10	0.87932	D	0	.	19.4499	0.94862	0.0:1.0:0.0:0.0	.	1744;1494;1745;1632	O75179-2;G5E964;O75179;E7EUV3	.;.;ANR17_HUMAN;.	V	1745;1152;1494;1632;129	ENSP00000351416:G1745V;ENSP00000332265:G1494V;ENSP00000427151:G1632V	ENSP00000332265:G1494V	G	-	2	0	ANKRD17	74178753	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.416000	0.80143	2.582000	0.87167	0.585000	0.79938	GGC		0.348	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
CXCL5	6374	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	4	74863781	74863781	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr4:74863781G>T	ENST00000296027.4	-	3	471	c.274C>A	c.(274-276)Ctt>Att	p.L92I		NM_002994.3	NP_002985.1	P42830	CXCL5_HUMAN	chemokine (C-X-C motif) ligand 5	92					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			TCTGGATCAAGACAAATTTCC	0.428																																						.											0													85.0	93.0	91.0					4																	74863781		2203	4300	6503	SO:0001583	missense	6374			X78686	CCDS34006.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163735		"""Endogenous ligands"""	10642	protein-coding gene	gene with protein product		600324	"""small inducible cytokine subfamily B (Cys-X-Cys), member 5 (epithelial-derived neutrophil-activating peptide 78)"""	SCYB5		7929219	Standard	NM_002994		Approved	ENA-78	uc003hhk.4	P42830		ENST00000296027.4:c.274C>A	4.37:g.74863781G>T	ENSP00000296027:p.Leu92Ile		Q96QE1	Missense_Mutation	SNP	ENST00000296027.4	37	CCDS34006.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.887192	0.33348	.	.	ENSG00000163735	ENST00000296027	T	0.06068	3.35	3.78	2.9	0.33743	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.085998	0.48767	N	0.000175	T	0.26557	0.0649	M	0.90145	3.09	0.29520	N	0.853537	D	0.89917	1.0	D	0.87578	0.998	T	0.10154	-1.0642	10	0.62326	D	0.03	.	8.2023	0.31432	0.0:0.0:0.7615:0.2385	.	92	P42830	CXCL5_HUMAN	I	92	ENSP00000296027:L92I	ENSP00000296027:L92I	L	-	1	0	CXCL5	75082645	0.992000	0.36948	0.539000	0.28077	0.233000	0.25261	2.704000	0.47118	0.759000	0.33084	0.306000	0.20318	CTT		0.428	CXCL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362749.1	NM_002994	
SEMA3C	10512	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	7	80458056	80458056	+	Nonsense_Mutation	SNP	G	G	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr7:80458056G>A	ENST00000265361.3	-	3	670	c.109C>T	c.(109-111)Cga>Tga	p.R37*	SEMA3C_ENST00000536800.1_Intron|SEMA3C_ENST00000544525.1_Nonsense_Mutation_p.R55*|SEMA3C_ENST00000419255.2_Nonsense_Mutation_p.R37*	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	37	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R37*(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTGGTTTCTCGAAGTTCTGAA	0.348																																						.											1	Substitution - Nonsense(1)	skin(1)											93.0	91.0	92.0					7																	80458056		2203	4300	6503	SO:0001587	stop_gained	10512			AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.109C>T	7.37:g.80458056G>A	ENSP00000265361:p.Arg37*		B4DRL8	Nonsense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	40	8.392540	0.98791	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	.	.	.	5.77	4.89	0.63831	.	0.171329	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	14.7854	0.69800	0.069:0.0:0.931:0.0	.	.	.	.	X	37;37;55	.	ENSP00000265361:R37X	R	-	1	2	SEMA3C	80295992	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	4.197000	0.58413	1.447000	0.47661	-0.142000	0.14014	CGA		0.348	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
ZNF789	285989	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	7	99084964	99084964	+	Silent	SNP	G	G	A	rs148718204	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr7:99084964G>A	ENST00000331410.5	+	5	1401	c.1131G>A	c.(1129-1131)acG>acA	p.T377T	ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_Intron	NM_213603.2	NP_998768.2	Q5FWF6	ZN789_HUMAN	zinc finger protein 789	377					regulation of transcription, DNA-templated (GO:0006355)|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)			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)	11	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GTGGGAAAACGTTTAGTTTTA	0.403																																						.											0								G		7,4399	12.9+/-30.5	0,7,2196	138.0	136.0	137.0		1131	-5.8	0.2	7	dbSNP_134	137	0,8600		0,0,4300	no	coding-synonymous	ZNF789	NM_213603.2		0,7,6496	AA,AG,GG		0.0,0.1589,0.0538		377/426	99084964	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	285989			AK093141	CCDS34693.1, CCDS34694.1	7q22.1	2013-01-08			ENSG00000198556	ENSG00000198556		"""Zinc fingers, C2H2-type"", ""-"""	27801	protein-coding gene	gene with protein product						12477932	Standard	XM_005250281		Approved		uc003uqq.1	Q5FWF6	OTTHUMG00000154601	ENST00000331410.5:c.1131G>A	7.37:g.99084964G>A			A4D282|A6NH61|Q6ZMZ9	Silent	SNP	ENST00000331410.5	37	CCDS34693.1																																																																																				0.403	ZNF789-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336266.1	NM_213603	
GPSM1	26086	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	9	139231484	139231484	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr9:139231484C>T	ENST00000440944.1	+	4	753	c.533C>T	c.(532-534)cCg>cTg	p.P178L	GPSM1_ENST00000392945.3_Missense_Mutation_p.P178L	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	178	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GGGCACCTGCCGCCCGATGTC	0.662																																						.											0													39.0	36.0	37.0					9																	139231484		2115	4176	6291	SO:0001583	missense	26086			AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.533C>T	9.37:g.139231484C>T	ENSP00000392828:p.Pro178Leu		A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Missense_Mutation	SNP	ENST00000440944.1	37	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473531	0.63737	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	D;D;D	0.90444	-2.65;-2.65;-2.67	3.79	3.79	0.43588	Tetratricopeptide-like helical (1);	0.068976	0.64402	U	0.000013	D	0.93910	0.8051	M	0.74647	2.275	0.80722	D	1	D;D	0.89917	1.0;0.999	P;P	0.61328	0.887;0.85	D	0.94277	0.7516	10	0.52906	T	0.07	-12.041	15.5081	0.75757	0.0:1.0:0.0:0.0	.	178;178	Q86YR5;Q86YR5-3	GPSM1_HUMAN;.	L	178;178;155	ENSP00000376674:P178L;ENSP00000392828:P178L;ENSP00000346797:P155L	ENSP00000346797:P155L	P	+	2	0	GPSM1	138351305	0.998000	0.40836	0.940000	0.37924	0.889000	0.51656	3.792000	0.55476	2.050000	0.60909	0.563000	0.77884	CCG		0.662	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
AFF2	2334	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	X	147924508	147924508	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chrX:147924508C>T	ENST00000370460.2	+	6	1671	c.1192C>T	c.(1192-1194)Cca>Tca	p.P398S	AFF2_ENST00000286437.5_Missense_Mutation_p.P39S|AFF2_ENST00000342251.3_Missense_Mutation_p.P365S|AFF2_ENST00000370457.5_Missense_Mutation_p.P365S|AFF2_ENST00000370458.1_Missense_Mutation_p.P365S	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	398					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GCATCTGACCCCAGGATTCAC	0.348																																						.											0													92.0	87.0	89.0					X																	147924508		2203	4299	6502	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1192C>T	X.37:g.147924508C>T	ENSP00000359489:p.Pro398Ser		A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	8.659	0.900042	0.17686	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458;ENST00000286437	T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06	5.67	4.7	0.59300	.	0.229244	0.38005	N	0.001852	T	0.32823	0.0842	N	0.03930	-0.32	0.31930	N	0.612348	B;B;B;B;B;B;B	0.33583	0.418;0.165;0.165;0.165;0.165;0.198;0.017	B;B;B;B;B;B;B	0.34873	0.191;0.121;0.121;0.121;0.121;0.191;0.023	T	0.31998	-0.9923	10	0.32370	T	0.25	.	3.4715	0.07569	0.0:0.6736:0.0:0.3264	.	39;369;365;365;394;398;365	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;.;AFF2_HUMAN;.	S	398;365;365;365;39	ENSP00000359489:P398S;ENSP00000359486:P365S;ENSP00000345459:P365S;ENSP00000359487:P365S;ENSP00000286437:P39S	ENSP00000286437:P39S	P	+	1	0	AFF2	147732200	1.000000	0.71417	0.978000	0.43139	0.873000	0.50193	2.680000	0.46918	2.374000	0.81015	0.540000	0.68198	CCA		0.348	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
PIK3C2B	5287	hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	1	204415184	204415184	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:204415184C>T	ENST00000367187.3	-	17	3134	c.2578G>A	c.(2578-2580)Gcc>Acc	p.A860T	PIK3C2B_ENST00000424712.2_Intron	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	860	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CAGCTGGGGGCGCTGGCGAGC	0.622											OREG0014135	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										.											0													64.0	66.0	65.0					1																	204415184		2203	4300	6503	SO:0001583	missense	5287			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2578G>A	1.37:g.204415184C>T	ENSP00000356155:p.Ala860Thr	2144	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	C	36	5.884921	0.97068	.	.	ENSG00000133056	ENST00000367187	T	0.61510	0.1	5.33	5.33	0.75918	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.74696	0.3750	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.75326	-0.3357	10	0.51188	T	0.08	.	18.6702	0.91508	0.0:1.0:0.0:0.0	.	860	O00750	P3C2B_HUMAN	T	860	ENSP00000356155:A860T	ENSP00000356155:A860T	A	-	1	0	PIK3C2B	202681807	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.942000	0.63547	2.516000	0.84829	0.460000	0.39030	GCC		0.622	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
MIER3	166968	hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	5	56229122	56229122	+	Missense_Mutation	SNP	T	T	G			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr5:56229122T>G	ENST00000381199.3	-	8	709	c.699A>C	c.(697-699)aaA>aaC	p.K233N	MIER3_ENST00000409421.1_Missense_Mutation_p.K170N|MIER3_ENST00000381213.3_Missense_Mutation_p.K233N|MIER3_ENST00000381226.3_Missense_Mutation_p.K238N			Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	233	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		TATCCATTATTTTTTCACTGC	0.398																																						.											0													237.0	228.0	231.0					5																	56229122		2203	4300	6503	SO:0001583	missense	166968			BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545			26678	protein-coding gene	gene with protein product						12477932	Standard	XM_005248448		Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000381199.3:c.699A>C	5.37:g.56229122T>G	ENSP00000370596:p.Lys233Asn		B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	Missense_Mutation	SNP	ENST00000381199.3	37		.	.	.	.	.	.	.	.	.	.	T	15.30	2.791476	0.50102	.	.	ENSG00000155545	ENST00000381226;ENST00000381213;ENST00000381199;ENST00000409421	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.5	0.519	0.17035	ELM2 domain (1);	0.046629	0.85682	D	0.000000	T	0.51550	0.1681	L	0.41710	1.295	0.38505	D	0.948324	D;D;P	0.76494	0.994;0.999;0.928	P;D;P	0.69479	0.81;0.964;0.775	T	0.47222	-0.9134	10	0.35671	T	0.21	-4.2485	9.0203	0.36195	0.0:0.2834:0.0:0.7166	.	233;238;233	Q7Z3K6;Q7Z3K6-2;Q7Z3K6-3	MIER3_HUMAN;.;.	N	238;233;233;170	ENSP00000370624:K238N;ENSP00000370611:K233N;ENSP00000370596:K233N;ENSP00000386584:K170N	ENSP00000370596:K233N	K	-	3	2	MIER3	56264879	0.096000	0.21769	0.251000	0.24312	0.991000	0.79684	0.502000	0.22594	0.078000	0.16900	-0.256000	0.11100	AAA		0.398	MIER3-004	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000132523.2	NM_152622	
OR2B2	81697	hgsc.bcm.edu	37	6	27879249	27879249	+	Silent	SNP	G	G	A	rs375078072		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr6:27879249G>A	ENST00000303324.2	-	1	925	c.849C>T	c.(847-849)ccC>ccT	p.P283P		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						GATTCAGCATGGGTGCAATGA	0.403																																						.											0								G		0,4406		0,0,2203	76.0	75.0	75.0		849	3.4	1.0	6		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR2B2	NM_033057.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		283/358	27879249	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	81697			Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.849C>T	6.37:g.27879249G>A			B2RNH2|Q9GZL2|Q9Y299	Silent	SNP	ENST00000303324.2	37	CCDS4641.1																																																																																				0.403	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
OR8H2	390151	broad.mit.edu;mdanderson.org	37	11	55872537	55872537	+	Missense_Mutation	SNP	A	A	G	rs61746549	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr11:55872537A>G	ENST00000313503.1	+	1	19	c.19A>G	c.(19-21)Aac>Gac	p.N7D		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N7D(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					TAGAAGGAATAACACAAATGT	0.438										HNSCC(53;0.14)			N|||	4	0.000798722	0.0008	0.0014	5008	,	,		18426	0.0		0.0	False		,,,				2504	0.002					.											1	Substitution - Missense(1)	kidney(1)											196.0	187.0	190.0					11																	55872537		2201	4296	6497	SO:0001583	missense	390151			AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.19A>G	11.37:g.55872537A>G	ENSP00000323982:p.Asn7Asp		Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	N	7.027	0.559788	0.13436	.	.	ENSG00000181767	ENST00000313503	T	0.00509	6.91	3.74	-2.34	0.06704	.	1.169330	0.06223	N	0.687064	T	0.00300	0.0009	N	0.17723	0.515	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	10	0.30854	T	0.27	.	0.2174	0.00164	0.3775:0.1477:0.1868:0.288	rs61746549	7	Q8N162	OR8H2_HUMAN	D	7	ENSP00000323982:N7D	ENSP00000323982:N7D	N	+	1	0	OR8H2	55629113	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.679000	0.01940	-0.566000	0.06054	-1.639000	0.00775	AAC		0.438	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
TAF1D	79101	broad.mit.edu	37	11	93471453	93471453	+	Frame_Shift_Del	DEL	T	T	-			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr11:93471453delT	ENST00000448108.2	-	3	931	c.281delA	c.(280-282)aagfs	p.K96fs	TAF1D_ENST00000546088.1_5'Flank	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	96					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						CCTCTTTTTCTTTTTTTTATA	0.348																																						.											0													109.0	116.0	114.0					11																	93471453		2201	4298	6499	SO:0001589	frameshift_variant	79101				CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"""Josephin domain containing 3"""	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.281delA	11.37:g.93471453delT	ENSP00000410409:p.Lys96fs		Q6I9Y6	Frame_Shift_Del	DEL	ENST00000448108.2	37	CCDS8293.1																																																																																				0.348	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116	
CASC5	57082	broad.mit.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	15	40944268	40944268	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr15:40944268C>T	ENST00000346991.5	+	22	6848	c.6458C>T	c.(6457-6459)aCg>aTg	p.T2153M	CASC5_ENST00000399668.2_Missense_Mutation_p.T2127M			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	2153	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GTTTATGACACGATACAACTC	0.378																																						.											0													114.0	102.0	106.0					15																	40944268		1897	4129	6026	SO:0001583	missense	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.6458C>T	15.37:g.40944268C>T	ENSP00000335463:p.Thr2153Met		Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863076	0.51482	.	.	ENSG00000137812	ENST00000346991;ENST00000399668	T;T	0.06933	3.24;3.24	5.4	5.4	0.78164	.	0.206901	0.41500	D	0.000876	T	0.19208	0.0461	L	0.36672	1.1	0.30216	N	0.797228	D;D	0.89917	1.0;0.999	D;P	0.63703	0.917;0.882	T	0.00630	-1.1636	10	0.87932	D	0	.	16.0887	0.81076	0.0:1.0:0.0:0.0	.	2127;2153	Q8NG31-2;Q8NG31	.;CASC5_HUMAN	M	2153;2127	ENSP00000335463:T2153M;ENSP00000382576:T2127M	ENSP00000335463:T2153M	T	+	2	0	CASC5	38731560	0.996000	0.38824	0.728000	0.30774	0.203000	0.24098	4.362000	0.59467	2.523000	0.85059	0.655000	0.94253	ACG		0.378	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
PIEZO1	9780	broad.mit.edu	37	16	88781785	88781785	+	3'UTR	DEL	A	A	-	rs113700874		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr16:88781785delA	ENST00000301015.9	-	0	8040				CTU2_ENST00000312060.5_3'UTR|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000453996.2_3'UTR|CTU2_ENST00000567949.1_3'UTR|PIEZO1_ENST00000327397.7_3'UTR	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						ttttttaattaaaaaaaaaaC	0.547																																						.											0																																										SO:0001624	3_prime_UTR_variant	348180			D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.*228T>-	16.37:g.88781785delA			A6NHT9|A7E2B7|Q0KKZ9	Splice_Site	DEL	ENST00000301015.9	37	CCDS54058.1																																																																																				0.547	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
RNMT	8731	broad.mit.edu	37	18	13746253	13746253	+	Frame_Shift_Del	DEL	A	A	-			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr18:13746253delA	ENST00000383314.2	+	9	1414	c.1174delA	c.(1174-1176)aaafs	p.K393fs	RNMT_ENST00000589866.1_Frame_Shift_Del_p.K393fs|RNMT_ENST00000262173.3_Frame_Shift_Del_p.K393fs|RNMT_ENST00000592764.1_Frame_Shift_Del_p.K393fs|RNMT_ENST00000535051.1_Frame_Shift_Del_p.K151fs|RNMT_ENST00000543302.2_Frame_Shift_Del_p.K393fs			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	393	mRNA cap 0 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00895}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)	p.T394fs*19(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						ACTAGTCTACAAAAAAACATT	0.308																																					GBM(29;474 594 19092 36647 41529)	.											1	Deletion - Frameshift(1)	large_intestine(1)											65.0	70.0	68.0					18																	13746253		2202	4299	6501	SO:0001589	frameshift_variant	8731			AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.1174delA	18.37:g.13746253delA	ENSP00000372804:p.Lys393fs		B0YJ90|D3DUJ5|O94996|Q9UIJ9	Frame_Shift_Del	DEL	ENST00000383314.2	37	CCDS11867.1																																																																																				0.308	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799	
RABL3	285282	broad.mit.edu	37	3	120417415	120417415	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:120417415T>C	ENST00000273375.3	-	5	418	c.389A>G	c.(388-390)tAt>tGt	p.Y130C	RABL3_ENST00000491398.1_5'UTR|RABL3_ENST00000483733.1_Missense_Mutation_p.Y130C	NM_173825.3	NP_776186.2	Q5HYI8	RABL3_HUMAN	RAB, member of RAS oncogene family-like 3	130	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)	17				GBM - Glioblastoma multiforme(114;0.151)		TTCTTGATCATAATCCCTGTG	0.338																																						.											0													190.0	207.0	202.0					3																	120417415		2203	4296	6499	SO:0001583	missense	285282			BC020832	CCDS3001.1	3q13.33	2008-02-05			ENSG00000144840	ENSG00000144840			18072	protein-coding gene	gene with protein product						12477932	Standard	NM_173825		Approved	MGC23920	uc003edx.3	Q5HYI8	OTTHUMG00000159668	ENST00000273375.3:c.389A>G	3.37:g.120417415T>C	ENSP00000273375:p.Tyr130Cys		Q8WUD3	Missense_Mutation	SNP	ENST00000273375.3	37	CCDS3001.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.112522	0.77210	.	.	ENSG00000144840	ENST00000273375;ENST00000483733	T;T	0.71103	-0.54;-0.51	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.81592	0.4855	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82598	-0.0378	10	0.56958	D	0.05	-12.3624	15.1734	0.72894	0.0:0.0:0.0:1.0	.	130	Q5HYI8	RABL3_HUMAN	C	130	ENSP00000273375:Y130C;ENSP00000419986:Y130C	ENSP00000273375:Y130C	Y	-	2	0	RABL3	121900105	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.572000	0.82409	2.176000	0.68965	0.455000	0.32223	TAT		0.338	RABL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356776.1	NM_173825	
MUC4	4585	broad.mit.edu;mdanderson.org	37	3	195509308	195509308	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:195509308G>A	ENST00000463781.3	-	2	9602	c.9143C>T	c.(9142-9144)tCa>tTa	p.S3048L	MUC4_ENST00000475231.1_Missense_Mutation_p.S3048L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	989					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)		TGTGGATGCTGAGGAAGTGTC	0.607																																						.											0																																										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.9143C>T	3.37:g.195509308G>A	ENSP00000417498:p.Ser3048Leu		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	.	.	.	.	.	.	.	.	.	.	g	8.283	0.816093	0.16607	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.44;1.43	.	.	.	.	.	.	.	.	T	0.15869	0.0382	N	0.19112	0.55	0.20975	N	0.999814	B	0.22480	0.07	B	0.14023	0.01	T	0.26360	-1.0105	7	.	.	.	.	5.4195	0.16392	0.0:0.0:1.0:0.0	.	2920	E7ESK3	.	L	3048	ENSP00000417498:S3048L;ENSP00000420243:S3048L	.	S	-	2	0	MUC4	196994087	0.286000	0.24305	0.013000	0.15412	0.000000	0.00434	2.555000	0.45854	0.497000	0.27926	0.000000	0.15137	TCA		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
VCAN	1462	broad.mit.edu;ucsc.edu;mdanderson.org	37	5	82841438	82841438	+	Silent	SNP	G	G	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr5:82841438G>T	ENST00000265077.3	+	9	9913	c.9348G>T	c.(9346-9348)gtG>gtT	p.V3116V	VCAN_ENST00000343200.5_Silent_p.V2129V|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Silent_p.V1314V|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Silent_p.V375V|VCAN_ENST00000342785.4_Silent_p.V1362V|VCAN-AS1_ENST00000512090.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3116	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GCACCTGTGTGCCAGGATACA	0.463																																						.											0													185.0	175.0	178.0					5																	82841438		2203	4300	6503	SO:0001819	synonymous_variant	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9348G>T	5.37:g.82841438G>T			P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																				0.463	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
OLFML2A	169611	broad.mit.edu	37	9	127572090	127572090	+	Missense_Mutation	SNP	G	G	A	rs201784600		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr9:127572090G>A	ENST00000373580.3	+	8	1358	c.1358G>A	c.(1357-1359)cGc>cAc	p.R453H	OLFML2A_ENST00000288815.5_Missense_Mutation_p.R239H	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	453	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CCTGCAGGCCGCTGGAGTAAC	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17402	0.0		0.001	False		,,,				2504	0.0					.											0								G	HIS/ARG	0,4406		0,0,2203	93.0	85.0	88.0		1358	6.2	1.0	9		88	1,8599	1.2+/-3.3	0,1,4299	no	missense	OLFML2A	NM_182487.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	453/653	127572090	1,13005	2203	4300	6503	SO:0001583	missense	169611			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.1358G>A	9.37:g.127572090G>A	ENSP00000362682:p.Arg453His		Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	37	CCDS6857.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.504096	0.96371	0.0	1.16E-4	ENSG00000185585	ENST00000342100;ENST00000373580;ENST00000288815	D;D	0.89617	-2.54;-2.54	6.17	6.17	0.99709	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95548	0.8553	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.975;0.999	D	0.95312	0.8413	10	0.87932	D	0	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	239;453	Q68BL7-3;Q68BL7	.;OLM2A_HUMAN	H	145;453;239	ENSP00000362682:R453H;ENSP00000288815:R239H	ENSP00000288815:R239H	R	+	2	0	OLFML2A	126611911	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGC		0.617	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487	
FBXW10	10517	ucsc.edu	37	17	18682505	18682505	+	Missense_Mutation	SNP	T	T	C	rs1024657	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr17:18682505T>C	ENST00000395665.4	+	14	3274	c.3053T>C	c.(3052-3054)gTc>gCc	p.V1018A	TVP23B_ENST00000476139.1_5'Flank|FBXW10_ENST00000301938.4_Missense_Mutation_p.V965A|TVP23B_ENST00000307767.8_5'Flank|TVP23B_ENST00000574226.1_5'Flank|FBXW10_ENST00000308799.4_Missense_Mutation_p.V1027A|FBXW10_ENST00000395667.1_Missense_Mutation_p.V1017A			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	1018								p.V1017A(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						CCAGGAAAAGTCAGCAAAGCT	0.488													N|||	744	0.148562	0.1846	0.2147	5008	,	,		13486	0.0903		0.2018	False		,,,				2504	0.0583					.											1	Substitution - Missense(1)	prostate(1)											42.0	40.0	41.0					17																	18682505		1906	3581	5487	SO:0001583	missense	10517			BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.3053T>C	17.37:g.18682505T>C	ENSP00000379025:p.Val1018Ala		C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	498	0.22802197802197802	92	0.18699186991869918	107	0.2955801104972376	65	0.11363636363636363	234	0.3087071240105541	C	0.015	-1.557317	0.00910	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	3.38	2.36	0.29203	.	0.000000	0.31936	N	0.006834	T	0.00012	0.0000	N	0.00128	-2.045	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.24693	-1.0153	9	0.02654	T	1	.	4.0906	0.09968	0.4063:0.4743:0.0:0.1194	.	965;1027;1018;1017	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	A	1017;1027;965;1018	ENSP00000379026:V1017A;ENSP00000310382:V1027A;ENSP00000306937:V965A;ENSP00000379025:V1018A	ENSP00000306937:V965A	V	+	2	0	FBXW10	18623230	0.407000	0.25352	0.286000	0.24833	0.737000	0.42083	0.661000	0.25023	0.116000	0.18110	-0.473000	0.04963	GTC		0.488	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
GPR146	115330	ucsc.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr7:1097895A>G	ENST00000397095.1	+	2	967	c.744A>G	c.(742-744)ccA>ccG	p.P248P	C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397100.2_Intron|GPR146_ENST00000297468.3_Silent_p.P248P|C7orf50_ENST00000357429.6_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		TCTGGACGCCACACTATCTGA	0.647													G|||	345	0.0688898	0.0204	0.0821	5008	,	,		17834	0.0		0.1262	False		,,,				2504	0.137					.											0									,,,	206,4198	800.2+/-415.6	2,202,1998	59.0	48.0	52.0		,,,744	-10.2	0.0	7	dbSNP_129	52	1354,7244	751.8+/-407.4	106,1142,3051	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	108,1344,5049	GG,GA,AA		15.7478,4.6776,11.9982	,,,	,,,248/334	1097895	1560,11442	2202	4299	6501	SO:0001819	synonymous_variant	115330			BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.744A>G	7.37:g.1097895A>G			Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																				0.647	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
GREB1	9687	ucsc.edu	37	2	11775503	11775503	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr2:11775503G>T	ENST00000381486.2	+	30	5618	c.5318G>T	c.(5317-5319)gGc>gTc	p.G1773V	GREB1_ENST00000396123.1_Missense_Mutation_p.G771V|GREB1_ENST00000234142.5_Missense_Mutation_p.G1773V	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1773						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GTGGTGGGCGGCCACAGGTCC	0.627																																					Ovarian(39;850 945 2785 23371 33093)	.											0													57.0	63.0	61.0					2																	11775503		2071	4202	6273	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.5318G>T	2.37:g.11775503G>T	ENSP00000370896:p.Gly1773Val		A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.717454	0.89205	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.28255	2.94;2.94;1.62	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.55545	0.1927	M	0.74647	2.275	0.80722	D	1	D	0.63880	0.993	D	0.64595	0.927	T	0.62469	-0.6848	10	0.87932	D	0	-30.8708	17.7214	0.88352	0.0:0.0:1.0:0.0	.	1773	Q4ZG55	GREB1_HUMAN	V	1773;1773;771	ENSP00000370896:G1773V;ENSP00000234142:G1773V;ENSP00000379429:G771V	ENSP00000234142:G1773V	G	+	2	0	GREB1	11692954	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	9.147000	0.94646	2.194000	0.70268	0.655000	0.94253	GGC		0.627	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
PEBP1	5037	ucsc.edu	37	12	118574067	118574067	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr12:118574067A>G	ENST00000261313.2	+	1	405	c.53A>G	c.(52-54)gAc>gGc	p.D18G		NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	18						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAAGAAGTGGACGAGCAGCCG	0.711																																					NSCLC(44;94 1357 12187 49467)	.											0													12.0	13.0	13.0					12																	118574067		1894	3543	5437	SO:0001583	missense	5037			X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"""Raf kinase inhibitory protein"", ""hippocampal cholinergic neurostimulating peptide"""	604591	"""prostatic binding protein"""	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.53A>G	12.37:g.118574067A>G	ENSP00000261313:p.Asp18Gly		B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	37	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	A	30	5.049727	0.93740	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.33865	1.39	4.75	4.75	0.60458	.	0.301525	0.39615	N	0.001304	T	0.59101	0.2169	M	0.85373	2.75	0.42300	D	0.992176	D;P	0.67145	0.996;0.931	P;P	0.58820	0.846;0.585	T	0.66763	-0.5841	10	0.52906	T	0.07	.	14.4148	0.67142	1.0:0.0:0.0:0.0	.	18;18	B4DRT4;P30086	.;PEBP1_HUMAN	G	18	ENSP00000261313:D18G	ENSP00000261313:D18G	D	+	2	0	PEBP1	117058450	1.000000	0.71417	0.953000	0.39169	0.740000	0.42216	8.273000	0.89887	2.009000	0.58944	0.402000	0.26972	GAC		0.711	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567	
PIKFYVE	200576	ucsc.edu;bcgsc.ca	37	2	209198216	209198216	+	Splice_Site	SNP	A	A	G			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr2:209198216A>G	ENST00000264380.4	+	24	4299	c.4141A>G	c.(4141-4143)Agt>Ggt	p.S1381G		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1381					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GGCGTCTTTCAGGTAAGAAAT	0.403																																						.											0													69.0	65.0	66.0					2																	209198216		2203	4300	6503	SO:0001630	splice_region_variant	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.4142+1A>G	2.37:g.209198216A>G			Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.398979	0.83120	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.29655	1.56;1.73	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.47525	0.1450	L	0.50333	1.59	0.80722	D	1	D;D	0.58268	0.982;0.969	D;D	0.67548	0.952;0.914	T	0.29640	-1.0005	10	0.28530	T	0.3	-13.6451	15.2597	0.73613	1.0:0.0:0.0:0.0	.	1381;1325	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	G	1381;957;1325	ENSP00000264380:S1381G;ENSP00000405736:S1325G	ENSP00000264380:S1381G	S	+	1	0	PIKFYVE	208906461	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.962000	0.93254	2.018000	0.59344	0.454000	0.30748	AGT		0.403	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	Missense_Mutation
TRABD	80305	ucsc.edu	37	22	50636349	50636349	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr22:50636349T>C	ENST00000303434.4	+	8	888	c.769T>C	c.(769-771)Tcg>Ccg	p.S257P	TRABD_ENST00000380909.4_Missense_Mutation_p.S257P|RP3-402G11.26_ENST00000608025.1_RNA|TRABD_ENST00000395829.1_Missense_Mutation_p.S257P|TRABD_ENST00000395827.1_Missense_Mutation_p.S257P	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	257										breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		CACCATCGTCTCGGAGCGCGA	0.657																																						.											0													141.0	106.0	118.0					22																	50636349		2203	4300	6503	SO:0001583	missense	80305			AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.769T>C	22.37:g.50636349T>C	ENSP00000305664:p.Ser257Pro		Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	Missense_Mutation	SNP	ENST00000303434.4	37	CCDS14086.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.584092	0.28268	.	.	ENSG00000170638	ENST00000380909;ENST00000303434;ENST00000395827;ENST00000395829	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.1	2.87	0.33458	.	0.190451	0.46442	D	0.000281	T	0.39410	0.1077	L	0.44542	1.39	0.48236	D	0.999612	B;P	0.39071	0.305;0.658	B;P	0.45428	0.242;0.48	T	0.10451	-1.0629	10	0.48119	T	0.1	-13.5527	8.1305	0.31024	0.1339:0.0:0.1404:0.7257	.	211;257	Q9H4I3-2;Q9H4I3	.;TRABD_HUMAN	P	257	ENSP00000370295:S257P;ENSP00000305664:S257P;ENSP00000379171:S257P;ENSP00000379173:S257P	ENSP00000305664:S257P	S	+	1	0	TRABD	48978476	1.000000	0.71417	0.027000	0.17364	0.040000	0.13550	2.494000	0.45329	0.235000	0.21160	-0.516000	0.04426	TCG		0.657	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204	
ANKRD30BL	554226	mdanderson.org	37	2	132919099	132919099	+	Silent	SNP	C	C	T	rs199974298		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr2:132919099C>T	ENST00000409867.1	-	1	429	c.180G>A	c.(178-180)aaG>aaA	p.K60K	ANKRD30BL_ENST00000470729.1_Intron			A7E2S9	A30BL_HUMAN	ankyrin repeat domain 30B-like	60										endometrium(1)|kidney(3)	4						CCATTGTCGTCTTCTTCATCA	0.582																																						.											0																																										SO:0001819	synonymous_variant	554226					2q21.2	2013-01-22	2010-06-14	2010-06-14	ENSG00000163046	ENSG00000163046		"""Ankyrin repeat domain containing"""	35167	protein-coding gene	gene with protein product			"""non-protein coding RNA 164"", ""ankyrin repeat domain 30B pseudogene 3"""	NCRNA00164, ANKRD30BP3		17114284	Standard	NR_027019		Approved		uc002tti.3	A7E2S9	OTTHUMG00000153491	ENST00000409867.1:c.180G>A	2.37:g.132919099C>T			B8ZZL7	RNA	SNP	ENST00000409867.1	37																																																																																					0.582	ANKRD30BL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331353.2	NR_027019	
DNAH14	127602	mdanderson.org;bcgsc.ca	37	1	225534219	225534219	+	Missense_Mutation	SNP	T	T	C	rs7527925	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:225534219T>C	ENST00000445597.2	+	49	8471	c.8471T>C	c.(8470-8472)gTa>gCa	p.V2824A	DNAH14_ENST00000430092.1_Missense_Mutation_p.V3627A|DNAH14_ENST00000439375.2_Missense_Mutation_p.V3627A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2824					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CTTTGCACTGTAATCATGCAA	0.323													C|||	2650	0.529153	0.6407	0.4697	5008	,	,		17450	0.5089		0.4046	False		,,,				2504	0.5695					.											0								C	ALA/VAL	842,542		268,306,118	70.0	60.0	63.0		10880	3.5	0.2	1	dbSNP_116	63	1404,1770		323,758,506	yes	missense	DNAH14	NM_001373.1	64	591,1064,624	CC,CT,TT		44.2344,39.1618,49.276	benign	3627/4516	225534219	2246,2312	692	1587	2279	SO:0001583	missense	127602			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8471T>C	1.37:g.225534219T>C	ENSP00000409472:p.Val2824Ala		A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	2.312	-0.357714	0.05138	0.608382	0.442344	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.50001	0.76;0.76;0.76	5.48	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.45086	-0.9285	7	0.15066	T	0.55	.	3.7279	0.08481	0.1327:0.5895:0.1289:0.1488	rs7527925;rs52797267;rs56543759;rs61045802;rs7527925	3627	Q0VDD8-4	.	A	2824;3627;3627	ENSP00000409472:V2824A;ENSP00000414402:V3627A;ENSP00000392061:V3627A	ENSP00000414402:V3627A	V	+	2	0	DNAH14	223600842	0.000000	0.05858	0.155000	0.22561	0.949000	0.60115	0.067000	0.14510	0.662000	0.31006	-0.294000	0.09567	GTA		0.323	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
HLA-B	3106	mdanderson.org	37	6	31324046	31324046	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr6:31324046C>T	ENST00000412585.2	-	3	545	c.517G>A	c.(517-519)Gcg>Acg	p.A173T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	173	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCACGGGCCGCCTCCCACTTG	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																													.											0													29.0	20.0	23.0					6																	31324046		2157	4214	6371	SO:0001583	missense	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.517G>A	6.37:g.31324046C>T	ENSP00000399168:p.Ala173Thr		Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	12.69	2.013055	0.35511	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00010	9.41;9.41	3.18	1.27	0.21489	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.413983	0.16697	U	0.203317	T	0.00144	0.0004	M	0.87758	2.905	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.994;0.998	T	0.15983	-1.0418	10	0.56958	D	0.05	.	5.8476	0.18675	0.0:0.6711:0.2073:0.1215	.	173;173	P30480;P01889	1B42_HUMAN;1B07_HUMAN	T	173;52;52;184	ENSP00000399168:A173T;ENSP00000405931:A184T	ENSP00000399168:A173T	A	-	1	0	HLA-B	31432025	0.000000	0.05858	0.017000	0.16124	0.005000	0.04900	-0.597000	0.05713	0.174000	0.19809	0.297000	0.19635	GCG		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
HLA-DRB5	3127	mdanderson.org	37	6	32497975	32497975	+	Silent	SNP	A	A	G	rs114195860	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr6:32497975A>G	ENST00000374975.3	-	1	89	c.27T>C	c.(25-27)ggT>ggC	p.G9G		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CCATGTAGGAACCTCCAGGGA	0.582																																						.											0													58.0	65.0	63.0					6																	32497975		2198	4282	6480	SO:0001819	synonymous_variant	3127				CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.27T>C	6.37:g.32497975A>G				Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																				0.582	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
MN1	4330	mdanderson.org	37	22	28194900	28194900	+	Silent	SNP	T	T	C	rs202212250|rs530519178	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr22:28194900T>C	ENST00000302326.4	-	1	2586	c.1632A>G	c.(1630-1632)caA>caG	p.Q544Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	544	Poly-Gln.				intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						gctgctgctgttgctgttgct	0.647			T	ETV6	"""AML, meningioma"""								C|||	5	0.000998403	0.0023	0.0	5008	,	,		12597	0.0		0.0	False		,,,				2504	0.002					.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	0																																										SO:0001819	synonymous_variant	4330			X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.1632A>G	22.37:g.28194900T>C			A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																				0.647	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
MUC4	4585	mdanderson.org	37	3	195510758	195510758	+	Missense_Mutation	SNP	C	C	T	rs200554304	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:195510758C>T	ENST00000463781.3	-	2	8152	c.7693G>A	c.(7693-7695)Gac>Aac	p.D2565N	MUC4_ENST00000475231.1_Missense_Mutation_p.D2565N|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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)		GCGGAAGTGTCGGTGACAGGA	0.582													.|||	229	0.0457268	0.1218	0.0187	5008	,	,		10272	0.002		0.0328	False		,,,				2504	0.0204					.											0													40.0	37.0	38.0					3																	195510758		660	1586	2246	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.7693G>A	3.37:g.195510758C>T	ENSP00000417498:p.Asp2565Asn		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	.	.	.	.	.	.	.	.	.	.	-	7.384	0.629375	0.14257	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.64;1.55	.	.	.	.	.	.	.	.	T	0.10981	0.0268	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.26780	-1.0093	7	.	.	.	.	1.9402	0.03345	0.3047:0.4382:0.0:0.257	.	2565	E7ESK3	.	N	2565	ENSP00000417498:D2565N;ENSP00000420243:D2565N	.	D	-	1	0	MUC4	196995153	0.005000	0.15991	0.003000	0.11579	0.000000	0.00434	-0.154000	0.10130	-1.037000	0.03283	0.000000	0.15137	GAC		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR13G1	441933	mdanderson.org;bcgsc.ca	37	1	247835950	247835950	+	Missense_Mutation	SNP	T	T	C	rs1151640	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:247835950T>C	ENST00000359688.2	-	1	415	c.394A>G	c.(394-396)Att>Gtt	p.I132V	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	132			I -> V (in dbSNP:rs1151640).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGTTCATAATAGTACTGTAA	0.468													T|||	2033	0.40595	0.1286	0.5937	5008	,	,		22510	0.6032		0.4195	False		,,,				2504	0.4305					.											0			GRCh37	CM053366	OR13G1	M	rs1151640	T	VAL/ILE	739,3667	305.5+/-289.0	58,623,1522	101.0	84.0	90.0		394	-3.4	0.0	1	dbSNP_87	90	3654,4946	525.3+/-380.7	772,2110,1418	yes	missense	OR13G1	NM_001005487.1	29	830,2733,2940	CC,CT,TT		42.4884,16.7726,33.7767	benign	132/308	247835950	4393,8613	2203	4300	6503	SO:0001583	missense	441933			AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.394A>G	1.37:g.247835950T>C	ENSP00000352717:p.Ile132Val		B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	960	0.43956043956043955	65	0.13211382113821138	204	0.56353591160221	372	0.6503496503496503	319	0.420844327176781	T	3.452	-0.111750	0.06881	0.167726	0.424884	ENSG00000197437	ENST00000359688	T	0.00695	5.83	4.2	-3.4	0.04853	GPCR, rhodopsin-like superfamily (1);	0.680368	0.12654	N	0.450235	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.07404	-1.0774	9	0.17832	T	0.49	-11.8146	5.9215	0.19084	0.0:0.1648:0.4093:0.4259	rs1151640;rs52796519;rs57652947;rs1151640	132	Q8NGZ3	O13G1_HUMAN	V	132	ENSP00000352717:I132V	ENSP00000352717:I132V	I	-	1	0	OR13G1	245902573	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	-0.022000	0.12480	-0.755000	0.04709	0.460000	0.39030	ATT		0.468	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
UBTF	7343	mdanderson.org	37	17	42287519	42287519	+	Silent	SNP	C	C	T	rs2071167	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr17:42287519C>T	ENST00000302904.4	-	15	2091	c.1599G>A	c.(1597-1599)aaG>aaA	p.K533K	UBTF_ENST00000527034.1_Silent_p.K496K|UBTF_ENST00000533177.1_Silent_p.K496K|UBTF_ENST00000529383.1_Silent_p.K533K|UBTF_ENST00000393606.3_Silent_p.K496K|UBTF_ENST00000343638.5_Silent_p.K496K|UBTF_ENST00000436088.1_Silent_p.K533K|UBTF_ENST00000526094.1_Silent_p.K496K|CTB-175E5.7_ENST00000586560.1_RNA			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	533					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CTTCGGCTGCCTTCTTAATCC	0.512											OREG0024456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2261	0.451478	0.6157	0.3646	5008	,	,		21021	0.6915		0.2416	False		,,,				2504	0.2597					.											0								C	,,	2335,2071	605.8+/-390.6	617,1101,485	187.0	195.0	192.0		1488,1488,1599	3.3	1.0	17	dbSNP_96	192	2174,6426	372.0+/-336.5	280,1614,2406	no	coding-synonymous,coding-synonymous,coding-synonymous	UBTF	NM_001076683.1,NM_001076684.2,NM_014233.3	,,	897,2715,2891	TT,TC,CC		25.2791,47.0041,34.6686	,,	496/728,496/728,533/765	42287519	4509,8497	2203	4300	6503	SO:0001819	synonymous_variant	7343			BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.1599G>A	17.37:g.42287519C>T		907	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1																																																																																				0.512	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
LEPR	3953	bcgsc.ca	37	1	66058516	66058516	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:66058516C>T	ENST00000349533.6	+	6	856	c.671C>T	c.(670-672)tCa>tTa	p.S224L	LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371060.3_Missense_Mutation_p.S224L|LEPR_ENST00000344610.8_Missense_Mutation_p.S224L|LEPR_ENST00000371058.1_Missense_Mutation_p.S224L|LEPR_ENST00000371059.3_Missense_Mutation_p.S224L|LEPR_ENST00000406510.3_Intron	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		ATTTTCCAGTCACCTCTAATG	0.368																																						.											0													94.0	92.0	93.0					1																	66058516		2203	4300	6503	SO:0001583	missense	3953			U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.671C>T	1.37:g.66058516C>T	ENSP00000330393:p.Ser224Leu		Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657442	0.88154	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.66099	-0.15;-0.16;-0.14;-0.19;-0.15	5.96	5.05	0.67936	.	0.189176	0.48286	D	0.000188	T	0.75882	0.3910	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.81391	-0.0954	10	0.87932	D	0	-8.9527	14.8905	0.70606	0.0:0.9306:0.0:0.0694	.	224;224;224	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	L	224	ENSP00000340884:S224L;ENSP00000330393:S224L;ENSP00000360099:S224L;ENSP00000360098:S224L;ENSP00000360097:S224L	ENSP00000340884:S224L	S	+	2	0	LEPR	65831104	0.997000	0.39634	1.000000	0.80357	0.937000	0.57800	3.676000	0.54612	1.536000	0.49237	0.650000	0.86243	TCA		0.368	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
RPAP2	79871	bcgsc.ca	37	1	92799023	92799023	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:92799023A>G	ENST00000610020.1	+	9	1640	c.1531A>G	c.(1531-1533)Agt>Ggt	p.S511G		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	511					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		TGAAAAGTTGAGTAAAGTGTA	0.333																																						.											0													119.0	117.0	118.0					1																	92799023		2203	4300	6503	SO:0001583	missense	79871			AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"""chromosome 1 open reading frame 82"""	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1531A>G	1.37:g.92799023A>G	ENSP00000476948:p.Ser511Gly		C9JKB5|Q49AS7|Q9H8Y2	Missense_Mutation	SNP	ENST00000610020.1	37	CCDS740.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.490173	0.44249	.	.	ENSG00000122484	ENST00000370343;ENST00000394482	.	.	.	5.49	4.35	0.52113	.	0.373385	0.36268	N	0.002681	T	0.36799	0.0980	L	0.54323	1.7	0.29479	N	0.856522	B	0.28713	0.22	B	0.28139	0.086	T	0.36261	-0.9755	8	0.59425	D	0.04	-3.388	12.1141	0.53856	0.7298:0.2702:0.0:0.0	.	511	Q8IXW5	RPAP2_HUMAN	G	511	.	ENSP00000359368:S511G	S	+	1	0	RPAP2	92571611	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.397000	0.52572	0.905000	0.36596	0.397000	0.26171	AGT		0.333	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813	
TCHH	7062	bcgsc.ca	37	1	152084663	152084663	+	Missense_Mutation	SNP	C	C	G	rs201434724		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:152084663C>G	ENST00000368804.1	-	2	1029	c.1030G>C	c.(1030-1032)Gag>Cag	p.E344Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	344	5 X 13 AA tandem repeats of R-R-E-Q-E-E- E-R-R-E-Q-Q-L.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.E344Q(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			cgcctctcctcctgctcgcgc	0.716																																						.											1	Substitution - Missense(1)	large_intestine(1)											11.0	15.0	14.0					1																	152084663		1908	3961	5869	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1030G>C	1.37:g.152084663C>G	ENSP00000357794:p.Glu344Gln		Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	6.972	0.549273	0.13374	.	.	ENSG00000159450	ENST00000368804	T	0.05786	3.39	4.13	-0.118	0.13547	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.46062	-0.9218	9	0.13853	T	0.58	.	9.5633	0.39383	0.0:0.3175:0.5938:0.0887	.	344	Q07283	TRHY_HUMAN	Q	344	ENSP00000357794:E344Q	ENSP00000357794:E344Q	E	-	1	0	TCHH	150351287	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.233000	0.09041	-0.165000	0.10908	-1.996000	0.00446	GAG		0.716	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TCHH	7062	bcgsc.ca	37	1	152084677	152084677	+	Missense_Mutation	SNP	A	A	T	rs199649490		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr1:152084677A>T	ENST00000368804.1	-	2	1015	c.1016T>A	c.(1015-1017)cTg>cAg	p.L339Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	339	5 X 13 AA tandem repeats of R-R-E-Q-E-E- E-R-R-E-Q-Q-L.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ctcgcgcctcagctgctgctc	0.706																																						.											0													11.0	15.0	14.0					1																	152084677		1976	4035	6011	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1016T>A	1.37:g.152084677A>T	ENSP00000357794:p.Leu339Gln		Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	6.735	0.504431	0.12822	.	.	ENSG00000159450	ENST00000368804	T	0.06218	3.33	3.82	-4.1	0.03940	.	.	.	.	.	T	0.00666	0.0022	N	0.08118	0	0.09310	N	1	B	0.21905	0.062	B	0.14023	0.01	T	0.48031	-0.9070	9	0.13470	T	0.59	.	4.258	0.10726	0.2515:0.0:0.1873:0.5612	.	339	Q07283	TRHY_HUMAN	Q	339	ENSP00000357794:L339Q	ENSP00000357794:L339Q	L	-	2	0	TCHH	150351301	0.000000	0.05858	0.024000	0.17045	0.001000	0.01503	-1.403000	0.02497	-0.646000	0.05452	-2.794000	0.00115	CTG		0.706	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
ZNF624	57547	bcgsc.ca	37	17	16527795	16527795	+	Missense_Mutation	SNP	C	C	A	rs8065506	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr17:16527795C>A	ENST00000311331.7	-	6	496	c.405G>T	c.(403-405)aaG>aaT	p.K135N		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	135			K -> N (in dbSNP:rs8065506). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|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(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTCGTGTAGCCTTCTTGGTTG	0.413													A|||	2443	0.487819	0.6906	0.3847	5008	,	,		17540	0.5347		0.2674	False		,,,				2504	0.4652				NSCLC(186;1023 2134 13330 38202 39800)	.											0			GRCh37	CM067489	ZNF624	M	rs8065506	A	ASN/LYS	2841,1565	491.1+/-362.0	916,1009,278	93.0	88.0	90.0		405	2.9	0.2	17	dbSNP_116	90	2334,6266	704.8+/-405.4	301,1732,2267	yes	missense	ZNF624	NM_020787.3	94	1217,2741,2545	AA,AC,CC		27.1395,35.5197,39.7893	benign	135/866	16527795	5175,7831	2203	4300	6503	SO:0001583	missense	57547			AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"""Zinc fingers, C2H2-type"", ""-"""	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.405G>T	17.37:g.16527795C>A	ENSP00000310472:p.Lys135Asn		Q3SY62|Q3SY63|Q6ZN27	Missense_Mutation	SNP	ENST00000311331.7	37	CCDS11180.1	939	0.42994505494505497	319	0.6483739837398373	128	0.35359116022099446	301	0.5262237762237763	191	0.2519788918205805	A	0.062	-1.222243	0.01530	0.644803	0.271395	ENSG00000197566	ENST00000311331	T	0.05382	3.45	2.92	2.92	0.33932	.	.	.	.	.	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10314	-1.0635	8	0.16896	T	0.51	.	7.3813	0.26858	0.5465:0.4535:0.0:0.0	rs8065506;rs52795751;rs61430075;rs8065506	135	Q9P2J8	ZN624_HUMAN	N	135	ENSP00000310472:K135N	ENSP00000310472:K135N	K	-	3	2	ZNF624	16468520	0.001000	0.12720	0.193000	0.23327	0.310000	0.27922	0.419000	0.21247	0.537000	0.28751	-0.262000	0.10625	AAG		0.413	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617	
FUT3	2525	bcgsc.ca	37	19	5843877	5843877	+	Missense_Mutation	SNP	G	G	A	rs28381969	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr19:5843877G>A	ENST00000303225.6	-	3	1608	c.974C>T	c.(973-975)aCg>aTg	p.T325M	FUT3_ENST00000589918.1_Missense_Mutation_p.T325M|FUT3_ENST00000458379.2_Missense_Mutation_p.T325M|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000589620.1_Missense_Mutation_p.T325M	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	325			T -> M (in dbSNP:rs28381969). {ECO:0000269|Ref.5}.		cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						AGGCCGCAGCGTCTCCCGCCA	0.637													G|||	37	0.00738818	0.025	0.0043	5008	,	,		19604	0.001		0.0	False		,,,				2504	0.0				Esophageal Squamous(82;745 1728 24593 44831)	.											0													42.0	45.0	44.0					19																	5843877		2203	4300	6503	SO:0001583	missense	2525				CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.974C>T	19.37:g.5843877G>A	ENSP00000305603:p.Thr325Met		B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	36	0.016483516483516484	18	0.036585365853658534	1	0.0027624309392265192	6	0.01048951048951049	11	0.014511873350923483	G	12.11	1.838692	0.32513	.	.	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.24350	1.86;1.86	2.29	1.18	0.20946	.	0.943966	0.08680	N	0.909636	T	0.07413	0.0187	M	0.79805	2.47	0.09310	N	1	P;P;P;P	0.38617	0.64;0.483;0.483;0.483	B;B;B;B	0.36186	0.219;0.148;0.148;0.148	T	0.11494	-1.0585	10	0.37606	T	0.19	.	5.4124	0.16356	0.1897:0.0:0.8103:0.0	rs28381969	325;325;325;325	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	M	325	ENSP00000305603:T325M;ENSP00000416443:T325M	ENSP00000305603:T325M	T	-	2	0	FUT3	5794877	0.000000	0.05858	0.620000	0.29132	0.507000	0.33981	-1.150000	0.03178	0.242000	0.21303	0.194000	0.17425	ACG		0.637	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
OTOF	9381	bcgsc.ca	37	2	26698856	26698856	+	Missense_Mutation	SNP	A	A	G	rs397515596		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr2:26698856A>G	ENST00000272371.2	-	24	3043	c.2917T>C	c.(2917-2919)Ttt>Ctt	p.F973L	OTOF_ENST00000339598.3_Missense_Mutation_p.F226L|OTOF_ENST00000338581.6_Missense_Mutation_p.F226L|OTOF_ENST00000403946.3_Missense_Mutation_p.F973L|OTOF_ENST00000402415.3_Missense_Mutation_p.F283L	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	973	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCGGCGGCAAAGAGGCTGCGG	0.652																																					GBM(102;732 1451 20652 24062 31372)	.											0													43.0	38.0	39.0					2																	26698856		2200	4295	6495	SO:0001583	missense	9381			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2917T>C	2.37:g.26698856A>G	ENSP00000272371:p.Phe973Leu		B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.325696	0.60743	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	5.41	5.41	0.78517	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.36690	0.0976	N	0.00303	-1.675	0.80722	D	1	P;B;P;B	0.48764	0.711;0.024;0.915;0.007	B;B;P;B	0.48952	0.356;0.018;0.596;0.018	T	0.56535	-0.7963	10	0.05620	T	0.96	-4.735	15.0966	0.72238	1.0:0.0:0.0:0.0	.	973;226;283;226	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	L	226;226;283;973;973	ENSP00000345137:F226L;ENSP00000344521:F226L;ENSP00000383906:F283L;ENSP00000272371:F973L;ENSP00000385255:F973L	ENSP00000272371:F973L	F	-	1	0	OTOF	26552360	1.000000	0.71417	0.999000	0.59377	0.751000	0.42716	6.119000	0.71590	2.059000	0.61396	0.459000	0.35465	TTT		0.652	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
PECR	55825	bcgsc.ca	37	2	216923679	216923679	+	Missense_Mutation	SNP	C	C	T	rs1429148	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr2:216923679C>T	ENST00000265322.7	-	4	519	c.445G>A	c.(445-447)Gag>Aag	p.E149K	PECR_ENST00000497889.1_5'UTR	NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	149			E -> K (in dbSNP:rs1429148).		fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CCTCCATGCTCTTTCATCCAG	0.393													C|||	877	0.17512	0.2451	0.1167	5008	,	,		19157	0.1935		0.0497	False		,,,				2504	0.2321					.											0								C	LYS/GLU	941,3465	358.6+/-314.5	97,747,1359	111.0	107.0	108.0		445	-1.0	0.2	2	dbSNP_88	108	508,8092	145.1+/-200.9	12,484,3804	yes	missense	PECR	NM_018441.5	56	109,1231,5163	TT,TC,CC		5.907,21.3572,11.141	benign	149/304	216923679	1449,11557	2203	4300	6503	SO:0001583	missense	55825			AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18281	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 29C, member 1"""	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.445G>A	2.37:g.216923679C>T	ENSP00000265322:p.Glu149Lys		B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Missense_Mutation	SNP	ENST00000265322.7	37	CCDS33375.1	334	0.15293040293040294	118	0.23983739837398374	37	0.10220994475138122	141	0.2465034965034965	38	0.05013192612137203	C	8.624	0.892018	0.17613	0.213572	0.05907	ENSG00000115425	ENST00000265322	T	0.42513	0.97	5.77	-1.01	0.10169	Apoptosis regulator, Bcl-2, BH (1);NAD(P)-binding domain (1);	0.630718	0.17997	N	0.155025	T	0.00012	0.0000	N	0.02775	-0.495	0.28925	P	0.891905	B;B	0.15930	0.005;0.015	B;B	0.25614	0.027;0.062	T	0.34650	-0.9820	9	0.10377	T	0.69	.	6.3072	0.21145	0.0:0.4753:0.1195:0.4052	rs1429148;rs3732029;rs59553324;rs1429148	149;3	Q9BY49;Q9BY49-2	PECR_HUMAN;.	K	149	ENSP00000265322:E149K	ENSP00000265322:E149K	E	-	1	0	PECR	216631924	0.024000	0.19004	0.180000	0.23079	0.930000	0.56654	-0.209000	0.09358	-0.531000	0.06340	-1.106000	0.02097	GAG		0.393	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441	
EDEM2	55741	bcgsc.ca	37	20	33711701	33711701	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr20:33711701A>G	ENST00000374492.3	-	9	1211	c.1106T>C	c.(1105-1107)cTt>cCt	p.L369P	EDEM2_ENST00000540582.1_Missense_Mutation_p.L328P|EDEM2_ENST00000374491.3_Missense_Mutation_p.L332P|EDEM2_ENST00000541621.1_Missense_Mutation_p.L148P|EDEM2_ENST00000542871.1_Missense_Mutation_p.L93P	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	369					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			ACCTGGCCGAAGTGGGTAGCC	0.542																																					Esophageal Squamous(51;906 1021 24535 36410 39145)	.											0													91.0	79.0	83.0					20																	33711701		2203	4300	6503	SO:0001583	missense	55741			AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.1106T>C	20.37:g.33711701A>G	ENSP00000363616:p.Leu369Pro		B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	37	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.886671	0.91814	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000541621;ENST00000542871;ENST00000540582	T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.83691	0.5309	H	0.98664	4.295	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.90157	0.4225	10	0.87932	D	0	-15.4479	16.3662	0.83325	1.0:0.0:0.0:0.0	.	328;148;332;369	F5GZ44;G3V1Q0;Q9BV94-2;Q9BV94	.;.;.;EDEM2_HUMAN	P	332;369;148;93;328	ENSP00000363615:L332P;ENSP00000363616:L369P;ENSP00000443528:L148P;ENSP00000441642:L93P;ENSP00000441548:L328P	ENSP00000363615:L332P	L	-	2	0	EDEM2	33175362	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	9.339000	0.96797	2.274000	0.75844	0.533000	0.62120	CTT		0.542	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
MUC4	4585	bcgsc.ca	37	3	195511334	195511334	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:195511334T>C	ENST00000463781.3	-	2	7576	c.7117A>G	c.(7117-7119)Agc>Ggc	p.S2373G	MUC4_ENST00000475231.1_Missense_Mutation_p.S2373G|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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)	p.S2373G(2)		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)		GAGGAAGAGCTGGTGACAGGA	0.592																																						.											2	Substitution - Missense(2)	skin(2)											25.0	28.0	27.0					3																	195511334		682	1585	2267	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.7117A>G	3.37:g.195511334T>C	ENSP00000417498:p.Ser2373Gly		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	.	.	.	.	.	.	.	.	.	.	t	0.378	-0.930247	0.02359	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.48;1.47	.	.	.	.	.	.	.	.	T	0.10680	0.0261	N	0.08118	0	0.09310	N	1	P	0.37985	0.613	B	0.35899	0.213	T	0.13629	-1.0502	7	.	.	.	.	2.3131	0.04191	0.0:0.2713:0.2996:0.4291	.	2373	E7ESK3	.	G	2373	ENSP00000417498:S2373G;ENSP00000420243:S2373G	.	S	-	1	0	MUC4	196995729	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-0.538000	0.06120	-1.841000	0.01183	-2.075000	0.00382	AGC		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	bcgsc.ca	37	3	195511925	195511925	+	Missense_Mutation	SNP	A	A	G	rs78031084	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr3:195511925A>G	ENST00000463781.3	-	2	6985	c.6526T>C	c.(6526-6528)Tct>Cct	p.S2176P	MUC4_ENST00000475231.1_Missense_Mutation_p.S2176P|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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)	p.S2176P(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)		ACAGGAAGAGAGGTGGCGTGA	0.587													.|||	274	0.0547125	0.0189	0.0288	5008	,	,		15474	0.122		0.0805	False		,,,				2504	0.0256					.											1	Substitution - Missense(1)	kidney(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.6526T>C	3.37:g.195511925A>G	ENSP00000417498:p.Ser2176Pro		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	.	.	.	.	.	.	.	.	.	.	a	3.373	-0.127914	0.06753	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.44881	0.91;0.97	.	.	.	.	.	.	.	.	T	0.12390	0.0301	N	0.02539	-0.55	0.09310	N	0.999998	B	0.19817	0.039	B	0.23018	0.043	T	0.16129	-1.0413	7	.	.	.	.	2.133	0.03754	0.2597:0.0:0.2591:0.4812	.	2176	E7ESK3	.	P	2176	ENSP00000417498:S2176P;ENSP00000420243:S2176P	.	S	-	1	0	MUC4	196996320	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-2.972000	0.00667	-2.644000	0.00427	-2.094000	0.00368	TCT		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNPY3	10695	bcgsc.ca	37	6	42906384	42906384	+	Missense_Mutation	SNP	G	G	T	rs9471969	byFrequency	TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr6:42906384G>T	ENST00000372836.4	+	6	1063	c.692G>T	c.(691-693)aGc>aTc	p.S231I	RP3-475N16.1_ENST00000450671.1_RNA|CNPY3_ENST00000394142.3_3'UTR	NM_006586.3	NP_006577.2	Q9BT09	CNPY3_HUMAN	canopy FGF signaling regulator 3	231	Saposin B-type.		S -> I (in dbSNP:rs9471969).		innate immune response (GO:0045087)|toll-like receptor signaling pathway (GO:0002224)	endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)	6	Colorectal(47;0.196)		all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			AAGAAGAGCAGCAGGGCCAAG	0.622													G|||	1071	0.213858	0.3328	0.2075	5008	,	,		19202	0.0149		0.2744	False		,,,				2504	0.2004					.											0								G	ILE/SER	1419,2987	449.8+/-349.2	230,959,1014	79.0	80.0	80.0		692	5.0	0.6	6	dbSNP_119	80	2199,6399	362.9+/-332.9	263,1673,2363	yes	missense	CNPY3	NM_006586.3	142	493,2632,3377	TT,TG,GG		25.5757,32.2061,27.8222	benign	231/279	42906384	3618,9386	2203	4299	6502	SO:0001583	missense	10695			U80744	CCDS4875.1	6p21.1	2013-09-19	2013-07-23	2007-10-22	ENSG00000137161	ENSG00000137161		"""Trinucleotide (CAG) repeat containing"""	11968	protein-coding gene	gene with protein product		610774	"""trinucleotide repeat containing 5"", ""canopy 3 homolog (zebrafish)"""	TNRC5		9225980	Standard	NM_006586		Approved	CAG4A	uc003ota.4	Q9BT09	OTTHUMG00000014708	ENST00000372836.4:c.692G>T	6.37:g.42906384G>T	ENSP00000361926:p.Ser231Ile		O15412|Q0P6I2|Q8NF54|Q8WTU8|Q9P0F2	Missense_Mutation	SNP	ENST00000372836.4	37	CCDS4875.1	463	0.211996336996337	158	0.32113821138211385	81	0.22375690607734808	13	0.022727272727272728	211	0.2783641160949868	G	16.53	3.149626	0.57151	0.322061	0.255757	ENSG00000137161	ENST00000372836	T	0.24723	1.84	5.02	5.02	0.67125	.	0.433550	0.25747	N	0.028570	T	0.06690	0.0171	N	0.08118	0	0.09310	P	1.0	B	0.32693	0.38	B	0.28011	0.085	T	0.15607	-1.0431	9	0.39692	T	0.17	-13.8584	15.6126	0.76737	0.0:0.0:1.0:0.0	rs9471969;rs52835372;rs58234738;rs9471969	231	Q9BT09	CNPY3_HUMAN	I	231	ENSP00000361926:S231I	ENSP00000361926:S231I	S	+	2	0	CNPY3	43014362	1.000000	0.71417	0.631000	0.29282	0.974000	0.67602	4.641000	0.61375	2.504000	0.84457	0.462000	0.41574	AGC		0.622	CNPY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040564.1	NM_006586	
CSMD3	114788	bcgsc.ca	37	8	113516067	113516067	+	Missense_Mutation	SNP	G	G	A	rs368685063		TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chr8:113516067G>A	ENST00000297405.5	-	30	5279	c.5035C>T	c.(5035-5037)Cgg>Tgg	p.R1679W	CSMD3_ENST00000455883.2_Missense_Mutation_p.R1575W|CSMD3_ENST00000343508.3_Missense_Mutation_p.R1639W|CSMD3_ENST00000352409.3_Missense_Mutation_p.R1679W	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1679	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCATCACTCCGAAAAGCCAAA	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																												.											0								G	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	160.0	144.0	149.0		4723,5035,4915	5.1	1.0	8		149	0,8600		0,0,4300	no	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	101,101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	1575/3539,1679/3708,1639/3668	113516067	1,13005	2203	4300	6503	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5035C>T	8.37:g.113516067G>A	ENSP00000297405:p.Arg1679Trp		Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687673	0.88639	2.27E-4	0.0	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02	5.08	5.08	0.68730	CUB (5);	0.000000	0.64402	D	0.000002	T	0.54854	0.1884	M	0.89095	3.005	0.50813	D	0.999892	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.99;0.994;0.998	T	0.61530	-0.7044	10	0.52906	T	0.07	.	18.6626	0.91477	0.0:0.0:1.0:0.0	.	1575;1679;1639	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	W	1639;1679;1019;1575;1679	ENSP00000345799:R1639W;ENSP00000297405:R1679W;ENSP00000341558:R1019W;ENSP00000412263:R1575W;ENSP00000343124:R1679W	ENSP00000297405:R1679W	R	-	1	2	CSMD3	113585243	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.538000	0.98072	2.629000	0.89072	0.650000	0.86243	CGG		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
MT-CYB	4519	bcgsc.ca	37	M	15216	15216	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8338-01A-11D-2310-10	TCGA-KL-8338-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e9966607-f842-41ec-8d4a-dff22bec65f6	511dfe93-0a8e-4ff1-8724-6f87ec952e5c	g.chrM:15216G>A	ENST00000361789.2	+	1	470	c.470G>A	c.(469-471)gGg>gAg	p.G157E	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	157					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CCCATACATTGGGACAGACCT	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																										.											0																																										SO:0001583	missense	0					mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.470G>A	M.37:g.15216G>A	ENSP00000354554:p.Gly157Glu	585	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																					0.453	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
