#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_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
PHTF1	10745	hgsc.bcm.edu	37	1	114254606	114254606	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:114254606C>A	ENST00000369604.1	-	9	1396	c.913G>T	c.(913-915)Gtt>Ttt	p.V305F	PHTF1_ENST00000357783.2_Missense_Mutation_p.V305F|PHTF1_ENST00000393357.2_Missense_Mutation_p.V305F|PHTF1_ENST00000447664.2_3'UTR|PHTF1_ENST00000369596.2_Missense_Mutation_p.V252F|PHTF1_ENST00000369600.1_Missense_Mutation_p.V252F|PHTF1_ENST00000369598.1_Missense_Mutation_p.V260F|PHTF1_ENST00000474926.1_5'UTR			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	305					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTATTCTTAACTTCACAACCA	0.378																																					p.V305F		Atlas-SNP	.											.	PHTF1	69	.	0			c.G913T						.						124.0	118.0	120.0					1																	114254606		2203	4300	6503	SO:0001583	missense	10745	exon8			TCTTAACTTCACA	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.913G>T	chr1.hg19:g.114254606C>A	ENSP00000358617:p.Val305Phe	106.0	0.0		108.0	62.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Missense_Mutation	SNP	ENST00000369604.1	hg19	CCDS861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.27|11.27	1.588763|1.588763	0.28357|0.28357	.|.	.|.	ENSG00000116793|ENSG00000116793	ENST00000412670|ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604;ENST00000357783	.|.	.|.	.|.	5.72|5.72	0.704|0.704	0.18121|0.18121	.|.	.|0.572283	.|0.18251	.|N	.|0.146927	T|T	0.08582|0.08582	0.0213|0.0213	N|N	0.14661|0.14661	0.345|0.345	0.24930|0.24930	N|N	0.991922|0.991922	.|B;B;B	.|0.10296	.|0.0;0.003;0.0	.|B;B;B	.|0.08055	.|0.0;0.003;0.002	T|T	0.26503|0.26503	-1.0101|-1.0101	5|9	.|0.49607	.|T	.|0.09	-7.6242|-7.6242	5.5222|5.5222	0.16939|0.16939	0.127:0.4715:0.0:0.4015|0.127:0.4715:0.0:0.4015	.|.	.|305;60;305	.|Q9UMS5;Q5TCR1;Q9UMS5-2	.|PHTF1_HUMAN;.;.	N|F	60|260;305;252;260;252;305;305	.|.	.|ENSP00000350428:V305F	K|V	-|-	3|1	2|0	PHTF1|PHTF1	114056129|114056129	0.841000|0.841000	0.29509|0.29509	0.989000|0.989000	0.46669|0.46669	0.748000|0.748000	0.42578|0.42578	0.063000|0.063000	0.14410|0.14410	0.363000|0.363000	0.24346|0.24346	0.460000|0.460000	0.39030|0.39030	AAG|GTT	.	.		0.378	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608	
TDRD5	163589	hgsc.bcm.edu	37	1	179609571	179609571	+	Silent	SNP	A	A	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:179609571A>G	ENST00000367614.1	+	11	2150	c.1791A>G	c.(1789-1791)agA>agG	p.R597R	TDRD5_ENST00000294848.8_Silent_p.R597R|TDRD5_ENST00000444136.1_Silent_p.R597R	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	597					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CTTGGGTGAGACCAGTAGAGG	0.408																																					p.R597R		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1791G						.						192.0	157.0	169.0					1																	179609571		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon11			GGTGAGACCAGTA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1791A>G	chr1.hg19:g.179609571A>G		64.0	0.0		72.0	20.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.408	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
PTGS2	5743	hgsc.bcm.edu	37	1	186647479	186647479	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:186647479C>G	ENST00000367468.5	-	4	507	c.371G>C	c.(370-372)aGc>aCc	p.S124T	PTGS2_ENST00000490885.2_5'UTR|RP5-973M2.2_ENST00000608917.1_lincRNA	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	124					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GGCTTCCCAGCTTTTGTAGCC	0.408																																					p.S124T		Atlas-SNP	.											.	PTGS2	144	.	0			c.G371C						.						82.0	73.0	76.0					1																	186647479		2203	4300	6503	SO:0001583	missense	5743	exon4			TCCCAGCTTTTGT	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.371G>C	chr1.hg19:g.186647479C>G	ENSP00000356438:p.Ser124Thr	140.0	0.0		161.0	12.0	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	hg19	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828035	0.50845	.	.	ENSG00000073756	ENST00000367468	T	0.18657	2.2	5.52	3.66	0.41972	.	0.156380	0.64402	D	0.000001	T	0.19167	0.0460	L	0.56340	1.77	0.47476	D	0.999436	B	0.12630	0.006	B	0.23018	0.043	T	0.04781	-1.0927	10	0.20519	T	0.43	-13.0003	8.9337	0.35686	0.0:0.7395:0.123:0.1375	.	124	P35354	PGH2_HUMAN	T	124	ENSP00000356438:S124T	ENSP00000356438:S124T	S	-	2	0	PTGS2	184914102	0.644000	0.27277	1.000000	0.80357	0.976000	0.68499	-0.111000	0.10807	0.698000	0.31739	-0.136000	0.14681	AGC	.	.		0.408	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963	
KIF21B	23046	hgsc.bcm.edu	37	1	200946498	200946498	+	Silent	SNP	C	C	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:200946498C>A	ENST00000422435.2	-	31	4483	c.4167G>T	c.(4165-4167)tcG>tcT	p.S1389S	KIF21B_ENST00000332129.2_Silent_p.S1376S|KIF21B_ENST00000360529.5_Silent_p.S1376S|KIF21B_ENST00000461742.2_Silent_p.S1389S	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1389					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TCACCTGGCCCGAGGACCTGC	0.562																																					p.S1389S		Atlas-SNP	.											.	KIF21B	208	.	0			c.G4167T						.						85.0	81.0	82.0					1																	200946498		2203	4300	6503	SO:0001819	synonymous_variant	23046	exon31			CTGGCCCGAGGAC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4167G>T	chr1.hg19:g.200946498C>A		111.0	0.0		96.0	52.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.562	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
CACNA1S	779	hgsc.bcm.edu	37	1	201017755	201017755	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:201017755T>A	ENST00000362061.3	-	36	4622	c.4396A>T	c.(4396-4398)Aca>Tca	p.T1466S	CACNA1S_ENST00000367338.3_Missense_Mutation_p.T1447S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1466					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCAAAGAGTGTGGCATTGAAG	0.607																																					p.T1466S		Atlas-SNP	.											.	CACNA1S	249	.	0			c.A4396T						.						139.0	108.0	119.0					1																	201017755		2203	4300	6503	SO:0001583	missense	779	exon36			AGAGTGTGGCATT	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4396A>T	chr1.hg19:g.201017755T>A	ENSP00000355192:p.Thr1466Ser	47.0	0.0		50.0	29.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	31	5.065373	0.93898	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.09255	3.0;3.0	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.41190	0.1148	M	0.89904	3.07	0.58432	D	0.999993	D	0.76494	0.999	D	0.83275	0.996	T	0.51996	-0.8634	10	0.87932	D	0	.	15.2557	0.73582	0.0:0.0:0.0:1.0	.	1466	Q13698	CAC1S_HUMAN	S	1466;1447	ENSP00000355192:T1466S;ENSP00000356307:T1447S	ENSP00000355192:T1466S	T	-	1	0	CACNA1S	199284378	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	7.965000	0.87945	2.060000	0.61445	0.455000	0.32223	ACA	.	.		0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
EXO1	9156	hgsc.bcm.edu	37	1	242035468	242035468	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr1:242035468A>G	ENST00000366548.3	+	12	1995	c.1402A>G	c.(1402-1404)Act>Gct	p.T468A	EXO1_ENST00000518483.1_Missense_Mutation_p.T468A|EXO1_ENST00000348581.5_Missense_Mutation_p.T468A	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	468	Interaction with MLH1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAATGGACCTACTAACAAAAA	0.378								Editing and processing nucleases																													p.T468A		Atlas-SNP	.											.	EXO1	103	.	0			c.A1402G						.						82.0	82.0	82.0					1																	242035468		2203	4300	6503	SO:0001583	missense	9156	exon12			GGACCTACTAACA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1402A>G	chr1.hg19:g.242035468A>G	ENSP00000355506:p.Thr468Ala	329.0	0.0		381.0	130.0	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	hg19	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.837237	0.00579	.	.	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.31769	1.48;1.48;1.48	5.85	-0.853	0.10709	.	1.139940	0.06337	N	0.707193	T	0.12902	0.0313	N	0.05383	-0.06	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.29397	-1.0013	10	0.08381	T	0.77	-21.1506	5.8209	0.18526	0.3839:0.0:0.4283:0.1877	.	467;468;468	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	A	468	ENSP00000355506:T468A;ENSP00000311873:T468A;ENSP00000430251:T468A	ENSP00000311873:T468A	T	+	1	0	EXO1	240102091	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.178000	0.09782	0.141000	0.18875	-0.280000	0.10049	ACT	.	.		0.378	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
ZDBF2	57683	hgsc.bcm.edu	37	2	207172701	207172701	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr2:207172701T>C	ENST00000374423.3	+	5	3835	c.3449T>C	c.(3448-3450)gTt>gCt	p.V1150A		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1150							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TACTTGGAAGTTAAGAACAGC	0.378																																					p.V1150A		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T3449C						.						75.0	72.0	73.0					2																	207172701		1855	4096	5951	SO:0001583	missense	57683	exon5			TGGAAGTTAAGAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3449T>C	chr2.hg19:g.207172701T>C	ENSP00000363545:p.Val1150Ala	124.0	0.0		124.0	50.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	T	8.634	0.894421	0.17613	.	.	ENSG00000204186	ENST00000374423	T	0.41758	0.99	4.25	0.388	0.16264	.	.	.	.	.	T	0.20495	0.0493	N	0.14661	0.345	0.09310	N	1	B	0.17268	0.021	B	0.15052	0.012	T	0.22243	-1.0222	9	0.21540	T	0.41	.	3.968	0.09441	0.5866:0.0:0.1134:0.2999	.	1150	Q9HCK1	ZDBF2_HUMAN	A	1150	ENSP00000363545:V1150A	ENSP00000363545:V1150A	V	+	2	0	ZDBF2	206880946	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.194000	0.17135	0.057000	0.16193	0.528000	0.53228	GTT	.	.		0.378	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
DGKD	8527	hgsc.bcm.edu	37	2	234360641	234360641	+	Silent	SNP	C	C	T	rs375913920		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr2:234360641C>T	ENST00000264057.2	+	18	2211	c.2199C>T	c.(2197-2199)ccC>ccT	p.P733P	DGKD_ENST00000409813.3_Silent_p.P689P	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	733					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	GTTCCTTACCCGGTGGCTCAG	0.498													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17823	0.0		0.0	False		,,,				2504	0.0				p.P733P		Atlas-SNP	.											.	DGKD	106	.	0			c.C2199T						.	C	,	3,4403	6.2+/-15.9	0,3,2200	127.0	118.0	121.0		2067,2199	-9.6	0.1	2		121	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DGKD	NM_003648.2,NM_152879.2	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	689/1171,733/1215	234360641	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8527	exon18			CTTACCCGGTGGC	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2851	protein-coding gene	gene with protein product	"""diglyceride kinase"""	601826	"""diacylglycerol kinase, delta (130kD)"""			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2199C>T	chr2.hg19:g.234360641C>T		59.0	0.0		65.0	26.0	NM_152879	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	hg19	CCDS2504.1																																																																																			.	.		0.498	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648	
ZFYVE20	64145	hgsc.bcm.edu	37	3	15115634	15115634	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:15115634C>A	ENST00000253699.3	-	14	2623	c.2010G>T	c.(2008-2010)gaG>gaT	p.E670D	ZFYVE20_ENST00000476527.2_Missense_Mutation_p.E670D	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	670	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB5A.|Poly-Glu.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						CTGCTTCCTCCTCCTCGTCCT	0.562																																					p.E670D		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G2010T						.						144.0	148.0	146.0					3																	15115634		2203	4300	6503	SO:0001583	missense	64145	exon14			TTCCTCCTCCTCG	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"""Zinc fingers, FYVE domain containing"""	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.2010G>T	chr3.hg19:g.15115634C>A	ENSP00000253699:p.Glu670Asp	70.0	0.0		48.0	22.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	hg19	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	3.450	-0.112244	0.06881	.	.	ENSG00000131381	ENST00000253699;ENST00000476527	T;T	0.54071	0.59;0.59	5.02	-3.86	0.04230	.	0.312584	0.33290	N	0.005077	T	0.23249	0.0562	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.07501	-1.0769	10	0.19147	T	0.46	-5.8485	0.7989	0.01072	0.2115:0.1569:0.1957:0.4359	.	670	Q9H1K0	RBNS5_HUMAN	D	670	ENSP00000253699:E670D;ENSP00000422551:E670D	ENSP00000253699:E670D	E	-	3	2	ZFYVE20	15090638	0.002000	0.14202	0.001000	0.08648	0.009000	0.06853	-0.282000	0.08445	-0.575000	0.05982	0.591000	0.81541	GAG	.	.		0.562	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125856710	125856710	+	Silent	SNP	C	C	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:125856710C>A	ENST00000393434.2	-	10	1519	c.1170G>T	c.(1168-1170)ctG>ctT	p.L390L	ALDH1L1_ENST00000393431.2_Silent_p.L390L|ALDH1L1_ENST00000452905.2_Silent_p.L289L|ALDH1L1_ENST00000273450.3_Silent_p.L400L|ALDH1L1_ENST00000472186.1_Silent_p.L390L	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	390	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	TCCTCACTAACAGCTGGATGA	0.582																																					p.L400L		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1200T						.						137.0	101.0	113.0					3																	125856710		2203	4300	6503	SO:0001819	synonymous_variant	10840	exon10			CACTAACAGCTGG	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1170G>T	chr3.hg19:g.125856710C>A		113.0	0.0		107.0	36.0	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	hg19	CCDS3034.1																																																																																			.	.		0.582	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
SLC9A9	285195	hgsc.bcm.edu	37	3	142987725	142987725	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:142987725C>A	ENST00000316549.6	-	15	1910	c.1702G>T	c.(1702-1704)Gcc>Tcc	p.A568S		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	568					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						ACCCCATAGGCTTGAGGACTG	0.493																																					p.A568S		Atlas-SNP	.											SLC9A9,NS,carcinoma,0,1	SLC9A9	117	.	0			c.G1702T						.						144.0	139.0	141.0					3																	142987725		2203	4300	6503	SO:0001583	missense	285195	exon15			CATAGGCTTGAGG	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1702G>T	chr3.hg19:g.142987725C>A	ENSP00000320246:p.Ala568Ser	113.0	0.0		87.0	41.0	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	hg19	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600024	0.87055	.	.	ENSG00000181804	ENST00000316549	T	0.57595	0.39	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000001	T	0.71796	0.3382	M	0.78637	2.42	0.47276	D	0.999378	D	0.63880	0.993	D	0.72625	0.978	T	0.66212	-0.5980	10	0.10902	T	0.67	.	19.6526	0.95823	0.0:1.0:0.0:0.0	.	568	Q8IVB4	SL9A9_HUMAN	S	568	ENSP00000320246:A568S	ENSP00000320246:A568S	A	-	1	0	SLC9A9	144470415	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.634000	0.67833	2.641000	0.89580	0.655000	0.94253	GCC	.	.		0.493	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
PLSCR1	5359	hgsc.bcm.edu	37	3	146234856	146234856	+	Silent	SNP	G	G	T	rs377240309		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:146234856G>T	ENST00000342435.4	-	8	1247	c.837C>A	c.(835-837)atC>atA	p.I279I	PLSCR1_ENST00000484560.1_5'UTR|PLSCR1_ENST00000448205.1_5'UTR|PLSCR1_ENST00000487389.1_Silent_p.I272I|PLSCR1_ENST00000448787.2_Silent_p.I198I	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	279					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						AAGGGAACTGGATTCCAAAGT	0.368																																					p.I279I		Atlas-SNP	.											.	PLSCR1	35	.	0			c.C837A						.						126.0	120.0	122.0					3																	146234856		2203	4300	6503	SO:0001819	synonymous_variant	5359	exon8			GAACTGGATTCCA	AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.837C>A	chr3.hg19:g.146234856G>T		167.0	0.0		169.0	32.0	NM_021105	B2R8H8|B4DTE8	Silent	SNP	ENST00000342435.4	hg19	CCDS3135.1	.	.	.	.	.	.	.	.	.	.	.	9.900	1.206612	0.22205	.	.	ENSG00000188313	ENST00000483300	.	.	.	4.84	0.891	0.19224	.	.	.	.	.	T	0.53498	0.1800	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42515	-0.9447	4	.	.	.	.	6.5816	0.22598	0.2178:0.0:0.6543:0.1279	.	.	.	.	Y	146	.	.	S	-	2	0	PLSCR1	147717546	1.000000	0.71417	0.951000	0.38953	0.988000	0.76386	0.690000	0.25451	0.183000	0.20059	0.555000	0.69702	TCC	.	.		0.368	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105	
MFSD1	64747	hgsc.bcm.edu	37	3	158531837	158531837	+	Silent	SNP	C	C	T	rs147447476		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr3:158531837C>T	ENST00000264266.8	+	7	695	c.633C>T	c.(631-633)ctC>ctT	p.L211L	MFSD1_ENST00000415822.2_Silent_p.L260L|MFSD1_ENST00000392813.4_Silent_p.L221L			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	211					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACACAACCCTCGGGATCACAC	0.453																																					p.L260L	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											MFSD1_ENST00000415822,right_lower_lobe,carcinoma,0,2	MFSD1	88	.	0			c.C780T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	175.0	137.0	150.0		663,780	-2.8	0.9	3	dbSNP_134	150	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MFSD1	NM_001167903.1,NM_022736.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	221/476,260/515	158531837	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64747	exon7			AACCCTCGGGATC	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.633C>T	chr3.hg19:g.158531837C>T		73.0	0.0		55.0	33.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	hg19																																																																																				.	C|1.000;T|0.000		0.453	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
ZCCHC4	29063	hgsc.bcm.edu	37	4	25314444	25314444	+	Silent	SNP	A	A	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr4:25314444A>C	ENST00000302874.4	+	1	37	c.13A>C	c.(13-15)Agg>Cgg	p.R5R	ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	5							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				GGCGGCCTCCAGGAATGGGTT	0.662											OREG0016141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R5R		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.A13C						.						81.0	97.0	92.0					4																	25314444		1985	4154	6139	SO:0001819	synonymous_variant	29063	exon1			GCCTCCAGGAATG	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"""Zinc fingers, CCHC domain containing"""	22917	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 4"""	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.13A>C	chr4.hg19:g.25314444A>C		55.0	0.0	778	44.0	19.0	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Silent	SNP	ENST00000302874.4	hg19	CCDS43218.1																																																																																			.	.		0.662	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1		
PDLIM4	8572	hgsc.bcm.edu	37	5	131606786	131606786	+	Splice_Site	SNP	G	G	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:131606786G>T	ENST00000253754.3	+	4	570	c.506G>T	c.(505-507)aGc>aTc	p.S169I	PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Splice_Site_p.S169I|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	169							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCACCCCCCAGGTAGCACAGA	0.587																																					p.S169I		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G506T						.						124.0	122.0	123.0					5																	131606786		2203	4300	6503	SO:0001630	splice_region_variant	8572	exon4			CCCCCAGGTAGCA	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.506+1G>T	chr5.hg19:g.131606786G>T		98.0	0.0		99.0	4.0	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	hg19	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930457	0.73327	.	.	ENSG00000131435	ENST00000253754;ENST00000379018;ENST00000418373	T;T;T	0.48522	2.58;1.91;0.81	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.67674	0.2918	M	0.68952	2.095	0.80722	D	1	D;D;B	0.89917	1.0;1.0;0.293	D;D;B	0.97110	1.0;0.997;0.095	T	0.69636	-0.5092	10	0.72032	D	0.01	-31.8443	16.2992	0.82801	0.0:0.0:1.0:0.0	.	169;110;169	P50479-2;C9J542;P50479	.;.;PDLI4_HUMAN	I	169;169;110	ENSP00000253754:S169I;ENSP00000368303:S169I;ENSP00000411753:S110I	ENSP00000253754:S169I	S	+	2	0	PDLIM4	131634685	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	5.142000	0.64820	2.631000	0.89168	0.455000	0.32223	AGC	.	.		0.587	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	Missense_Mutation
UNC5A	90249	hgsc.bcm.edu	37	5	176306745	176306745	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:176306745A>T	ENST00000329542.4	+	15	2661	c.2387A>T	c.(2386-2388)aAg>aTg	p.K796M	UNC5A_ENST00000261961.3_Missense_Mutation_p.K756M	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	796	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTGCCTCCAAGCCCAGCCCC	0.697																																					p.K796M		Atlas-SNP	.											.	UNC5A	76	.	0			c.A2387T						.						44.0	47.0	46.0					5																	176306745		2203	4300	6503	SO:0001583	missense	90249	exon15			CCTCCAAGCCCAG	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"""Immunoglobulin superfamily / I-set domain containing"""	12567	protein-coding gene	gene with protein product		607869	"""unc5 (C.elegans homolog) a"""				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.2387A>T	chr5.hg19:g.176306745A>T	ENSP00000332737:p.Lys796Met	85.0	0.0		73.0	13.0	NM_133369	B2RXE6|Q8TF26|Q96GP4	Missense_Mutation	SNP	ENST00000329542.4	hg19	CCDS34299.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848309	0.71603	.	.	ENSG00000113763	ENST00000329542;ENST00000261961	D;D	0.86164	-2.08;-2.08	4.51	4.51	0.55191	Death (2);DEATH-like (2);	0.000000	0.85682	D	0.000000	D	0.93000	0.7772	M	0.80746	2.51	0.53688	D	0.999972	D	0.89917	1.0	D	0.81914	0.995	D	0.93934	0.7217	10	0.87932	D	0	-31.7076	13.66	0.62361	1.0:0.0:0.0:0.0	.	796	Q6ZN44	UNC5A_HUMAN	M	796;756	ENSP00000332737:K796M;ENSP00000261961:K756M	ENSP00000261961:K756M	K	+	2	0	UNC5A	176239351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.664000	0.91139	1.898000	0.54952	0.383000	0.25322	AAG	.	.		0.697	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300	
C5orf45	51149	hgsc.bcm.edu	37	5	179274998	179274998	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:179274998T>G	ENST00000292586.6	-	3	285	c.195A>C	c.(193-195)caA>caC	p.Q65H	C5orf45_ENST00000518235.1_Missense_Mutation_p.Q65H|RN7SKP150_ENST00000410516.1_RNA|C5orf45_ENST00000376931.2_Intron|C5orf45_ENST00000520698.1_Intron|C5orf45_ENST00000403396.2_Missense_Mutation_p.Q107H|C5orf45_ENST00000518219.1_Missense_Mutation_p.Q65H|Y_RNA_ENST00000516393.1_RNA|C5orf45_ENST00000523084.1_Intron|C5orf45_ENST00000521333.1_Missense_Mutation_p.Q65H	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	65										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GCTCTGAAACTTGTCCCTGTA	0.418																																					p.Q65H		Atlas-SNP	.											.	C5orf45	23	.	0			c.A195C						.						117.0	112.0	114.0					5																	179274998		2203	4300	6503	SO:0001583	missense	51149	exon3			TGAAACTTGTCCC		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.195A>C	chr5.hg19:g.179274998T>G	ENSP00000292586:p.Gln65His	105.0	0.0		81.0	32.0	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	hg19	CCDS34319.1	.	.	.	.	.	.	.	.	.	.	T	9.433	1.086065	0.20390	.	.	ENSG00000161010	ENST00000403396;ENST00000518235;ENST00000518219;ENST00000292586;ENST00000521333	T;T;T;T;T	0.23552	1.9;3.07;3.07;3.07;3.07	4.1	-2.01	0.07410	.	0.199418	0.31113	N	0.008234	T	0.38401	0.1039	M	0.71581	2.175	0.09310	N	0.999995	D;P;B	0.69078	0.997;0.662;0.385	D;B;B	0.70935	0.971;0.278;0.106	T	0.19418	-1.0306	10	0.66056	D	0.02	-6.5747	4.3111	0.10971	0.1636:0.3382:0.0:0.4981	.	65;65;107	B7Z1T6;Q6NTE8;Q6NTE8-2	.;CE045_HUMAN;.	H	107;65;65;65;65	ENSP00000384599:Q107H;ENSP00000430298:Q65H;ENSP00000428460:Q65H;ENSP00000292586:Q65H;ENSP00000429651:Q65H	ENSP00000292586:Q65H	Q	-	3	2	C5orf45	179207604	0.046000	0.20272	0.012000	0.15200	0.027000	0.11550	-0.031000	0.12287	-0.453000	0.07076	-2.065000	0.00396	CAA	.	.		0.418	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
DAXX	1616	hgsc.bcm.edu	37	6	33289254	33289254	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr6:33289254A>C	ENST00000374542.5	-	3	502	c.298T>G	c.(298-300)Ttg>Gtg	p.L100V	DAXX_ENST00000266000.6_Missense_Mutation_p.L100V|DAXX_ENST00000477162.1_Intron|DAXX_ENST00000414083.2_Missense_Mutation_p.L25V	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	100	Necessary for interaction with USP7 and ATRX.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						GCCGAGGCCAAAAACAGAGAG	0.547			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.L112V		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.T334G						.						69.0	75.0	73.0					6																	33289254		2203	4300	6503	SO:0001583	missense	1616	exon3			AGGCCAAAAACAG	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.298T>G	chr6.hg19:g.33289254A>C	ENSP00000363668:p.Leu100Val	79.0	0.0		83.0	33.0	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Missense_Mutation	SNP	ENST00000374542.5	hg19	CCDS4776.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.247371	0.59103	.	.	ENSG00000204209	ENST00000266000;ENST00000374542;ENST00000414083;ENST00000446403;ENST00000453407	.	.	.	5.11	0.0611	0.14339	Armadillo-like helical (1);	0.000000	0.64402	D	0.000001	T	0.51584	0.1683	L	0.44542	1.39	0.43412	D	0.995552	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.999	T	0.53272	-0.8462	9	0.49607	T	0.09	-6.2462	8.4696	0.32977	0.6545:0.0:0.3455:0.0	.	112;100;100	B4E1C1;B2R7M0;Q9UER7	.;.;DAXX_HUMAN	V	100;100;25;100;100	.	ENSP00000266000:L100V	L	-	1	2	DAXX	33397232	0.998000	0.40836	0.963000	0.40424	0.974000	0.67602	0.370000	0.20433	0.115000	0.18071	0.443000	0.29094	TTG	.	.		0.547	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
PRSS35	167681	hgsc.bcm.edu	37	6	84233828	84233828	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr6:84233828T>G	ENST00000369700.3	+	2	845	c.668T>G	c.(667-669)cTg>cGg	p.L223R	PRSS35_ENST00000536636.1_Missense_Mutation_p.L223R	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	223	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		AGAGAGCATCTGCGGGAGAGA	0.527																																					p.L223R		Atlas-SNP	.											.	PRSS35	60	.	0			c.T668G						.						58.0	67.0	64.0					6																	84233828		2203	4300	6503	SO:0001583	missense	167681	exon2			AGCATCTGCGGGA	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.668T>G	chr6.hg19:g.84233828T>G	ENSP00000358714:p.Leu223Arg	161.0	0.0		156.0	34.0	NM_153362	A8K7B3|Q9BQP6	Missense_Mutation	SNP	ENST00000369700.3	hg19	CCDS4999.1	.	.	.	.	.	.	.	.	.	.	T	0.038	-1.295115	0.01375	.	.	ENSG00000146250	ENST00000536636;ENST00000369700	T;T	0.42900	0.96;0.96	5.65	-0.0528	0.13820	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.840251	0.10503	N	0.667053	T	0.07458	0.0188	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36383	-0.9750	10	0.30078	T	0.28	-1.6262	5.01	0.14308	0.0:0.2526:0.2715:0.476	.	223	Q8N3Z0	PRS35_HUMAN	R	223	ENSP00000440870:L223R;ENSP00000358714:L223R	ENSP00000358714:L223R	L	+	2	0	PRSS35	84290547	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.266000	0.08631	0.055000	0.16094	0.379000	0.24179	CTG	.	.		0.527	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
FERD3L	222894	hgsc.bcm.edu	37	7	19184898	19184898	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:19184898G>A	ENST00000275461.3	-	1	146	c.88C>T	c.(88-90)Ctc>Ttc	p.L30F	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	30					cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L30F(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						AAGTCGCAGAGGAGAGGGCGT	0.672																																					p.L30F		Atlas-SNP	.											FERD3L,scalp,carcinoma,0,1	FERD3L	63	.	1	Substitution - Missense(1)	skin(1)	c.C88T						.						37.0	36.0	36.0					7																	19184898		2201	4300	6501	SO:0001583	missense	222894	exon1			CGCAGAGGAGAGG	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.88C>T	chr7.hg19:g.19184898G>A	ENSP00000275461:p.Leu30Phe	41.0	0.0		32.0	11.0	NM_152898	Q495K0	Missense_Mutation	SNP	ENST00000275461.3	hg19	CCDS5368.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188341	0.57909	.	.	ENSG00000146618	ENST00000275461	D	0.96802	-4.13	5.39	4.51	0.55191	.	0.325996	0.22051	N	0.065313	D	0.89860	0.6837	L	0.27053	0.805	0.25955	N	0.982706	B	0.18461	0.028	B	0.13407	0.009	T	0.76719	-0.2856	10	0.10111	T	0.7	-3.247	5.2416	0.15475	0.2375:0.1656:0.5968:0.0	.	30	Q96RJ6	FER3L_HUMAN	F	30	ENSP00000275461:L30F	ENSP00000275461:L30F	L	-	1	0	FERD3L	19151423	0.998000	0.40836	0.987000	0.45799	0.833000	0.47200	1.910000	0.39927	1.274000	0.44362	0.650000	0.86243	CTC	.	.		0.672	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1		
IGF2BP3	10643	hgsc.bcm.edu	37	7	23509595	23509595	+	Silent	SNP	C	C	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:23509595C>T	ENST00000258729.3	-	1	491	c.135G>A	c.(133-135)ccG>ccA	p.P45P	IGF2BP3_ENST00000491719.1_5'Flank	NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	45	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						AGCTCTCGTCCGGGCAGTCCA	0.697																																					p.P45P		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.G135A						.						40.0	46.0	44.0					7																	23509595		2203	4300	6503	SO:0001819	synonymous_variant	10643	exon1			CTCGTCCGGGCAG	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"""RNA binding motif (RRM) containing"""	28868	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 3"", ""cancer/testis antigen 98"""	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.135G>A	chr7.hg19:g.23509595C>T		48.0	0.0		51.0	13.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Silent	SNP	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.		0.697	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547	
ABCA13	154664	hgsc.bcm.edu	37	7	48313643	48313643	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:48313643T>G	ENST00000435803.1	+	17	4404	c.4380T>G	c.(4378-4380)aaT>aaG	p.N1460K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1460					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTGTGTCAATATTTACTTGA	0.249																																					p.N1460K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T4380G						.						27.0	30.0	29.0					7																	48313643		1787	4029	5816	SO:0001583	missense	154664	exon17			TGTCAATATTTAC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4380T>G	chr7.hg19:g.48313643T>G	ENSP00000411096:p.Asn1460Lys	116.0	0.0		127.0	49.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	9.564	1.119347	0.20877	.	.	ENSG00000179869	ENST00000435803	D	0.86030	-2.06	5.44	1.67	0.24075	.	0.425529	0.20048	N	0.100369	D	0.85999	0.5828	M	0.62723	1.935	0.09310	N	1	D	0.63880	0.993	P	0.53954	0.738	T	0.77032	-0.2738	9	.	.	.	.	8.8855	0.35400	0.0:0.3008:0.0:0.6992	.	1460	Q86UQ4	ABCAD_HUMAN	K	1460	ENSP00000411096:N1460K	.	N	+	3	2	ABCA13	48284189	0.047000	0.20315	0.200000	0.23457	0.219000	0.24729	0.652000	0.24888	0.099000	0.17552	-0.400000	0.06385	AAT	.	.		0.249	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
LETM2	137994	hgsc.bcm.edu	37	8	38257839	38257839	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:38257839T>A	ENST00000379957.4	+	5	822	c.695T>A	c.(694-696)tTt>tAt	p.F232Y	LETM2_ENST00000524874.1_Missense_Mutation_p.F184Y|LETM2_ENST00000527710.1_Missense_Mutation_p.F18Y|LETM2_ENST00000297720.5_Missense_Mutation_p.F137Y|LETM2_ENST00000523983.2_Missense_Mutation_p.F185Y|RP11-350N15.3_ENST00000533301.1_RNA	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	232	LETM1.					integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.F137C(1)		NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			CTAGCAAAATTTCTTCAAGAA	0.398																																					p.F185Y		Atlas-SNP	.											LETM2,rectum,carcinoma,0,1	LETM2	57	.	1	Substitution - Missense(1)	large_intestine(1)	c.T554A						.						78.0	70.0	73.0					8																	38257839		2203	4300	6503	SO:0001583	missense	137994	exon5			CAAAATTTCTTCA	AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"""EF-hand domain containing"""	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.695T>A	chr8.hg19:g.38257839T>A	ENSP00000369291:p.Phe232Tyr	66.0	0.0		40.0	12.0	NM_001199659	A6NMG3|Q8NCR2|Q96LL1	Missense_Mutation	SNP	ENST00000379957.4	hg19		.	.	.	.	.	.	.	.	.	.	T	33	5.207499	0.95033	.	.	ENSG00000165046	ENST00000297720;ENST00000524874;ENST00000379957;ENST00000523983;ENST00000527710	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.77	5.77	0.91146	LETM1-like (1);	0.000000	0.85682	D	0.000000	T	0.71896	0.3394	M	0.83312	2.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.76680	-0.2870	10	0.87932	D	0	-15.1134	16.0892	0.81080	0.0:0.0:0.0:1.0	.	29;232;184	B7Z7T4;Q2VYF4;E9PMA4	.;LETM2_HUMAN;.	Y	137;184;232;185;18	ENSP00000297720:F137Y;ENSP00000431211:F184Y;ENSP00000369291:F232Y;ENSP00000428765:F185Y;ENSP00000434867:F18Y	ENSP00000297720:F137Y	F	+	2	0	LETM2	38376996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.584000	0.82572	2.208000	0.71279	0.454000	0.30748	TTT	.	.		0.398	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652	
ADAM18	8749	hgsc.bcm.edu	37	8	39468133	39468133	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:39468133A>G	ENST00000265707.5	+	6	475	c.430A>G	c.(430-432)Aaa>Gaa	p.K144E	ADAM18_ENST00000379866.1_Missense_Mutation_p.K144E|ADAM18_ENST00000520772.1_Missense_Mutation_p.K144E|ADAM18_ENST00000541111.1_Intron	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	144					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TTATCAAATGAAAAATAATGA	0.328																																					p.K144E		Atlas-SNP	.											.	ADAM18	169	.	0			c.A430G						.						48.0	50.0	49.0					8																	39468133		2203	4298	6501	SO:0001583	missense	8749	exon6			CAAATGAAAAATA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.430A>G	chr8.hg19:g.39468133A>G	ENSP00000265707:p.Lys144Glu	444.0	1.0		308.0	142.0	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.858578	0.51376	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.11495	5.35;4.95;2.77	5.25	5.25	0.73442	.	0.123619	0.37219	N	0.002183	T	0.07818	0.0196	N	0.08118	0	0.80722	D	1	P;P;B	0.45634	0.863;0.784;0.217	P;B;B	0.49528	0.614;0.41;0.109	T	0.38286	-0.9668	10	0.07990	T	0.79	.	11.4678	0.50249	1.0:0.0:0.0:0.0	.	144;144;144	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	E	144;144;144;100	ENSP00000265707:K144E;ENSP00000369195:K144E;ENSP00000429908:K144E	ENSP00000265707:K144E	K	+	1	0	ADAM18	39587290	0.996000	0.38824	0.986000	0.45419	0.146000	0.21551	1.900000	0.39828	2.206000	0.71126	0.533000	0.62120	AAA	.	.		0.328	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
DENND3	22898	hgsc.bcm.edu	37	8	142151392	142151392	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:142151392T>C	ENST00000262585.2	+	4	630	c.352T>C	c.(352-354)Tat>Cat	p.Y118H	DENND3_ENST00000519811.1_Missense_Mutation_p.Y198H|DENND3_ENST00000424248.1_Missense_Mutation_p.Y118H|DENND3_ENST00000518347.1_Missense_Mutation_p.Y198H	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	118	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGGTTTCCCTATTACAACTC	0.587																																					p.Y118H		Atlas-SNP	.											.	DENND3	127	.	0			c.T352C						.						146.0	119.0	128.0					8																	142151392		2203	4300	6503	SO:0001583	missense	22898	exon4			TTTCCCTATTACA	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.352T>C	chr8.hg19:g.142151392T>C	ENSP00000262585:p.Tyr118His	51.0	0.0		73.0	8.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	hg19	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.1|20.1	3.940896|3.940896	0.73557|0.73557	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000518347;ENST00000262585;ENST00000424248;ENST00000519811;ENST00000523058;ENST00000518249	.|T;T;T;T	.|0.11495	.|2.77;2.77;2.77;2.77	5.24|5.24	5.24|5.24	0.73138|0.73138	.|DENN (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.34366|0.34366	0.0895|0.0895	M|M	0.78049|0.78049	2.395|2.395	0.51767|0.51767	D|D	0.999936|0.999936	.|D;D;D	.|0.89917	.|1.0;1.0;0.999	.|D;D;D	.|0.97110	.|1.0;1.0;0.996	T|T	0.07770|0.07770	-1.0755|-1.0755	5|9	.|.	.|.	.|.	-13.0908|-13.0908	15.15|15.15	0.72689|0.72689	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|198;118;198	.|E9PF32;A2RUS2;E5RIR7	.|.;DEND3_HUMAN;.	P|H	174|198;118;118;198;198;31	.|ENSP00000262585:Y118H;ENSP00000410594:Y118H;ENSP00000428714:Y198H;ENSP00000430786:Y198H	.|.	L|Y	+|+	2|1	0|0	DENND3|DENND3	142220574|142220574	1.000000|1.000000	0.71417|0.71417	0.467000|0.467000	0.27180|0.27180	0.540000|0.540000	0.34992|0.34992	6.209000|6.209000	0.72171|0.72171	1.972000|1.972000	0.57404|0.57404	0.533000|0.533000	0.62120|0.62120	CTA|TAT	.	.		0.587	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
CCIN	881	hgsc.bcm.edu	37	9	36170372	36170372	+	Silent	SNP	C	C	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr9:36170372C>T	ENST00000335119.2	+	1	984	c.873C>T	c.(871-873)ggC>ggT	p.G291G		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	291					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			AGGCCCACGGCCAGTTCAATG	0.582																																					p.G291G		Atlas-SNP	.											.	CCIN	56	.	0			c.C873T						.						75.0	71.0	72.0					9																	36170372		2203	4300	6503	SO:0001819	synonymous_variant	881	exon1			CCACGGCCAGTTC	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"""BTB/POZ domain containing"""	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.873C>T	chr9.hg19:g.36170372C>T		56.0	0.0		35.0	19.0	NM_005893	Q9BXG7	Silent	SNP	ENST00000335119.2	hg19	CCDS6599.1																																																																																			.	.		0.582	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893	
ANK3	288	hgsc.bcm.edu	37	10	61828727	61828727	+	Missense_Mutation	SNP	G	G	A	rs368539157		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr10:61828727G>A	ENST00000280772.2	-	37	12103	c.11912C>T	c.(11911-11913)aCt>aTt	p.T3971I	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3971	Thr-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						agtggtggtagtggtggtggt	0.468																																					p.T3971I		Atlas-SNP	.											.,2	ANK3	703	.	0			c.C11912T						.						78.0	86.0	83.0					10																	61828727		2202	4300	6502	SO:0001583	missense	288	exon37			GTGGTAGTGGTGG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11912C>T	chr10.hg19:g.61828727G>A	ENSP00000280772:p.Thr3971Ile	62.0	1.0		52.0	4.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	1.592	-0.528734	0.04112	.	.	ENSG00000151150	ENST00000280772	T	0.42513	0.97	3.29	3.29	0.37713	.	0.251972	0.20684	U	0.087593	T	0.20495	0.0493	N	0.08118	0	0.80722	D	1	P	0.49783	0.928	B	0.39119	0.291	T	0.03296	-1.1051	10	0.39692	T	0.17	.	10.3334	0.43835	0.0:0.0:1.0:0.0	.	3971	Q12955	ANK3_HUMAN	I	3971	ENSP00000280772:T3971I	ENSP00000280772:T3971I	T	-	2	0	ANK3	61498733	1.000000	0.71417	1.000000	0.80357	0.165000	0.22458	2.153000	0.42282	2.149000	0.67028	0.563000	0.77884	ACT	.	.		0.468	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
PALD1	27143	hgsc.bcm.edu	37	10	72326463	72326463	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr10:72326463C>T	ENST00000263563.6	+	20	2813	c.2545C>T	c.(2545-2547)Ccc>Tcc	p.P849S		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	849						cytosol (GO:0005829)											CAGCCTCGAGCCCTCTGCCCC	0.687																																					p.P849S		Atlas-SNP	.											.	.	.	.	0			c.C2545T						.						26.0	26.0	26.0					10																	72326463		2201	4299	6500	SO:0001583	missense	27143	exon20			CTCGAGCCCTCTG	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2545C>T	chr10.hg19:g.72326463C>T	ENSP00000263563:p.Pro849Ser	26.0	0.0		13.0	7.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.15|17.15	3.316980|3.316980	0.60524|0.60524	.|.	.|.	ENSG00000107719|ENSG00000107719	ENST00000426268|ENST00000263563;ENST00000373214	.|T	.|0.32988	.|1.43	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|0.064498	.|0.64402	.|D	.|0.000006	T|T	0.51805|0.51805	0.1696|0.1696	M|M	0.66939|0.66939	2.045|2.045	0.52099|0.52099	D|D	0.999945|0.999945	.|D	.|0.61080	.|0.989	.|D	.|0.66084	.|0.941	T|T	0.54146|0.54146	-0.8337|-0.8337	5|10	.|0.72032	.|D	.|0.01	-10.2785|-10.2785	14.1938|14.1938	0.65656|0.65656	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|849	.|Q9ULE6	.|PALD_HUMAN	V|S	229|849;825	.|ENSP00000263563:P849S	.|ENSP00000263563:P849S	A|P	+|+	2|1	0|0	KIAA1274|KIAA1274	71996469|71996469	0.281000|0.281000	0.24258|0.24258	0.971000|0.971000	0.41717|0.41717	0.081000|0.081000	0.17604|0.17604	0.696000|0.696000	0.25541|0.25541	2.415000|2.415000	0.81967|0.81967	0.491000|0.491000	0.48974|0.48974	GCC|CCC	.	.		0.687	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249530	71249530	+	Silent	SNP	T	T	C	rs532438179|rs369043826	byFrequency	TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr11:71249530T>C	ENST00000398534.3	+	1	460	c.429T>C	c.(427-429)tgT>tgC	p.C143C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	143	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						AGCCCTGCTGTTCCCAGTCCA	0.612																																					p.C143C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.T429C						.						146.0	159.0	155.0					11																	71249530		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CTGCTGTTCCCAG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.429T>C	chr11.hg19:g.71249530T>C		79.0	0.0		99.0	15.0	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	hg19	CCDS41683.1																																																																																			.	.		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788188	3788188	+	Missense_Mutation	SNP	C	C	A	rs3803135	byFrequency	TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr12:3788188C>A	ENST00000252322.1	-	6	885	c.417G>T	c.(415-417)aaG>aaT	p.K139N	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.K139N|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.K139N	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		139					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			ACAGATACACCTTCTCTTCAT	0.557																																					p.K139N		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G417T						.						188.0	152.0	164.0					12																	3788188		2203	4300	6503	SO:0001583	missense	84766	exon6			ATACACCTTCTCT																												ENST00000252322.1:c.417G>T	chr12.hg19:g.3788188C>A	ENSP00000252322:p.Lys139Asn	88.0	0.0		49.0	18.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	C	5.197	0.221924	0.09863	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.61980	0.06;2.5;2.51	4.9	2.65	0.31530	EF-hand-like domain (1);	0.350601	0.31041	N	0.008369	T	0.55049	0.1896	M	0.75447	2.3	0.36095	P	0.156231	B;B;B	0.12013	0.004;0.005;0.003	B;B;B	0.10450	0.005;0.003;0.003	T	0.55768	-0.8089	9	0.18276	T	0.48	-21.8852	7.1665	0.25693	0.0:0.7457:0.0:0.2543	.	139;139;139	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	N	139	ENSP00000409382:K139N;ENSP00000412496:K139N;ENSP00000252322:K139N	ENSP00000252322:K139N	K	-	3	2	EFCAB4B	3658449	0.995000	0.38212	0.988000	0.46212	0.279000	0.26890	0.436000	0.21526	1.026000	0.39733	0.561000	0.74099	AAG	.	C|0.862;T|0.138		0.557	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
SOX5	6660	hgsc.bcm.edu	37	12	24048957	24048957	+	Splice_Site	SNP	T	T	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr12:24048957T>C	ENST00000451604.2	-	2	141	c.40A>G	c.(40-42)Atg>Gtg	p.M14V	SOX5_ENST00000541847.1_Splice_Site_p.M4V|SOX5_ENST00000546136.1_Start_Codon_SNP_p.M1V|SOX5_ENST00000545921.1_Splice_Site_p.M4V|SOX5_ENST00000541536.1_Start_Codon_SNP_p.M1V|SOX5_ENST00000537393.1_Splice_Site_p.M14V|SOX5_ENST00000309359.1_Splice_Site_p.M1V|SOX5_ENST00000441133.2_Splice_Site_p.M14V|SOX5_ENST00000381381.2_Splice_Site_p.M1V			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	14					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TTGGAAGACATCCTGGAAGGA	0.473																																					p.M14V		Atlas-SNP	.											.	SOX5	134	.	0			c.A40G						.						107.0	105.0	106.0					12																	24048957		2203	4300	6503	SO:0001630	splice_region_variant	6660	exon2			AAGACATCCTGGA	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"""SRY (sex determining region Y)-boxes"""	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.39-1A>G	chr12.hg19:g.24048957T>C		48.0	0.0		45.0	17.0	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.983197	0.53827	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083	D;D;D;D;D;D;D	0.98602	-4.81;-4.81;-4.89;-4.83;-5.02;-4.89;-4.81	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.98842	0.9609	M	0.77103	2.36	0.80722	D	1	P;D;B;D	0.61080	0.811;0.989;0.219;0.98	P;D;P;D	0.75484	0.828;0.986;0.455;0.968	D	0.99861	1.1083	10	0.87932	D	0	.	16.2948	0.82765	0.0:0.0:0.0:1.0	.	14;14;1;14	G3V0H1;F5H0I3;P35711-4;P35711	.;.;.;SOX5_HUMAN	V	1;1;1;14;1;14;1;4;4;14;1	ENSP00000437487:M1V;ENSP00000308927:M1V;ENSP00000370788:M1V;ENSP00000398273:M14V;ENSP00000439832:M14V;ENSP00000441973:M1V;ENSP00000443520:M4V	ENSP00000308927:M1V	M	-	1	0	SOX5	23940224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.378000	0.79679	2.253000	0.74438	0.455000	0.32223	ATG	.	.		0.473	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940	Missense_Mutation
IL31	386653	hgsc.bcm.edu	37	12	122657036	122657036	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr12:122657036T>C	ENST00000377035.1	-	3	444	c.418A>G	c.(418-420)Att>Gtt	p.I140V		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	140					immune system process (GO:0002376)	extracellular space (GO:0005615)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TGTTGAGAAATAGTCAGGATG	0.448																																					p.I140V		Atlas-SNP	.											.	IL31	23	.	0			c.A418G						.						175.0	160.0	165.0					12																	122657036		2203	4300	6503	SO:0001583	missense	386653	exon3			GAGAAATAGTCAG	AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"""Interleukins and interleukin receptors"""	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.418A>G	chr12.hg19:g.122657036T>C	ENSP00000366234:p.Ile140Val	102.0	0.0		72.0	26.0	NM_001014336	A2RUQ1	Missense_Mutation	SNP	ENST00000377035.1	hg19	CCDS31919.1	.	.	.	.	.	.	.	.	.	.	T	7.013	0.557194	0.13436	.	.	ENSG00000204671	ENST00000377035	.	.	.	4.18	-8.36	0.00980	.	1.491180	0.04518	N	0.384050	T	0.21631	0.0521	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.15052	0.012	T	0.23119	-1.0197	9	0.13853	T	0.58	-2.3243	9.5938	0.39563	0.1742:0.6206:0.0878:0.1173	.	140	Q6EBC2	IL31_HUMAN	V	140	.	ENSP00000366234:I140V	I	-	1	0	IL31	121222989	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.865000	0.01649	-3.932000	0.00090	-0.371000	0.07208	ATT	.	.		0.448	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336	
DACH1	1602	hgsc.bcm.edu	37	13	72440337	72440337	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr13:72440337T>C	ENST00000359684.2	-	1	570	c.571A>G	c.(571-573)Aaa>Gaa	p.K191E	DACH1_ENST00000354591.4_Missense_Mutation_p.K191E|DACH1_ENST00000313174.7_Missense_Mutation_p.K191E|DACH1_ENST00000305425.4_Missense_Mutation_p.K191E			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	191	DACHbox-N.|Interaction with SIX6 and HDAC3. {ECO:0000250}.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TCCACCATTTTGCACTCATTA	0.602																																					p.K191E		Atlas-SNP	.											.	DACH1	123	.	0			c.A571G						.						39.0	42.0	41.0					13																	72440337		1956	4147	6103	SO:0001583	missense	1602	exon1			CCATTTTGCACTC	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"""dachshund homolog (Drosophila)"", ""dachshund homolog 1 (Drosophila)"""	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.571A>G	chr13.hg19:g.72440337T>C	ENSP00000352712:p.Lys191Glu	89.0	0.0		48.0	35.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.25	3.340931	0.60963	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63	3.9	3.9	0.45041	.	0.275476	0.33875	U	0.004472	D	0.84347	0.5452	L	0.61218	1.895	0.54753	D	0.999985	P;P;P	0.52061	0.827;0.827;0.95	B;B;P	0.49999	0.271;0.271;0.628	D	0.86050	0.1525	10	0.87932	D	0	-6.9207	12.3897	0.55352	0.0:0.0:0.0:1.0	.	189;189;189	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	E	191	ENSP00000304994:K191E;ENSP00000318506:K191E;ENSP00000346604:K191E;ENSP00000352712:K191E	ENSP00000304994:K191E	K	-	1	0	DACH1	71338338	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.498000	0.66931	1.396000	0.46663	0.254000	0.18369	AAA	.	.		0.602	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392	
PSMB11	122706	hgsc.bcm.edu	37	14	23512059	23512059	+	Missense_Mutation	SNP	G	G	A	rs368929459		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr14:23512059G>A	ENST00000408907.2	+	1	684	c.625G>A	c.(625-627)Gtg>Atg	p.V209M		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	209					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		TCGCTGCGCCGTGGCCCACGC	0.627																																					p.V209M		Atlas-SNP	.											.	PSMB11	40	.	0			c.G625A						.	G	MET/VAL	0,4238		0,0,2119	40.0	42.0	41.0		625	4.1	0.4	14		41	2,8484		0,2,4241	no	missense	PSMB11	NM_001099780.1	21	0,2,6360	AA,AG,GG		0.0236,0.0,0.0157	probably-damaging	209/301	23512059	2,12722	2119	4243	6362	SO:0001583	missense	122706	exon1			TGCGCCGTGGCCC		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.625G>A	chr14.hg19:g.23512059G>A	ENSP00000386212:p.Val209Met	48.0	0.0		35.0	20.0	NM_001099780		Missense_Mutation	SNP	ENST00000408907.2	hg19	CCDS41923.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.232866	0.39498	0.0	2.36E-4	ENSG00000222028	ENST00000408907	T	0.23552	1.9	5.02	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.52613	0.1745	M	0.83692	2.655	0.37205	D	0.904548	D	0.89917	1.0	D	0.97110	1.0	T	0.65005	-0.6273	10	0.87932	D	0	-12.6072	12.3151	0.54951	0.0833:0.0:0.9167:0.0	.	209	A5LHX3	PSB11_HUMAN	M	209	ENSP00000386212:V209M	ENSP00000386212:V209M	V	+	1	0	PSMB11	22581899	1.000000	0.71417	0.362000	0.25862	0.002000	0.02628	3.680000	0.54641	1.135000	0.42183	-0.136000	0.14681	GTG	.	.		0.627	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780	
STON2	85439	hgsc.bcm.edu	37	14	81744593	81744593	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr14:81744593G>T	ENST00000267540.2	-	4	1262	c.1062C>A	c.(1060-1062)agC>agA	p.S354R	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Missense_Mutation_p.S354R	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	354					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		AATCTCTTTGGCTTTTGCCCG	0.468																																					p.S354R		Atlas-SNP	.											.	STON2	94	.	0			c.C1062A						.						115.0	119.0	118.0					14																	81744593		2203	4300	6503	SO:0001583	missense	85439	exon6			TCTTTGGCTTTTG	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.1062C>A	chr14.hg19:g.81744593G>T	ENSP00000267540:p.Ser354Arg	121.0	0.0		96.0	5.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.349891	0.24426	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.12465	2.68;2.69	6.17	4.36	0.52297	.	0.145674	0.64402	D	0.000006	T	0.14614	0.0353	L	0.57536	1.79	0.34730	D	0.729635	B;B	0.18461	0.016;0.028	B;B	0.17433	0.005;0.018	T	0.11060	-1.0603	10	0.25106	T	0.35	-24.6284	11.0372	0.47808	0.1977:0.0:0.8023:0.0	.	354;354	Q8WXE9;G3V2T7	STON2_HUMAN;.	R	354;366;354	ENSP00000450857:S354R;ENSP00000267540:S354R	ENSP00000267540:S354R	S	-	3	2	STON2	80814346	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	4.432000	0.59922	0.943000	0.37553	0.655000	0.94253	AGC	.	.		0.468	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104	
ATG2B	55102	hgsc.bcm.edu	37	14	96779699	96779699	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr14:96779699T>C	ENST00000359933.4	-	24	4609	c.3716A>G	c.(3715-3717)cAt>cGt	p.H1239R	ATG2B_ENST00000261834.5_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1239					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AAGATGAACATGAAAAGTTGT	0.279																																					p.H1239R		Atlas-SNP	.											.	ATG2B	169	.	0			c.A3716G						.						57.0	58.0	58.0					14																	96779699		2203	4297	6500	SO:0001583	missense	55102	exon24			TGAACATGAAAAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3716A>G	chr14.hg19:g.96779699T>C	ENSP00000353010:p.His1239Arg	387.0	0.0		367.0	143.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	T	25.1	4.600303	0.87055	.	.	ENSG00000066739	ENST00000359933	T	0.20332	2.08	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.48801	-0.9003	10	0.59425	D	0.04	.	16.0133	0.80420	0.0:0.0:0.0:1.0	.	1239	Q96BY7	ATG2B_HUMAN	R	1239	ENSP00000353010:H1239R	ENSP00000353010:H1239R	H	-	2	0	ATG2B	95849452	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.424000	0.80242	2.179000	0.69175	0.533000	0.62120	CAT	.	.		0.279	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
EIF3J	8669	hgsc.bcm.edu	37	15	44849749	44849749	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr15:44849749G>T	ENST00000261868.5	+	6	610	c.472G>T	c.(472-474)Gag>Tag	p.E158*	EIF3J_ENST00000424492.3_Nonsense_Mutation_p.E109*|EIF3J_ENST00000535391.1_Intron|RP11-151N17.1_ENST00000558006.1_RNA	NM_003758.2	NP_003749.2			eukaryotic translation initiation factor 3, subunit J											endometrium(1)|large_intestine(5)|liver(2)|skin(1)	9		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		TGACTTTACAGAGTTTGGAAA	0.333																																					p.E158X		Atlas-SNP	.											.	EIF3J	29	.	0			c.G472T						.						70.0	76.0	74.0					15																	44849749		2198	4296	6494	SO:0001587	stop_gained	8669	exon6			TTTACAGAGTTTG	U97670	CCDS10111.1, CCDS61612.1, CCDS61613.1	15q21.1	2014-05-13	2007-07-27	2007-07-27	ENSG00000104131	ENSG00000104131			3270	protein-coding gene	gene with protein product		603910	"""eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa"""	EIF3S1		9822659	Standard	NM_001284335		Approved	eIF3-p35, eIF3-alpha, eIF3j	uc001ztv.3	O75822	OTTHUMG00000131158	ENST00000261868.5:c.472G>T	chr15.hg19:g.44849749G>T	ENSP00000261868:p.Glu158*	66.0	0.0		77.0	27.0	NM_003758		Nonsense_Mutation	SNP	ENST00000261868.5	hg19	CCDS10111.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.591824|5.591824	0.96590|0.96590	.|.	.|.	ENSG00000104131|ENSG00000104131	ENST00000261868;ENST00000424492|ENST00000536248	.|.	.|.	.|.	5.77|5.77	3.89|3.89	0.44902|0.44902	.|.	0.097124|.	0.64402|.	D|.	0.000001|.	.|T	.|0.62441	.|0.2428	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.58951	.|-0.7545	.|4	0.25106|.	T|.	0.35|.	.|.	11.564|11.564	0.50794|0.50794	0.0672:0.1254:0.8074:0.0|0.0672:0.1254:0.8074:0.0	.|.	.|.	.|.	.|.	X|I	158;109|36	.|.	ENSP00000261868:E158X|.	E|R	+|+	1|2	0|0	EIF3J|EIF3J	42637041|42637041	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.611000|7.611000	0.82962|0.82962	0.779000|0.779000	0.33543|0.33543	0.555000|0.555000	0.69702|0.69702	GAG|AGA	.	.		0.333	EIF3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253850.1	NM_003758	
ADAD2	161931	hgsc.bcm.edu	37	16	84228736	84228736	+	Silent	SNP	G	G	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr16:84228736G>T	ENST00000315906.5	+	4	721	c.669G>T	c.(667-669)ctG>ctT	p.L223L	ADAD2_ENST00000268624.3_Silent_p.L295L|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	223					RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						TTGACCTCCTGTTGGACGAGC	0.672																																					p.L295L		Atlas-SNP	.											.	ADAD2	46	.	0			c.G885T						.						38.0	39.0	39.0					16																	84228736		2200	4300	6500	SO:0001819	synonymous_variant	161931	exon5			CCTCCTGTTGGAC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.669G>T	chr16.hg19:g.84228736G>T		125.0	0.0		56.0	37.0	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	hg19	CCDS45536.1																																																																																			.	.		0.672	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
KRT10	3858	hgsc.bcm.edu	37	17	38975317	38975317	+	Silent	SNP	G	G	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr17:38975317G>A	ENST00000269576.5	-	7	1479	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				tgccgccgtggccgccgccgt	0.796																																					p.G490G		Atlas-SNP	.											.	KRT10	56	.	0			c.C1470T						.																																			SO:0001819	synonymous_variant	3858	exon7			GCCGTGGCCGCCG	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1470C>T	chr17.hg19:g.38975317G>A		27.0	0.0		77.0	9.0	NM_000421	Q14664|Q8N175	Silent	SNP	ENST00000269576.5	hg19	CCDS11377.1																																																																																			.	.		0.796	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
KRT10	3858	hgsc.bcm.edu	37	17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	27.0	0.0		74.0	8.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
UBTF	7343	hgsc.bcm.edu	37	17	42289011	42289011	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr17:42289011T>G	ENST00000302904.4	-	10	1502	c.1010A>C	c.(1009-1011)cAg>cCg	p.Q337P	UBTF_ENST00000343638.5_Missense_Mutation_p.Q300P|UBTF_ENST00000527034.1_Missense_Mutation_p.Q300P|UBTF_ENST00000393606.3_Missense_Mutation_p.Q300P|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000526094.1_Missense_Mutation_p.Q300P|UBTF_ENST00000436088.1_Missense_Mutation_p.Q337P|UBTF_ENST00000533177.1_Missense_Mutation_p.Q300P|UBTF_ENST00000529383.1_Missense_Mutation_p.Q337P			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	337					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)		CTTCTCCTTCTGGGACAGCAG	0.577																																					p.Q337P		Atlas-SNP	.											.	UBTF	65	.	0			c.A1010C						.						103.0	98.0	100.0					17																	42289011		2203	4300	6503	SO:0001583	missense	7343	exon10			TCCTTCTGGGACA	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.1010A>C	chr17.hg19:g.42289011T>G	ENSP00000302640:p.Gln337Pro	26.0	0.0		23.0	8.0	NM_014233	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	hg19	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	t	19.89	3.911255	0.72983	.	.	ENSG00000108312	ENST00000343638;ENST00000302904;ENST00000527034;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383	T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	4.4	4.4	0.53042	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	T	0.47303	0.1438	N	0.17312	0.475	0.80722	D	1	D;D;D	0.76494	0.99;0.994;0.999	D;D;D	0.91635	0.999;0.941;0.999	T	0.51301	-0.8723	10	0.51188	T	0.08	-38.8703	13.4552	0.61195	0.0:0.0:0.0:1.0	.	300;300;337	E9PKP7;P17480-2;P17480	.;.;UBF1_HUMAN	P	300;337;300;300;337;300;300;337	ENSP00000345297:Q300P;ENSP00000302640:Q337P;ENSP00000431539:Q300P;ENSP00000437180:Q300P;ENSP00000390669:Q337P;ENSP00000377231:Q300P;ENSP00000432925:Q300P;ENSP00000435708:Q337P	ENSP00000302640:Q337P	Q	-	2	0	UBTF	39644537	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.768000	0.85345	1.858000	0.53909	0.402000	0.26972	CAG	.	.		0.577	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
MUC16	94025	hgsc.bcm.edu	37	19	9076110	9076110	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:9076110G>C	ENST00000397910.4	-	3	11539	c.11336C>G	c.(11335-11337)tCt>tGt	p.S3779C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3780	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGCCCTATAGAGAAGGGCAA	0.527																																					p.S3779C		Atlas-SNP	.											.	MUC16	4315	.	0			c.C11336G						.						151.0	147.0	148.0					19																	9076110		2049	4206	6255	SO:0001583	missense	94025	exon3			CCTATAGAGAAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11336C>G	chr19.hg19:g.9076110G>C	ENSP00000381008:p.Ser3779Cys	83.0	0.0		49.0	32.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	1.751	-0.489244	0.04352	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	1.93	0.801	0.18679	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	.	.	.	D	0.71674	0.998	D	0.69307	0.963	T	0.43909	-0.9362	8	0.87932	D	0	.	4.0161	0.09644	0.246:0.0:0.754:0.0	.	3779	B5ME49	.	C	3779	ENSP00000381008:S3779C	ENSP00000381008:S3779C	S	-	2	0	MUC16	8937110	0.001000	0.12720	0.001000	0.08648	0.021000	0.10359	0.729000	0.26028	0.313000	0.23062	0.313000	0.20887	TCT	.	.		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DPF1	8193	hgsc.bcm.edu	37	19	38703032	38703032	+	Splice_Site	SNP	C	C	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:38703032C>T	ENST00000420980.2	-	10	987		c.e10-1		DPF1_ENST00000412732.1_Intron|DPF1_ENST00000416611.1_Splice_Site|DPF1_ENST00000414789.1_Intron|DPF1_ENST00000456296.1_Intron|DPF1_ENST00000355526.4_Intron	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1						apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGCTGGCACCCTGGGGGCACG	0.667																																					.		Atlas-SNP	.											.	DPF1	54	.	0			c.961-1G>A						.						7.0	7.0	7.0					19																	38703032		2059	4010	6069	SO:0001630	splice_region_variant	8193	exon11			GGCACCCTGGGGG	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"""Zinc fingers, PHD-type"""	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.961-1G>A	chr19.hg19:g.38703032C>T		81.0	0.0		109.0	38.0	NM_004647	B3KSY8|Q08AJ0	Splice_Site	SNP	ENST00000420980.2	hg19	CCDS33008.2	.	.	.	.	.	.	.	.	.	.	C	14.88	2.668539	0.47677	.	.	ENSG00000011332	ENST00000420980;ENST00000416611	.	.	.	4.01	1.71	0.24356	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7924	0.18367	0.1899:0.7045:0.0:0.1055	.	.	.	.	.	-1	.	.	.	-	.	.	DPF1	43394872	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.960000	0.40422	0.882000	0.36016	0.579000	0.79373	.	.	.		0.667	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1		Intron
TNNC2	7125	hgsc.bcm.edu	37	20	44451995	44451995	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr20:44451995C>G	ENST00000372555.3	-	6	567	c.475G>C	c.(475-477)Gtg>Ctg	p.V159L	TNNC2_ENST00000372557.1_Missense_Mutation_p.V144L	NM_003279.2	NP_003270.1	P02585	TNNC2_HUMAN	troponin C type 2 (fast)	159	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				muscle filament sliding (GO:0030049)|regulation of muscle contraction (GO:0006937)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.0122)			Felodipine(DB01023)	CCTTACTGCACGCCCTCCATC	0.652																																					p.V159L		Atlas-SNP	.											.	TNNC2	12	.	0			c.G475C						.						77.0	51.0	60.0					20																	44451995		2203	4299	6502	SO:0001583	missense	7125	exon6			ACTGCACGCCCTC		CCDS13375.1	20q12-q13.11	2013-01-10	2005-09-12		ENSG00000101470	ENSG00000101470		"""EF-hand domain containing"""	11944	protein-coding gene	gene with protein product		191039	"""troponin C2, fast"""			2373703	Standard	NM_003279		Approved		uc002xpr.3	P02585	OTTHUMG00000032623	ENST00000372555.3:c.475G>C	chr20.hg19:g.44451995C>G	ENSP00000361636:p.Val159Leu	38.0	0.0		39.0	21.0	NM_003279	Q6FH92	Missense_Mutation	SNP	ENST00000372555.3	hg19	CCDS13375.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.094030	0.56075	.	.	ENSG00000101470	ENST00000372557;ENST00000372555	T;T	0.75589	-0.95;-0.85	4.92	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.55353	0.1915	N	0.05467	-0.045	0.51767	D	0.999932	P	0.35612	0.512	B	0.37091	0.241	T	0.60342	-0.7282	10	0.87932	D	0	-40.8879	9.9765	0.41786	0.1553:0.6944:0.1502:0.0	.	159	P02585	TNNC2_HUMAN	L	144;159	ENSP00000361638:V144L;ENSP00000361636:V159L	ENSP00000361636:V159L	V	-	1	0	TNNC2	43885402	1.000000	0.71417	0.996000	0.52242	0.809000	0.45718	4.403000	0.59729	1.055000	0.40461	0.491000	0.48974	GTG	.	.		0.652	TNNC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079524.3	NM_003279	
SGSM1	129049	hgsc.bcm.edu	37	22	25308673	25308673	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr22:25308673G>A	ENST00000400359.4	+	23	3054	c.3047G>A	c.(3046-3048)gGa>gAa	p.G1016E	SGSM1_ENST00000400358.4_Missense_Mutation_p.G961E	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	1016	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TTCCCCCACGGAGGCGCCATG	0.507																																					p.G1016E		Atlas-SNP	.											.	SGSM1	150	.	0			c.G3047A						.						82.0	83.0	83.0					22																	25308673		2155	4277	6432	SO:0001583	missense	129049	exon23			CCCACGGAGGCGC	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.3047G>A	chr22.hg19:g.25308673G>A	ENSP00000383212:p.Gly1016Glu	95.0	0.0		85.0	11.0	NM_001039948	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	hg19	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	g	31	5.062794	0.93898	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.10477	2.87;2.87	5.3	5.3	0.74995	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.33089	0.0851	M	0.67700	2.07	0.80722	D	1	B;B;D;D	0.89917	0.335;0.176;0.971;1.0	B;B;P;D	0.97110	0.31;0.437;0.861;1.0	T	0.00797	-1.1562	10	0.46703	T	0.11	-16.8961	18.3333	0.90277	0.0:0.0:1.0:0.0	.	961;1016;1033;1016	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	E	1016;961;1016	ENSP00000383211:G961E;ENSP00000383212:G1016E	ENSP00000383211:G961E	G	+	2	0	SGSM1	23638673	1.000000	0.71417	0.978000	0.43139	0.991000	0.79684	9.779000	0.99018	2.663000	0.90544	0.655000	0.94253	GGA	.	.		0.507	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
RBM10	8241	hgsc.bcm.edu	37	X	47030582	47030582	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chrX:47030582G>T	ENST00000377604.3	+	4	1099	c.357G>T	c.(355-357)gaG>gaT	p.E119D	RBM10_ENST00000345781.6_Intron|RBM10_ENST00000329236.7_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	119	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggaggatgaggagg	0.662																																					p.E184D	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G552T						.						20.0	19.0	19.0					X																	47030582		2202	4294	6496	SO:0001583	missense	8241	exon4			GGAGGAGGATGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.357G>T	chrX.hg19:g.47030582G>T	ENSP00000366829:p.Glu119Asp	52.0	0.0		52.0	4.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	7.514	0.655267	0.14580	.	.	ENSG00000182872	ENST00000377604	T	0.11169	2.8	3.1	1.15	0.20763	Nucleotide-binding, alpha-beta plait (1);	0.859005	0.09469	N	0.797951	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38628	-0.9652	10	0.11182	T	0.66	-1.7872	6.9396	0.24486	0.0:0.0:0.4873:0.5127	.	184;119;119	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	D	119	ENSP00000366829:E119D	ENSP00000366829:E119D	E	+	3	2	RBM10	46915526	1.000000	0.71417	0.776000	0.31678	0.914000	0.54420	0.961000	0.29267	0.165000	0.19558	0.502000	0.49764	GAG	.	.		0.662	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
IRAK1	3654	hgsc.bcm.edu	37	X	153277357	153277357	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chrX:153277357C>A	ENST00000369980.3	-	14	2259	c.2092G>T	c.(2092-2094)Gaa>Taa	p.E698*	IRAK1_ENST00000369974.2_Nonsense_Mutation_p.E619*|IRAK1_ENST00000429936.2_Nonsense_Mutation_p.E694*|IRAK1_ENST00000393682.1_Nonsense_Mutation_p.E679*|IRAK1_ENST00000393687.2_Nonsense_Mutation_p.E668*|IRAK1_ENST00000477274.1_Intron	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	698					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGTCCTGTTCCAGGCCCAAG	0.567																																					p.E698X		Atlas-SNP	.											.	IRAK1	107	.	0			c.G2092T						.						61.0	62.0	62.0					X																	153277357		2203	4300	6503	SO:0001587	stop_gained	3654	exon14			CCTGTTCCAGGCC	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.2092G>T	chrX.hg19:g.153277357C>A	ENSP00000358997:p.Glu698*	19.0	0.0		24.0	16.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Nonsense_Mutation	SNP	ENST00000369980.3	hg19	CCDS14740.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	39|39|39	7.303695|7.303695|7.303695	0.98200|0.98200|0.98200	.|.|.	.|.|.	ENSG00000184216|ENSG00000184216|ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936|ENST00000444254|ENST00000455690;ENST00000437278	.|.|.	.|.|.	.|.|.	5.63|5.63|5.63	4.75|4.75|4.75	0.60458|0.60458|0.60458	.|.|.	0.959084|.|.	0.08611|.|.	N|.|.	0.920017|.|.	.|T|T	.|0.60983|0.60983	.|0.2311|0.2311	.|.|.	.|.|.	.|.|.	0.35444|0.35444|0.35444	D|D|D	0.795096|0.795096|0.795096	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.67662|0.67662	.|-0.5613|-0.5613	.|4|4	0.51188|.|.	T|.|.	0.08|.|.	0.3674|0.3674|0.3674	11.4292|11.4292|11.4292	0.50029|0.50029|0.50029	0.0:0.8225:0.1775:0.0|0.0:0.8225:0.1775:0.0|0.0:0.8225:0.1775:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|V|C	698;619;679;668;694|203|147;261	.|.|.	ENSP00000358991:E619X|.|.	E|G|W	-|-|-	1|2|3	0|0|0	IRAK1|IRAK1|IRAK1	152930551|152930551|152930551	0.006000|0.006000|0.006000	0.16342|0.16342|0.16342	0.005000|0.005000|0.005000	0.12908|0.12908|0.12908	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	2.036000|2.036000|2.036000	0.41165|0.41165|0.41165	1.125000|1.125000|1.125000	0.41998|0.41998|0.41998	0.525000|0.525000|0.525000	0.51046|0.51046|0.51046	GAA|GGA|TGG	.	.		0.567	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
CCNO	10309	hgsc.bcm.edu	37	5	54529209	54529209	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr5:54529209delG	ENST00000282572.4	-	1	299	c.143delC	c.(142-144)ccgfs	p.P48fs	RP11-506H20.1_ENST00000506435.1_RNA	NM_021147.3	NP_066970.3	P22674	CCNO_HUMAN	cyclin O	48					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cell cycle (GO:0007049)|cell division (GO:0051301)|cilium assembly (GO:0042384)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)|embryo development (GO:0009790)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	uracil DNA N-glycosylase activity (GO:0004844)			endometrium(1)|lung(3)|skin(1)	5		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)			GAGCGGGCACGGGTTCAGGGG	0.711																																					p.P48fs		Atlas-INDEL	.											.	CCNO	17	.	0			c.144delG						.																																			SO:0001589	frameshift_variant	10309	exon1			.	M87499	CCDS34157.1	5q11.2	2010-11-15	2007-07-26	2007-07-26	ENSG00000152669	ENSG00000152669			18576	protein-coding gene	gene with protein product		607752	"""cyclin U"""	CCNU			Standard	NR_125346		Approved	UDG2, FLJ22422, UNG2	uc003jpw.3	P22674	OTTHUMG00000162598	ENST00000282572.4:c.143delC	chr5.hg19:g.54529209delG	ENSP00000282572:p.Pro48fs	143.0	0.0		136.0	56.0	NM_021147	A8K1W5|Q0P6J2|Q9H6B0|Q9UMD5	Frame_Shift_Del	DEL	ENST00000282572.4	hg19	CCDS34157.1																																																																																			.	.		0.711	CCNO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369707.1	NM_021147	
TULP2	7288	hgsc.bcm.edu	37	19	49399799	49399816	+	Splice_Site	DEL	TTCAAACAGCCGCCGCTG	TTCAAACAGCCGCCGCTG	-	rs375021981|rs575577268		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	TTCAAACAGCCGCCGCTG	TTCAAACAGCCGCCGCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:49399799_49399816delTTCAAACAGCCGCCGCTG	ENST00000221399.3	-	4	229_243	c.85_99delCAGCGGCGGCTGTTTGAA	c.(85-99)cagcggcggctgtttdel	p.QRRLF29del		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	29					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GCTGCTTCTTTTCAAACAGCCGCCGCTGGGGAGATGGG	0.628																																					p.29_34del		Atlas-INDEL	.											.	TULP2	60	.	0			c.85_100del						.																																			SO:0001630	splice_region_variant	7288	exon4			.	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.85-1CAGCGGCGGCTGTTTGAA>-	chr19.hg19:g.49399799_49399816delTTCAAACAGCCGCCGCTG		36.0	0.0		30.0	10.0	NM_003323	Q8TC50	Frame_Shift_Del	DEL	ENST00000221399.3	hg19	CCDS12739.1																																																																																			.	.		0.628	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	In_Frame_Del
FRMD5	84978	hgsc.bcm.edu	37	15	44194417	44194418	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr15:44194417_44194418insT	ENST00000417257.1	-	7	770_771	c.594_595insA	c.(592-597)aaagcafs	p.A199fs	FRMD5_ENST00000484674.1_Frame_Shift_Ins_p.A110fs|FRMD5_ENST00000402883.1_Frame_Shift_Ins_p.A199fs	NM_032892.3	NP_116281.2	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5	199	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		AATGTCTGTGCTTTTCTTAAGA	0.465																																					p.A199fs		Atlas-INDEL	.											.	FRMD5	45	.	0			c.595_596insA						.																																			SO:0001589	frameshift_variant	84978	exon7			.	BC007796	CCDS10107.2, CCDS73715.1, CCDS73716.1	15q15.3	2005-08-09			ENSG00000171877	ENSG00000171877			28214	protein-coding gene	gene with protein product							Standard	XM_005254729		Approved	MGC14161	uc001ztl.3	Q7Z6J6	OTTHUMG00000060475	ENST00000417257.1:c.595dupA	chr15.hg19:g.44194421_44194421dupT	ENSP00000403067:p.Ala199fs	65.0	0.0		48.0	23.0	NM_032892	Q8NBG4	Frame_Shift_Ins	INS	ENST00000417257.1	hg19	CCDS10107.2																																																																																			.	.		0.465	FRMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133879.1	NM_032892	
ALB	213	hgsc.bcm.edu	37	4	74272435	74272440	+	De_novo_Start_InFrame	DEL	CATGTG	CATGTG	-	rs75152012		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	CATGTG	CATGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr4:74272435_74272440delCATGTG	ENST00000503124.1	+	0	196_201				ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000295897.4_In_Frame_Del_p.76_78TCV>I|ALB_ENST00000509063.1_In_Frame_Del_p.76_78TCV>I			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTGCAAAAACATGTGTTGCTGATGA	0.35																																					p.76_77del		Atlas-INDEL	.											.	ALB	132	.	0			c.226_231del	GRCh37	CD023226	ALB	D	rs75152012	.																																					213	exon3			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919		chr4.hg19:g.74272435_74272440delCATGTG		42.0	0.0		44.0	13.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.350	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
AKAP9	10142	hgsc.bcm.edu	37	7	91652251	91652251	+	Frame_Shift_Del	DEL	A	A	-	rs548801776		TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr7:91652251delA	ENST00000359028.2	+	15	4337	c.4112delA	c.(4111-4113)caafs	p.Q1371fs	AKAP9_ENST00000358100.2_Frame_Shift_Del_p.Q1371fs|AKAP9_ENST00000356239.3_Frame_Shift_Del_p.Q1359fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1371					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAAACTGAACAAAACTATGAG	0.393			T	BRAF	papillary thyroid																																p.Q1359fs		Atlas-INDEL	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.4075delC						.						98.0	91.0	93.0					7																	91652251		2203	4300	6503	SO:0001589	frameshift_variant	10142	exon14			.	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4112delA	chr7.hg19:g.91652251delA	ENSP00000351922:p.Gln1371fs	108.0	0.0		78.0	16.0	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	hg19																																																																																				.	.		0.393	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ODF1	4956	hgsc.bcm.edu	37	8	103573034	103573042	+	In_Frame_Del	DEL	CCCGTGCAG	CCCGTGCAG	-	rs143802899|rs199994329|rs568456031|rs372688769|rs59109601|rs377699584|rs11992195|rs62523273|rs386728348|rs58232162	byFrequency	TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	CCCGTGCAG	CCCGTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr8:103573034_103573042delCCCGTGCAG	ENST00000285402.3	+	2	831_839	c.675_683delCCCGTGCAG	c.(673-684)aacccgtgcagc>aac	p.PCS226del	ODF1_ENST00000518835.1_In_Frame_Del_p.PCS19del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	226	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			gcccctgcaacccgtgcagcccATATGAT	0.541																																					p.225_228del		Atlas-INDEL	.											ODF1,NS,carcinoma,0,1	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.674_682del						.																																			SO:0001651	inframe_deletion	4956	exon2			.	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.675_683delCCCGTGCAG	chr8.hg19:g.103573034_103573042delCCCGTGCAG	ENSP00000285402:p.Pro226_Ser228del	46.0	0.0		47.0	10.0	NM_024410	Q3SX72	In_Frame_Del	DEL	ENST00000285402.3	hg19	CCDS6293.1																																																																																			.	.		0.541	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
ALB	213	hgsc.bcm.edu	37	4	74286007	74286007	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr4:74286007delG	ENST00000503124.1	+	12	1579	c.1372delG	c.(1372-1374)ggcfs	p.G458fs	ALB_ENST00000401494.3_Frame_Shift_Del_p.G493fs|ALB_ENST00000415165.2_Frame_Shift_Del_p.G416fs|ALB_ENST00000295897.4_Frame_Shift_Del_p.G608fs|ALB_ENST00000509063.1_Intron|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGCTGCCTTAGGCTTATAACA	0.279																																					p.L607fs		Atlas-INDEL	.											.	ALB	132	.	0			c.1821delA						.						89.0	85.0	87.0					4																	74286007		2201	4300	6501	SO:0001589	frameshift_variant	213	exon14			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1372delG	chr4.hg19:g.74286007delG	ENSP00000421027:p.Gly458fs	155.0	0.0		134.0	70.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.279	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
KEAP1	9817	hgsc.bcm.edu	37	19	10600016	10600019	+	Frame_Shift_Del	DEL	ATAG	ATAG	-			TCGA-DD-AACO-01A-11D-A40R-10	TCGA-DD-AACO-10A-01D-A40U-10	ATAG	ATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42340dfc-2c44-47a6-b81d-99117a74110c	7b21aa0b-afe2-498f-890b-c71e1a5a372a	g.chr19:10600016_10600019delATAG	ENST00000171111.5	-	5	2104_2107	c.1557_1560delCTAT	c.(1555-1560)atctatfs	p.IY519fs	KEAP1_ENST00000393623.2_Frame_Shift_Del_p.IY519fs|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	519					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CCCCAGCAGCATAGATACAGTTGT	0.583																																					p.520_521del		Atlas-INDEL	.											.	KEAP1	182	.	0			c.1558_1561del						.																																			SO:0001589	frameshift_variant	9817	exon5			.	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1557_1560delCTAT	chr19.hg19:g.10600016_10600019delATAG	ENSP00000171111:p.Ile519fs	131.0	0.0		67.0	40.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Frame_Shift_Del	DEL	ENST00000171111.5	hg19	CCDS12239.1																																																																																			.	.		0.583	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
