#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
COL11A1	1301	broad.mit.edu	37	1	103470190	103470190	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr1:103470190C>T	ENST00000370096.3	-	19	2185	c.1873G>A	c.(1873-1875)Ggt>Agt	p.G625S	COL11A1_ENST00000461720.1_5'UTR|COL11A1_ENST00000358392.2_Missense_Mutation_p.G637S|COL11A1_ENST00000512756.1_Missense_Mutation_p.G509S|COL11A1_ENST00000353414.4_Missense_Mutation_p.G586S	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	625	Collagen-like 3.|Collagen-like 4.|Triple-helical region.		G -> V (in STL2). {ECO:0000269|PubMed:8872475}.		cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.G637S(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCAGGAGGACCTGGAGGACCT	0.323																																																1	Substitution - Missense(1)	ovary(1)	1											40.0	37.0	38.0					1																	103470190		2203	4300	6503	103242778	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1873G>A	1.37:g.103470190C>T	ENSP00000359114:p.Gly625Ser		103242778	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.990652	0.93106	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.99607	-6.27;-6.27;-6.27;-6.27	5.83	4.92	0.64577	.	0.052522	0.85682	N	0.000000	D	0.99492	0.9819	H	0.99650	4.68	0.80722	D	1	B;B;B;B	0.32245	0.106;0.087;0.361;0.234	B;B;B;B	0.31946	0.084;0.05;0.138;0.119	D	0.97964	1.0339	10	0.87932	D	0	.	14.9259	0.70878	0.0:0.9315:0.0:0.0685	.	509;586;637;625	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	S	625;637;586;509	ENSP00000359114:G625S;ENSP00000351163:G637S;ENSP00000302551:G586S;ENSP00000426533:G509S	ENSP00000302551:G586S	G	-	1	0	COL11A1	103242778	1.000000	0.71417	0.648000	0.29521	0.996000	0.88848	5.090000	0.64498	1.468000	0.48064	0.655000	0.94253	GGT		0.323	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
TDRD5	163589	broad.mit.edu	37	1	179609181	179609181	+	Silent	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr1:179609181C>T	ENST00000367614.1	+	10	2087	c.1728C>T	c.(1726-1728)ttC>ttT	p.F576F	TDRD5_ENST00000444136.1_Silent_p.F576F|TDRD5_ENST00000294848.8_Silent_p.F576F	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	576	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				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)		p.F576F(1)		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						CCCTGAGGTTCCTCAAGTGAG	0.408																																																1	Substitution - coding silent(1)	ovary(1)	1											118.0	116.0	117.0					1																	179609181		2203	4300	6503	177875804	SO:0001819	synonymous_variant	163589			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.1728C>T	1.37:g.179609181C>T			177875804	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	37	CCDS1332.1																																																																																				0.408	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
TPR	7175	broad.mit.edu	37	1	186312598	186312598	+	Nonsense_Mutation	SNP	G	G	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr1:186312598G>A	ENST00000367478.4	-	27	3906	c.3610C>T	c.(3610-3612)Cga>Tga	p.R1204*		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1204					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.R1205*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTTTCTCGTCGTATAAATCTA	0.333			T	NTRK1	papillary thyroid																																		Dom	yes		1	1q25	7175	translocated promoter region		E	1	Substitution - Nonsense(1)	ovary(1)	1											63.0	59.0	60.0					1																	186312598		1851	4093	5944	184579221	SO:0001587	stop_gained	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3610C>T	1.37:g.186312598G>A	ENSP00000356448:p.Arg1204*		184579221	Q15655|Q5SWY0|Q99968	Nonsense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	45	11.910955	0.99616	.	.	ENSG00000047410	ENST00000367478	.	.	.	5.07	5.07	0.68467	.	0.124249	0.56097	D	0.000031	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4489	0.90696	0.0:0.0:1.0:0.0	.	.	.	.	X	1204	.	ENSP00000356448:R1204X	R	-	1	2	TPR	184579221	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.644000	0.83416	2.372000	0.80975	0.561000	0.74099	CGA		0.333	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
C12orf40	283461	broad.mit.edu	37	12	40076668	40076668	+	Silent	SNP	G	G	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr12:40076668G>A	ENST00000324616.5	+	8	1096	c.942G>A	c.(940-942)agG>agA	p.R314R	C12orf40_ENST00000405531.3_Silent_p.R314R|C12orf40_ENST00000398716.1_Silent_p.R237R	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	314								p.R314R(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ATGAGCAAAGGATAAAGAAAA	0.328																																																1	Substitution - coding silent(1)	ovary(1)	12											101.0	96.0	98.0					12																	40076668		1863	4090	5953	38362935	SO:0001819	synonymous_variant	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.942G>A	12.37:g.40076668G>A			38362935	B7WNU1|Q8IXY6|Q8N818|V9HW02	Silent	SNP	ENST00000324616.5	37	CCDS41770.1																																																																																				0.328	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
WDR59	79726	broad.mit.edu	37	16	74920294	74920294	+	Splice_Site	SNP	G	G	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr16:74920294G>A	ENST00000262144.6	-	24	2550	c.2420C>T	c.(2419-2421)gCg>gTg	p.A807V		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	807								p.A807V(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CTCTCTTCCCGCTGAAGAAAA	0.512																																																1	Substitution - Missense(1)	ovary(1)	16											58.0	57.0	57.0					16																	74920294		2198	4300	6498	73477795	SO:0001630	splice_region_variant	79726			AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.2420-1C>T	16.37:g.74920294G>A			73477795	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	CCDS32488.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689193	0.29962	.	.	ENSG00000103091	ENST00000262144	T	0.68331	-0.32	5.29	3.07	0.35406	.	0.445679	0.25341	N	0.031370	T	0.46580	0.1400	N	0.22421	0.69	0.32492	N	0.5401	B;B	0.10296	0.0;0.003	B;B	0.08055	0.0;0.003	T	0.47736	-0.9094	10	0.25751	T	0.34	.	6.965	0.24617	0.3418:0.0:0.6582:0.0	.	807;252	Q6PJI9;Q6PJI9-4	WDR59_HUMAN;.	V	807	ENSP00000262144:A807V	ENSP00000262144:A807V	A	-	2	0	WDR59	73477795	0.998000	0.40836	0.991000	0.47740	0.391000	0.30476	2.607000	0.46300	1.177000	0.42855	0.505000	0.49811	GCG		0.512	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	Missense_Mutation
TP53	7157	broad.mit.edu	37	17	7576885	7576885	+	Nonsense_Mutation	SNP	T	T	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr17:7576885T>A	ENST00000269305.4	-	9	1150	c.961A>T	c.(961-963)Aaa>Taa	p.K321*	TP53_ENST00000445888.2_Nonsense_Mutation_p.K321*|TP53_ENST00000359597.4_Nonsense_Mutation_p.K321*|TP53_ENST00000455263.2_Nonsense_Mutation_p.K321*|TP53_ENST00000420246.2_Nonsense_Mutation_p.K321*|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	321	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.		K -> E (in kidney cancer; germline mutation).|K -> R (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.K321fs*24(3)|p.P318fs*15(2)|p.K321*(2)|p.P318fs*21(1)|p.S315fs*22(1)|p.?(1)|p.L308fs*15(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCCAGTGGTTTCTTCTTTGGC	0.458		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	19	Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Nonsense(2)|Unknown(1)	bone(4)|breast(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|ovary(2)|stomach(1)|soft_tissue(1)|endometrium(1)|lung(1)	17											129.0	119.0	122.0					17																	7576885		2203	4300	6503	7517610	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.961A>T	17.37:g.7576885T>A	ENSP00000269305:p.Lys321*		7517610	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	37|37	6.314282|6.314282	0.97467|0.97467	.|.	.|.	ENSG00000141510|ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690|ENST00000419024	.|.	.|.	.|.	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	0.806142|.	0.11658|.	N|.	0.542146|.	.|T	.|0.65523	.|0.2699	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77000	.|-0.2750	.|4	0.02654|0.87932	T|D	1|0	-22.8989|-22.8989	10.7895|10.7895	0.46424|0.46424	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|S	321;321;321;321;321;310;189|7	.|.	ENSP00000269305:K321X|ENSP00000402130:R7S	K|R	-|-	1|3	0|2	TP53|TP53	7517610|7517610	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	3.768000|3.768000	0.55295|0.55295	2.030000|2.030000	0.59900|0.59900	0.459000|0.459000	0.35465|0.35465	AAA|AGA		0.458	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
CARD14	79092	broad.mit.edu	37	17	78169003	78169003	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr17:78169003C>T	ENST00000573882.1	+	12	1906	c.1370C>T	c.(1369-1371)tCg>tTg	p.S457L	CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000344227.2_Missense_Mutation_p.S457L|CARD14_ENST00000392434.2_Missense_Mutation_p.S220L|CARD14_ENST00000570421.1_Missense_Mutation_p.S457L			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	457					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)	p.S457L(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CAGCTCTTGTCGGACCTGAGT	0.677																																																1	Substitution - Missense(1)	ovary(1)	17											44.0	42.0	43.0					17																	78169003		2203	4300	6503	75783598	SO:0001583	missense	79092			AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.1370C>T	17.37:g.78169003C>T	ENSP00000458715:p.Ser457Leu		75783598	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	C	6.016	0.371343	0.11409	.	.	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	T;T	0.36878	1.23;1.23	4.55	2.56	0.30785	.	1.811070	0.02701	N	0.111750	T	0.33585	0.0868	L	0.51422	1.61	0.09310	N	1	B;B;B	0.18013	0.004;0.025;0.002	B;B;B	0.09377	0.001;0.004;0.001	T	0.15549	-1.0433	10	0.21014	T	0.42	-3.8235	6.8276	0.23893	0.0:0.6697:0.2248:0.1055	.	457;220;457	B8QQJ3;E7ETJ2;Q9BXL6	.;.;CAR14_HUMAN	L	457;220;220	ENSP00000344549:S457L;ENSP00000376229:S220L	ENSP00000308507:S220L	S	+	2	0	CARD14	75783598	0.952000	0.32445	0.007000	0.13788	0.006000	0.05464	2.327000	0.43858	0.556000	0.29098	0.650000	0.86243	TCG		0.677	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
CD22	933	broad.mit.edu	37	19	35828818	35828818	+	Silent	SNP	G	G	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr19:35828818G>A	ENST00000085219.5	+	5	945	c.879G>A	c.(877-879)acG>acA	p.T293T	CD22_ENST00000419549.2_Silent_p.T121T|CD22_ENST00000341773.6_Intron|CD22_ENST00000544992.2_Silent_p.T293T|CD22_ENST00000594250.1_Intron|CD22_ENST00000270311.6_Silent_p.T173T|CD22_ENST00000536635.2_Silent_p.T293T	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	293	Ig-like C2-type 2.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.T293T(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ATACATTCACGCTAAACCTGC	0.567																																					Ovarian(42;1009 1133 23674 26041)											1	Substitution - coding silent(1)	ovary(1)	19											111.0	77.0	88.0					19																	35828818		2203	4300	6503	40520658	SO:0001819	synonymous_variant	933			X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.879G>A	19.37:g.35828818G>A			40520658	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																				0.567	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
ZNF227	7770	broad.mit.edu	37	19	44739757	44739757	+	Missense_Mutation	SNP	A	A	G			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr19:44739757A>G	ENST00000313040.7	+	6	1379	c.1174A>G	c.(1174-1176)Agt>Ggt	p.S392G	ZNF227_ENST00000391961.2_Missense_Mutation_p.S341G|ZNF227_ENST00000589005.1_Missense_Mutation_p.S341G	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	392					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S392G(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CTTCGGTTGGAGTGTTAATCT	0.448																																																1	Substitution - Missense(1)	ovary(1)	19											87.0	95.0	93.0					19																	44739757		2203	4300	6503	49431597	SO:0001583	missense	7770			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1174A>G	19.37:g.44739757A>G	ENSP00000321049:p.Ser392Gly		49431597	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.701403	0.48307	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.16324	2.35;2.87	4.54	2.35	0.29111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17066	0.0410	M	0.79343	2.45	0.09310	N	0.999996	B;B;B;B	0.33807	0.117;0.117;0.426;0.117	B;B;B;B	0.24701	0.007;0.015;0.055;0.015	T	0.15780	-1.0425	9	0.30854	T	0.27	.	6.1318	0.20209	0.7455:0.1651:0.0895:0.0	.	313;371;344;392	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	G	392;349;341;371;93	ENSP00000321049:S392G;ENSP00000375823:S341G	ENSP00000321049:S392G	S	+	1	0	ZNF227	49431597	0.000000	0.05858	0.998000	0.56505	0.983000	0.72400	0.130000	0.15850	0.659000	0.30945	0.460000	0.39030	AGT		0.448	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
SIGLEC11	114132	broad.mit.edu	37	19	50462666	50462666	+	Silent	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr19:50462666C>T	ENST00000447370.2	-	5	1098	c.1008G>A	c.(1006-1008)gcG>gcA	p.A336A	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Silent_p.A336A	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	336	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.A324A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		GCCTGTTCTCCGCTCGGCAGG	0.662																																																1	Substitution - coding silent(1)	ovary(1)	19											29.0	45.0	40.0					19																	50462666		1957	4292	6249	55154478	SO:0001819	synonymous_variant	114132			AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1008G>A	19.37:g.50462666C>T			55154478		Silent	SNP	ENST00000447370.2	37	CCDS12790.2	.	.	.	.	.	.	.	.	.	.	C	0.258	-1.001602	0.02128	.	.	ENSG00000161640	ENST00000426971	.	.	.	1.61	-3.23	0.05109	.	.	.	.	.	T	0.49508	0.1561	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	T	0.41858	-0.9485	4	.	.	.	.	6.2332	0.20747	0.0:0.5744:0.0:0.4256	.	.	.	.	Q	326	.	.	R	-	2	0	SIGLEC11	55154478	0.000000	0.05858	0.769000	0.31535	0.031000	0.12232	-3.504000	0.00449	-0.896000	0.03915	-1.219000	0.01604	CGG		0.662	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
CNTNAP5	129684	broad.mit.edu	37	2	125521567	125521567	+	Silent	SNP	C	C	T	rs566175180		TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr2:125521567C>T	ENST00000431078.1	+	16	2737	c.2373C>T	c.(2371-2373)aaC>aaT	p.N791N		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	791	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.N791N(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCTTCTGGAACGCCGTCTCAT	0.413													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18170	0.0		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	ovary(1)	2											124.0	118.0	120.0					2																	125521567		1883	4093	5976	125238037	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2373C>T	2.37:g.125521567C>T			125238037	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.413	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
SCN7A	6332	broad.mit.edu	37	2	167262119	167262119	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr2:167262119C>T	ENST00000409855.1	-	25	5146	c.5020G>A	c.(5020-5022)Gaa>Aaa	p.E1674K		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1674					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E1674K(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GGTGACTTTTCCTTAGCTTTG	0.353																																																1	Substitution - Missense(1)	ovary(1)	2											244.0	230.0	234.0					2																	167262119		1846	4097	5943	166970365	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.5020G>A	2.37:g.167262119C>T	ENSP00000386796:p.Glu1674Lys		166970365		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.115764	0.77323	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.96774	-4.12	4.75	4.75	0.60458	.	0.521196	0.17591	N	0.168756	D	0.92077	0.7489	N	0.22421	0.69	0.39221	D	0.963505	P	0.39060	0.657	B	0.35182	0.197	D	0.93094	0.6502	10	0.54805	T	0.06	.	15.1315	0.72527	0.0:1.0:0.0:0.0	.	1674	Q01118	SCN7A_HUMAN	K	1674	ENSP00000386796:E1674K	ENSP00000259060:E1674K	E	-	1	0	SCN7A	166970365	0.639000	0.27234	0.220000	0.23810	0.217000	0.24651	2.927000	0.48900	2.630000	0.89119	0.655000	0.94253	GAA		0.353	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
STX16	8675	broad.mit.edu	37	20	57251255	57251255	+	Nonsense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr20:57251255C>T	ENST00000371141.4	+	9	1610	c.886C>T	c.(886-888)Caa>Taa	p.Q296*	STX16-NPEPL1_ENST00000530122.1_Intron|STX16_ENST00000371132.4_Nonsense_Mutation_p.Q275*|STX16_ENST00000358029.4_Nonsense_Mutation_p.Q292*|STX16_ENST00000361830.3_Nonsense_Mutation_p.Q296*|STX16_ENST00000361770.5_Nonsense_Mutation_p.Q279*|STX16_ENST00000355957.5_Nonsense_Mutation_p.Q279*|STX16_ENST00000359617.4_Nonsense_Mutation_p.Q243*	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	296					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.Q275*(1)		breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			AGAACAGTATCAAAAGAAGAA	0.413																																																1	Substitution - Nonsense(1)	ovary(1)	20											201.0	200.0	200.0					20																	57251255		2203	4300	6503	56684661	SO:0001587	stop_gained	8675			AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.886C>T	20.37:g.57251255C>T	ENSP00000360183:p.Gln296*		56684661	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Nonsense_Mutation	SNP	ENST00000371141.4	37	CCDS13468.1	.	.	.	.	.	.	.	.	.	.	C	44	10.548866	0.99425	.	.	ENSG00000124222	ENST00000355957;ENST00000361770;ENST00000359617;ENST00000371141;ENST00000371138;ENST00000371132;ENST00000358029;ENST00000361830;ENST00000438253;ENST00000435446	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.2859	0.94069	0.0:1.0:0.0:0.0	.	.	.	.	X	279;279;243;296;243;275;292;296;190;110	.	ENSP00000360180:Q243X	Q	+	1	0	STX16	56684661	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.784000	0.75084	2.873000	0.98535	0.563000	0.77884	CAA		0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
PPM1F	9647	broad.mit.edu	37	22	22285650	22285650	+	Missense_Mutation	SNP	C	C	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	A	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr22:22285650C>A	ENST00000263212.5	-	6	866	c.761G>T	c.(760-762)gGc>gTc	p.G254V	PPM1F_ENST00000397495.4_Missense_Mutation_p.G254V|PPM1F_ENST00000407142.1_Missense_Mutation_p.G86V|PPM1F_ENST00000538191.1_Missense_Mutation_p.G150V	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	254					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)	p.G254V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		ACCTGTGGTGCCGCTCTGCAG	0.627																																																1	Substitution - Missense(1)	ovary(1)	22											40.0	33.0	36.0					22																	22285650		2203	4300	6503	20615650	SO:0001583	missense	9647			D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.761G>T	22.37:g.22285650C>A	ENSP00000263212:p.Gly254Val		20615650	A8K6G3|B7Z2C3|Q96PM2	Missense_Mutation	SNP	ENST00000263212.5	37	CCDS13796.1	.	.	.	.	.	.	.	.	.	.	C	33	5.225093	0.95173	.	.	ENSG00000100034	ENST00000263212;ENST00000407142;ENST00000406981;ENST00000538191;ENST00000397495;ENST00000445205	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	4.84	4.84	0.62591	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	D	0.89008	0.6593	H	0.98111	4.15	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.92947	0.6377	10	0.87932	D	0	-28.1433	18.5176	0.90941	0.0:1.0:0.0:0.0	.	150;254;254	B7Z2C3;A8MX49;P49593	.;.;PPM1F_HUMAN	V	254;86;86;150;254;86	ENSP00000263212:G254V;ENSP00000384930:G86V;ENSP00000439915:G150V;ENSP00000380632:G254V;ENSP00000392372:G86V	ENSP00000263212:G254V	G	-	2	0	PPM1F	20615650	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	7.567000	0.82357	2.700000	0.92200	0.561000	0.74099	GGC		0.627	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
C7	730	broad.mit.edu	37	5	40981517	40981517	+	Nonsense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr5:40981517C>T	ENST00000313164.9	+	18	2733	c.2374C>T	c.(2374-2376)Cga>Tga	p.R792*		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	792	Factor I module (FIM) 2.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.R792*(1)					Ovarian(839;0.0112)				ATGTGTCTGCCGAGAAGCATC	0.502																																																1	Substitution - Nonsense(1)	ovary(1)	5											54.0	55.0	54.0					5																	40981517		2070	4203	6273	41017274	SO:0001587	stop_gained	730			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.2374C>T	5.37:g.40981517C>T	ENSP00000322061:p.Arg792*		41017274	Q6P3T5|Q92489	Nonsense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	C	42	9.517932	0.99193	.	.	ENSG00000112936	ENST00000313164	.	.	.	5.83	1.47	0.22746	.	0.462043	0.21307	N	0.076703	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.0824	9.8439	0.41015	0.4699:0.381:0.149:0.0	.	.	.	.	X	792	.	ENSP00000322061:R792X	R	+	1	2	C7	41017274	0.896000	0.30565	0.996000	0.52242	0.982000	0.71751	0.108000	0.15396	0.241000	0.21283	0.563000	0.77884	CGA		0.502	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
CCL28	56477	broad.mit.edu	37	5	43381982	43381982	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr5:43381982C>T	ENST00000361115.4	-	3	438	c.364G>A	c.(364-366)Ggc>Agc	p.G122S	CCL28_ENST00000513525.1_Missense_Mutation_p.G75S	NM_148672.2	NP_683513.1	Q9NRJ3	CCL28_HUMAN	chemokine (C-C motif) ligand 28	122					cell chemotaxis (GO:0060326)|chemotaxis (GO:0006935)|immune response (GO:0006955)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	chemokine activity (GO:0008009)	p.G122S(1)		kidney(3)|lung(3)|ovary(1)	7						GTTTTATGGCCGTATGTTTCG	0.413																																					Esophageal Squamous(178;1549 1997 2043 22794 27051)											1	Substitution - Missense(1)	ovary(1)	5											291.0	264.0	273.0					5																	43381982		2203	4300	6503	43417739	SO:0001583	missense	56477			AF110384	CCDS3944.1	5p12	2013-02-25			ENSG00000151882	ENSG00000151882		"""Chemokine ligands"", ""Endogenous ligands"""	17700	protein-coding gene	gene with protein product	"""CC chemokine CCL28"", ""mucosae-associated epithelial chemokine"", ""small inducible cytokine subfamily A (Cys-Cys), member 28"", ""small inducible cytokine A28"""	605240				10781587, 11295038	Standard	XR_241707		Approved	SCYA28, MEC, CCK1	uc003jnu.3	Q9NRJ3	OTTHUMG00000094811	ENST00000361115.4:c.364G>A	5.37:g.43381982C>T	ENSP00000354416:p.Gly122Ser		43417739	D7RIE7	Missense_Mutation	SNP	ENST00000361115.4	37	CCDS3944.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.605969	0.28623	.	.	ENSG00000151882	ENST00000361115;ENST00000513525	T;T	0.45668	1.39;0.89	4.99	2.2	0.27929	.	1.281610	0.05413	N	0.542883	T	0.21881	0.0527	N	0.12182	0.205	0.09310	N	1	P	0.38195	0.622	B	0.24848	0.056	T	0.16070	-1.0415	10	0.34782	T	0.22	-0.5687	7.5798	0.27959	0.0:0.7291:0.0:0.2709	.	122	Q9NRJ3	CCL28_HUMAN	S	122;75	ENSP00000354416:G122S;ENSP00000422369:G75S	ENSP00000354416:G122S	G	-	1	0	CCL28	43417739	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.126000	0.10563	0.359000	0.24239	-0.145000	0.13849	GGC		0.413	CCL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211631.2	NM_148672	
PPP2CA	5515	broad.mit.edu	37	5	133541780	133541780	+	Nonsense_Mutation	SNP	G	G	A			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr5:133541780G>A	ENST00000481195.1	-	2	425	c.145C>T	c.(145-147)Cga>Tga	p.R49*	CDKL3_ENST00000609383.1_3'UTR|CTD-2410N18.4_ENST00000518409.1_RNA|CTD-2410N18.5_ENST00000519718.1_Intron|CDKL3_ENST00000609654.1_Nonsense_Mutation_p.R399*|PPP2CA_ENST00000231504.5_5'UTR	NM_002715.2	NP_002706.1	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha isozyme	49					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|meiotic nuclear division (GO:0007126)|mesoderm development (GO:0007498)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein dephosphorylation (GO:0006470)|protein heterotrimerization (GO:0070208)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of protein autophosphorylation (GO:0031952)|regulation of protein catabolic process (GO:0042176)|regulation of receptor activity (GO:0010469)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.R49*(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	ACTGGACATCGAACCTCTTGC	0.378																																																1	Substitution - Nonsense(1)	ovary(1)	5											154.0	136.0	142.0					5																	133541780		2203	4300	6503	133569679	SO:0001587	stop_gained	5515				CCDS4173.1	5q31.1	2013-01-24	2010-03-05		ENSG00000113575	ENSG00000113575	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9299	protein-coding gene	gene with protein product	"""protein phosphatase 2A catalytic subunit, alpha isoform"""	176915	"""protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform"""			8383590	Standard	NM_002715		Approved	PP2Calpha		P67775	OTTHUMG00000129119	ENST00000481195.1:c.145C>T	5.37:g.133541780G>A	ENSP00000418447:p.Arg49*		133569679	P05323|P13197	Nonsense_Mutation	SNP	ENST00000481195.1	37	CCDS4173.1	.	.	.	.	.	.	.	.	.	.	G	37	6.174370	0.97348	.	.	ENSG00000113575	ENST00000481195;ENST00000523082	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	-3.2523	19.3944	0.94601	0.0:0.0:1.0:0.0	.	.	.	.	X	49;36	.	ENSP00000418447:R49X	R	-	1	2	PPP2CA	133569679	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.333000	0.72939	2.665000	0.90641	0.591000	0.81541	CGA		0.378	PPP2CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251165.1	NM_002715	
ASTN2	23245	broad.mit.edu	37	9	119976858	119976858	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr9:119976858C>T	ENST00000313400.4	-	3	894	c.794G>A	c.(793-795)cGg>cAg	p.R265Q	ASTN2_ENST00000373996.3_Missense_Mutation_p.R265Q|ASTN2_ENST00000361209.2_Missense_Mutation_p.R265Q|ASTN2_ENST00000361477.3_5'UTR			O75129	ASTN2_HUMAN	astrotactin 2	265					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.R265Q(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GAAGCTCTCCCGCGCCTGGGG	0.597																																																1	Substitution - Missense(1)	ovary(1)	9											84.0	75.0	78.0					9																	119976858		2203	4300	6503	119016679	SO:0001583	missense	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.794G>A	9.37:g.119976858C>T	ENSP00000314038:p.Arg265Gln		119016679	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	C	18.17	3.565489	0.65651	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000361209	T;T;T	0.24350	2.03;2.02;1.86	5.51	4.6	0.57074	.	0.081526	0.49305	D	0.000150	T	0.36248	0.0960	N	0.24115	0.695	0.44117	D	0.99689	D;D;D	0.89917	0.999;0.996;1.0	D;P;D	0.77557	0.99;0.575;0.968	T	0.10776	-1.0615	9	.	.	.	-19.6359	15.8965	0.79338	0.0:0.864:0.136:0.0	.	265;265;265	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	Q	265	ENSP00000314038:R265Q;ENSP00000363108:R265Q;ENSP00000354504:R265Q	.	R	-	2	0	ASTN2	119016679	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.867000	0.69597	1.298000	0.44778	0.655000	0.94253	CGG		0.597	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
TEX13A	56157	broad.mit.edu	37	X	104464292	104464292	+	Missense_Mutation	SNP	C	C	G			TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	G	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chrX:104464292C>G	ENST00000413579.1	-	3	697	c.586G>C	c.(586-588)Gag>Cag	p.E196Q	TEX13A_ENST00000372578.3_Missense_Mutation_p.E196Q|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372575.1_Missense_Mutation_p.E196Q|IL1RAPL2_ENST00000344799.4_Intron			Q9BXU3	TX13A_HUMAN	testis expressed 13A	196							zinc ion binding (GO:0008270)	p.E196Q(1)		large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CCCCTCTGCTCTTCTTCTGCT	0.652																																																1	Substitution - Missense(1)	ovary(1)	X											23.0	26.0	25.0					X																	104464292		2092	4131	6223	104350948	SO:0001583	missense	56157			AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.586G>C	X.37:g.104464292C>G	ENSP00000399753:p.Glu196Gln		104350948	B1B1G8|Q32NB6	Missense_Mutation	SNP	ENST00000413579.1	37		.	.	.	.	.	.	.	.	.	.	C	0.013	-1.622647	0.00820	.	.	ENSG00000133149	ENST00000372578;ENST00000372575;ENST00000413579	.	.	.	1.69	-3.39	0.04868	.	1.807170	0.03666	N	0.243298	T	0.27134	0.0665	.	.	.	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.07966	-1.0745	8	0.34782	T	0.22	.	3.9763	0.09476	0.0:0.3334:0.3416:0.325	.	196;196	C9JWK0;Q9BXU3	.;TX13A_HUMAN	Q	196	.	ENSP00000361656:E196Q	E	-	1	0	TEX13A	104350948	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.013000	0.03645	-2.080000	0.00870	-0.735000	0.03563	GAG		0.652	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
CTSL	1514	broad.mit.edu	37	9	90343265	90343265	+	Frame_Shift_Del	DEL	C	C	-	rs76801214	byFrequency	TCGA-24-2271-01A-01W-0799-08	TCGA-24-2271-10A-01W-0799-08	C	C	-	-	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	42836db7-656d-43d6-a100-3f134642db36	5be0af72-07fd-4531-a2c1-606754f9445c	g.chr9:90343265delC	ENST00000343150.5	+	4	1240	c.350delC	c.(349-351)tctfs	p.S117fs	CTSL_ENST00000340342.6_Frame_Shift_Del_p.S117fs|CTSL_ENST00000495822.1_Intron|CTSL_ENST00000342020.5_Frame_Shift_Del_p.S117fs			P07711	CATL1_HUMAN	cathepsin L	117					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)	p.S117fs*10(1)									GCCCCCAGATCTGTGGATTGG	0.498																																																1	Deletion - Frameshift(1)	ovary(1)	9											65.0	62.0	63.0					9																	90343265		2203	4300	6503	89533085	SO:0001589	frameshift_variant	1514			X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"""Cathepsins"""	2537	protein-coding gene	gene with protein product		116880	"""cathepsin L1"""	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.350delC	9.37:g.90343265delC	ENSP00000345344:p.Ser117fs		89533085	Q6IAV1|Q96QJ0	Frame_Shift_Del	DEL	ENST00000343150.5	37	CCDS6675.1																																																																																				0.498	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912	
