#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
MTOR	2475	broad.mit.edu	37	1	11272938	11272938	+	Missense_Mutation	SNP	C	C	T	rs529153687		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr1:11272938C>T	ENST00000361445.4	-	22	3389	c.3313G>A	c.(3313-3315)Gcc>Acc	p.A1105T		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1105					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.A1105T(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCCAGGTTGGCGCCAAACAGC	0.512													C|||	1	0.000199681	0.0	0.0	5008	,	,		17392	0.0		0.0	False		,,,				2504	0.001															1	Substitution - Missense(1)	ovary(1)	1											102.0	87.0	92.0					1																	11272938		2203	4300	6503	11195525	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3313G>A	1.37:g.11272938C>T	ENSP00000354558:p.Ala1105Thr		11195525	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.754482	0.69648	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.64438	-0.1	5.48	5.48	0.80851	Armadillo-like helical (1);Armadillo-type fold (1);	0.122378	0.56097	D	0.000040	T	0.51873	0.1700	L	0.33753	1.03	0.80722	D	1	B	0.30211	0.273	B	0.17722	0.019	T	0.47302	-0.9128	10	0.31617	T	0.26	-17.9397	19.3587	0.94425	0.0:1.0:0.0:0.0	.	1105	P42345	MTOR_HUMAN	T	1105	ENSP00000354558:A1105T	ENSP00000354558:A1105T	A	-	1	0	MTOR	11195525	1.000000	0.71417	0.961000	0.40146	0.991000	0.79684	7.304000	0.78882	2.573000	0.86826	0.655000	0.94253	GCC		0.512	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
HAO2	51179	broad.mit.edu	37	1	119936413	119936413	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr1:119936413C>T	ENST00000325945.3	+	8	1079	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	HAO2_ENST00000361035.4_Missense_Mutation_p.R349W|HAO2_ENST00000482991.1_3'UTR	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	336	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)	p.R336W(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		TTTAGGCTGCCGGTCGGTCGC	0.483																																																1	Substitution - Missense(1)	ovary(1)	1											213.0	194.0	200.0					1																	119936413		2203	4300	6503	119737936	SO:0001583	missense	51179			AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"""(S)-2-hydroxy-acid oxidase"", ""glycolate oxidase"", ""long-chain L-2-hydroxy acid oxidase"", ""growth-inhibiting protein 16"""	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.1006C>T	1.37:g.119936413C>T	ENSP00000316339:p.Arg336Trp		119737936	Q2TU86|Q5QP00|Q9UJS6	Missense_Mutation	SNP	ENST00000325945.3	37	CCDS901.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.187497	0.38609	.	.	ENSG00000116882	ENST00000361035;ENST00000325945	T;T	0.33216	1.42;1.42	4.66	2.71	0.32032	Aldolase-type TIM barrel (1);FMN-dependent dehydrogenase (1);	0.384931	0.26673	N	0.023082	T	0.22475	0.0542	M	0.87547	2.89	0.49483	D	0.999795	P	0.35793	0.521	B	0.33254	0.16	T	0.06972	-1.0797	9	.	.	.	-9.7153	11.4768	0.50302	0.3256:0.6744:0.0:0.0	.	336	Q9NYQ3	HAOX2_HUMAN	W	349;336	ENSP00000354314:R349W;ENSP00000316339:R336W	.	R	+	1	2	HAO2	119737936	1.000000	0.71417	0.971000	0.41717	0.715000	0.41141	1.776000	0.38594	0.647000	0.30713	0.563000	0.77884	CGG		0.483	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783	
PGLYRP4	57115	broad.mit.edu	37	1	153317834	153317834	+	Missense_Mutation	SNP	G	G	A	rs200715095		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr1:153317834G>A	ENST00000359650.5	-	4	228	c.164C>T	c.(163-165)aCg>aTg	p.T55M	PGLYRP4_ENST00000490266.1_5'UTR|PGLYRP4_ENST00000368739.3_Missense_Mutation_p.T51M	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	55					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.T55M(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCGAGAGACCGTGGTGGAGAC	0.587																																																1	Substitution - Missense(1)	ovary(1)	1											127.0	98.0	108.0					1																	153317834		2203	4300	6503	151584458	SO:0001583	missense	57115			AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.164C>T	1.37:g.153317834G>A	ENSP00000352672:p.Thr55Met		151584458	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	G	0.539	-0.854573	0.02630	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.04603	3.61;3.59	3.2	-1.57	0.08506	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (2);	.	.	.	.	T	0.00468	0.0015	N	0.01576	-0.805	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.45848	-0.9233	9	0.24483	T	0.36	-17.5147	2.2658	0.04078	0.4913:0.0:0.2841:0.2246	.	51;55	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	M	51;55	ENSP00000357728:T51M;ENSP00000352672:T55M	ENSP00000352672:T55M	T	-	2	0	PGLYRP4	151584458	0.000000	0.05858	0.204000	0.23530	0.070000	0.16714	0.510000	0.22723	0.026000	0.15269	-0.657000	0.03884	ACG		0.587	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393	
DCST1	149095	broad.mit.edu	37	1	155014239	155014239	+	Silent	SNP	G	G	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr1:155014239G>A	ENST00000295542.1	+	8	894	c.798G>A	c.(796-798)aaG>aaA	p.K266K	DCST1_ENST00000368419.2_Silent_p.K266K|DCST1_ENST00000423025.2_Silent_p.K241K|DCST1_ENST00000392480.1_Silent_p.K266K	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	266						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.K266K(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TTGACCGCAAGCATGAACAGT	0.537																																																1	Substitution - coding silent(1)	ovary(1)	1											179.0	134.0	149.0					1																	155014239		2203	4300	6503	153280863	SO:0001819	synonymous_variant	149095			AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.798G>A	1.37:g.155014239G>A			153280863	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Silent	SNP	ENST00000295542.1	37	CCDS1083.1																																																																																				0.537	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
CHRM3	1131	broad.mit.edu	37	1	240072215	240072215	+	Silent	SNP	A	A	G			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr1:240072215A>G	ENST00000255380.4	+	5	2243	c.1464A>G	c.(1462-1464)aaA>aaG	p.K488K		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	488					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)	p.K488K(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGGAGAAGAAAGCGGCCCAGA	0.507																																																1	Substitution - coding silent(1)	ovary(1)	1											136.0	129.0	132.0					1																	240072215		2203	4300	6503	238138838	SO:0001819	synonymous_variant	1131			U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1464A>G	1.37:g.240072215A>G			238138838	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Silent	SNP	ENST00000255380.4	37	CCDS1616.1																																																																																				0.507	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
MYBPC3	4607	broad.mit.edu	37	11	47353745	47353745	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr11:47353745C>T	ENST00000545968.1	-	33	3746	c.3692G>A	c.(3691-3693)aGc>aAc	p.S1231N	MYBPC3_ENST00000256993.4_Missense_Mutation_p.S1230N|MYBPC3_ENST00000399249.2_Missense_Mutation_p.S1231N	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	1231	Ig-like C2-type 7.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.S1231N(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		TCCCTGCTTGCTGAACATGCG	0.552																																																1	Substitution - Missense(1)	ovary(1)	11	GRCh37	CI014153	MYBPC3	I							86.0	90.0	89.0					11																	47353745		1955	4140	6095	47310321	SO:0001583	missense	4607			X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.3692G>A	11.37:g.47353745C>T	ENSP00000442795:p.Ser1231Asn		47310321	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465593	0.43839	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.66460	-0.21;-0.21;-0.21	5.46	5.46	0.80206	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59293	0.2183	L	0.37697	1.125	0.53005	D	0.999965	B	0.09022	0.002	B	0.20955	0.032	T	0.52866	-0.8518	9	0.23302	T	0.38	.	18.0769	0.89430	0.0:1.0:0.0:0.0	.	1230	Q14896	MYPC3_HUMAN	N	1231;1231;1230	ENSP00000442795:S1231N;ENSP00000382193:S1231N;ENSP00000256993:S1230N	ENSP00000256993:S1230N	S	-	2	0	MYBPC3	47310321	0.383000	0.25156	1.000000	0.80357	0.995000	0.86356	0.350000	0.20079	2.556000	0.86216	0.561000	0.74099	AGC		0.552	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
HRASLS5	117245	broad.mit.edu	37	11	63233592	63233592	+	Missense_Mutation	SNP	C	C	T	rs144730159		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr11:63233592C>T	ENST00000301790.4	-	5	896	c.737G>A	c.(736-738)cGg>cAg	p.R246Q	HRASLS5_ENST00000540857.1_Missense_Mutation_p.R236Q|HRASLS5_ENST00000539221.1_Intron			Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5	246							transferase activity, transferring acyl groups (GO:0016746)	p.R246Q(2)		endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	14						CTGCTGGCTCCGGGGTACGCC	0.478																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	11						C	,GLN/ARG,GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	149.0	112.0	124.0		,707,737	4.2	1.0	11	dbSNP_134	124	1,8595	1.2+/-3.3	0,1,4297	no	intron,missense,missense	HRASLS5	NM_001146728.1,NM_001146729.1,NM_054108.3	,43,43	0,2,6497	TT,TC,CC		0.0116,0.0227,0.0154	,probably-damaging,probably-damaging	,236/270,246/280	63233592	2,12996	2201	4298	6499	62990168	SO:0001583	missense	117245			AJ416558	CCDS8044.1, CCDS53646.1, CCDS53647.1	11q13.2	2006-08-16			ENSG00000168004	ENSG00000168004			24978	protein-coding gene	gene with protein product		611474					Standard	NM_001146729		Approved	HRLP5	uc001nwy.2	Q96KN8	OTTHUMG00000167806	ENST00000301790.4:c.737G>A	11.37:g.63233592C>T	ENSP00000301790:p.Arg246Gln		62990168	B7X6T1|F5GZ87|F5H4Y9	Missense_Mutation	SNP	ENST00000301790.4	37	CCDS8044.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470291	0.63625	2.27E-4	1.16E-4	ENSG00000168004	ENST00000540857;ENST00000301790	T;T	0.28069	1.63;1.63	4.17	4.17	0.49024	NC (1);	0.215456	0.45867	D	0.000323	T	0.44519	0.1297	L	0.60455	1.87	0.26750	N	0.97021	D;D	0.65815	0.993;0.995	P;P	0.59171	0.771;0.853	T	0.23048	-1.0199	10	0.46703	T	0.11	-30.7947	12.2841	0.54783	0.0:1.0:0.0:0.0	.	236;246	F5H4Y9;Q96KN8	.;HRSL5_HUMAN	Q	236;246	ENSP00000444809:R236Q;ENSP00000301790:R246Q	ENSP00000301790:R246Q	R	-	2	0	HRASLS5	62990168	0.097000	0.21791	1.000000	0.80357	0.584000	0.36387	0.570000	0.23653	2.623000	0.88846	0.655000	0.94253	CGG		0.478	HRASLS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396375.1	NM_054108	
CLIP1	6249	broad.mit.edu	37	12	122838999	122838999	+	Splice_Site	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr12:122838999C>T	ENST00000540338.1	-	6	1349		c.e6+1		CLIP1_ENST00000361654.4_Splice_Site|CLIP1_ENST00000545889.1_Splice_Site|CLIP1_ENST00000537178.1_Splice_Site|CLIP1_ENST00000302528.7_Splice_Site|CLIP1_ENST00000358808.2_Splice_Site			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1						microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TCTGGGGTCACCTTTTCTCCT	0.512																																																1	Unknown(1)	ovary(1)	12											126.0	99.0	108.0					12																	122838999		2203	4300	6503	121404952	SO:0001630	splice_region_variant	6249				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.1307+1G>A	12.37:g.122838999C>T			121404952	A0AVD3|Q17RS4|Q29RG0	Splice_Site	SNP	ENST00000540338.1	37	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.832195	0.91036	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304;ENST00000450731;ENST00000537004	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1346	0.98019	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CLIP1	121404952	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.818000	0.86416	2.765000	0.95021	0.655000	0.94253	.		0.512	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	Intron
SCEL	8796	broad.mit.edu	37	13	78176834	78176834	+	Missense_Mutation	SNP	T	T	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr13:78176834T>A	ENST00000349847.3	+	17	1107	c.1023T>A	c.(1021-1023)aaT>aaA	p.N341K	SCEL_ENST00000377246.3_Missense_Mutation_p.N321K|SCEL_ENST00000535157.1_Missense_Mutation_p.N319K|SCEL-AS1_ENST00000457528.2_RNA|SCEL-AS1_ENST00000456280.2_RNA|SCEL_ENST00000469982.1_Intron	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	341	16 X approximate tandem repeats.				embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)	p.N341K(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		CCAGGATGAATAAAACGAGCA	0.348																																																1	Substitution - Missense(1)	ovary(1)	13											132.0	139.0	137.0					13																	78176834		2203	4300	6503	77074835	SO:0001583	missense	8796			AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1023T>A	13.37:g.78176834T>A	ENSP00000302579:p.Asn341Lys		77074835	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	37	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	T	9.936	1.216138	0.22373	.	.	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.21932	1.98;1.98;1.98	3.93	-4.19	0.03835	.	0.866901	0.09752	N	0.760489	T	0.12347	0.0300	L	0.39898	1.24	0.09310	N	1	B;B;B	0.24368	0.082;0.082;0.102	B;B;B	0.26770	0.053;0.053;0.073	T	0.34700	-0.9818	10	0.33940	T	0.23	-1.0741	0.8661	0.01204	0.1516:0.2302:0.3119:0.3063	.	319;321;341	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	K	319;321;341	ENSP00000437895:N319K;ENSP00000366454:N321K;ENSP00000302579:N341K	ENSP00000302579:N341K	N	+	3	2	SCEL	77074835	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.892000	0.04131	-0.861000	0.04094	-0.408000	0.06270	AAT		0.348	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
SRL	6345	broad.mit.edu	37	16	4242677	4242677	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr16:4242677G>A	ENST00000399609.3	-	6	911	c.899C>T	c.(898-900)cCg>cTg	p.P300L	SRL_ENST00000537996.1_Missense_Mutation_p.P258L	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	759	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.P300L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						ATGGGTGTCCGGCTTATACTC	0.532																																																1	Substitution - Missense(1)	ovary(1)	16											86.0	92.0	90.0					16																	4242677		1970	4151	6121	4182678	SO:0001583	missense	6345			AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.899C>T	16.37:g.4242677G>A	ENSP00000382518:p.Pro300Leu		4182678		Missense_Mutation	SNP	ENST00000399609.3	37	CCDS42113.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.146867	0.37923	.	.	ENSG00000185739	ENST00000399609;ENST00000330063;ENST00000537996	T;T	0.30448	1.53;1.54	5.18	5.18	0.71444	.	0.073557	0.56097	U	0.000036	T	0.26702	0.0653	L	0.31926	0.97	0.80722	D	1	B	0.16396	0.017	B	0.15052	0.012	T	0.03175	-1.1064	10	0.25751	T	0.34	-11.5064	18.4856	0.90828	0.0:0.0:1.0:0.0	.	300	Q86TD4-2	.	L	300;758;258	ENSP00000382518:P300L;ENSP00000440350:P258L	ENSP00000333285:P758L	P	-	2	0	SRL	4182678	1.000000	0.71417	0.965000	0.40720	0.820000	0.46376	6.508000	0.73721	2.679000	0.91253	0.655000	0.94253	CCG		0.532	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152	
CDH8	1006	broad.mit.edu	37	16	61854905	61854905	+	Missense_Mutation	SNP	G	G	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr16:61854905G>C	ENST00000577390.1	-	6	1902	c.948C>G	c.(946-948)atC>atG	p.I316M	CDH8_ENST00000584337.1_Missense_Mutation_p.I316M|CDH8_ENST00000299345.6_Missense_Mutation_p.I316M|CDH8_ENST00000577730.1_Missense_Mutation_p.I316M	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	316	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.I316M(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CATCTCCATCGATGATATCAT	0.428																																																1	Substitution - Missense(1)	ovary(1)	16											177.0	137.0	150.0					16																	61854905		2203	4300	6503	60412406	SO:0001583	missense	1006			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.948C>G	16.37:g.61854905G>C	ENSP00000462701:p.Ile316Met		60412406	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030372	0.35797	.	.	ENSG00000150394	ENST00000299345	T	0.01804	4.63	6.16	0.262	0.15597	Cadherin (4);Cadherin-like (1);	0.090329	0.64402	D	0.000001	T	0.03348	0.0097	N	0.25031	0.7	0.45097	D	0.99811	P;P	0.42456	0.736;0.78	P;P	0.58172	0.834;0.792	T	0.55173	-0.8182	10	0.51188	T	0.08	.	10.7217	0.46044	0.6986:0.0:0.3014:0.0	.	132;316	Q3LID3;P55286	.;CADH8_HUMAN	M	316	ENSP00000299345:I316M	ENSP00000299345:I316M	I	-	3	3	CDH8	60412406	0.866000	0.29940	0.996000	0.52242	0.867000	0.49689	0.068000	0.14531	0.207000	0.20607	-0.247000	0.11927	ATC		0.428	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
ATP2A3	489	broad.mit.edu	37	17	3850997	3850997	+	Silent	SNP	G	G	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr17:3850997G>T	ENST00000352011.3	-	8	837	c.783C>A	c.(781-783)tcC>tcA	p.S261S	ATP2A3_ENST00000309890.7_Silent_p.S261S|ATP2A3_ENST00000359983.3_Silent_p.S261S|ATP2A3_ENST00000397041.3_Silent_p.S261S|ATP2A3_ENST00000397043.3_Silent_p.S261S|ATP2A3_ENST00000397035.3_Silent_p.S261S|ATP2A3_ENST00000397039.1_5'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	261					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.S261S(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		AGATGGCGTGGGACAGCTGCC	0.672																																					GBM(32;29 774 15719 37967)											1	Substitution - coding silent(1)	ovary(1)	17											30.0	32.0	31.0					17																	3850997		2202	4296	6498	3797746	SO:0001819	synonymous_variant	489				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.783C>A	17.37:g.3850997G>T			3797746	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																				0.672	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
TP53	7157	broad.mit.edu	37	17	7577559	7577559	+	Missense_Mutation	SNP	G	G	A	rs397516437|rs28934573		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr17:7577559G>A	ENST00000269305.4	-	7	911	c.722C>T	c.(721-723)tCc>tTc	p.S241F	TP53_ENST00000413465.2_Missense_Mutation_p.S241F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.S241F|TP53_ENST00000359597.4_Missense_Mutation_p.S241F|TP53_ENST00000420246.2_Missense_Mutation_p.S241F|TP53_ENST00000445888.2_Missense_Mutation_p.S241F	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	241	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		S -> A (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|S -> C (in sporadic cancers; somatic mutation).|S -> F (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934573). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228}.|S -> P (in sporadic cancers; somatic mutation).|S -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; 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.S241F(85)|p.S241C(26)|p.0?(8)|p.S241Y(8)|p.C242fs*5(6)|p.?(5)|p.S241del(5)|p.S148F(4)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.S148C(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(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)	GCCCATGCAGGAACTGTTACA	0.572		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"""	160	Substitution - Missense(124)|Deletion - In frame(13)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(5)|Complex - deletion inframe(1)	urinary_tract(19)|large_intestine(18)|breast(17)|endometrium(15)|ovary(15)|lung(12)|skin(9)|biliary_tract(8)|central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(7)|upper_aerodigestive_tract(6)|stomach(6)|oesophagus(5)|bone(5)|liver(3)|pancreas(3)|eye(2)|thyroid(1)|kidney(1)	17	GRCh37	CM920673	TP53	M	rs28934573						139.0	108.0	118.0					17																	7577559		2203	4300	6503	7518284	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.722C>T	17.37:g.7577559G>A	ENSP00000269305:p.Ser241Phe		7518284	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404027	0.62288	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99857	-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22	4.62	3.64	0.41730	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.120078	0.56097	D	0.000022	D	0.99871	0.9939	M	0.92784	3.345	0.53688	A	0.999973	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.96525	0.9388	9	0.87932	D	0	-35.4617	12.8645	0.57932	0.0:0.1651:0.8349:0.0	rs28934573	241;241;148;241;241;241	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	F	241;241;241;241;241;241;230;148;109;148	ENSP00000410739:S241F;ENSP00000352610:S241F;ENSP00000269305:S241F;ENSP00000398846:S241F;ENSP00000391127:S241F;ENSP00000391478:S241F;ENSP00000425104:S109F;ENSP00000423862:S148F	ENSP00000269305:S241F	S	-	2	0	TP53	7518284	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.346000	0.44027	1.295000	0.44724	0.462000	0.41574	TCC		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
MYH1	4619	broad.mit.edu	37	17	10395823	10395823	+	Silent	SNP	G	G	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr17:10395823G>A	ENST00000226207.5	-	40	5824	c.5730C>T	c.(5728-5730)gcC>gcT	p.A1910A	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1910					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A1910A(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CCCGTTCCTCGGCCTCCTCCA	0.478																																																1	Substitution - coding silent(1)	ovary(1)	17											149.0	137.0	141.0					17																	10395823		2203	4300	6503	10336548	SO:0001819	synonymous_variant	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.5730C>T	17.37:g.10395823G>A			10336548	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																				0.478	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
MC5R	4161	broad.mit.edu	37	18	13826571	13826571	+	Silent	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr18:13826571C>T	ENST00000324750.3	+	1	1029	c.807C>T	c.(805-807)taC>taT	p.Y269Y	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	269					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)	p.Y269Y(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						AGAACCTCTACTGCTCTCGCT	0.512																																																1	Substitution - coding silent(1)	ovary(1)	18											239.0	193.0	208.0					18																	13826571		2203	4300	6503	13816571	SO:0001819	synonymous_variant	4161			AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"""GPCR / Class A : Melanocortin receptors"""	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.807C>T	18.37:g.13826571C>T			13816571	B0YJ34|Q502V1	Silent	SNP	ENST00000324750.3	37	CCDS11868.1																																																																																				0.512	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913	
DENND1C	79958	broad.mit.edu	37	19	6467577	6467577	+	Nonsense_Mutation	SNP	G	G	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr19:6467577G>A	ENST00000381480.2	-	23	2456	c.2344C>T	c.(2344-2346)Caa>Taa	p.Q782*	DENND1C_ENST00000543576.1_Nonsense_Mutation_p.Q738*	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	782					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.Q782*(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						TGGGACTTTTGACAGTTGCTG	0.597																																																1	Substitution - Nonsense(1)	ovary(1)	19											42.0	45.0	44.0					19																	6467577		1902	4135	6037	6418577	SO:0001587	stop_gained	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.2344C>T	19.37:g.6467577G>A	ENSP00000370889:p.Gln782*		6418577	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Nonsense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831393	0.71258	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	.	.	.	4.52	3.46	0.39613	.	1.102580	0.07247	N	0.865293	.	.	.	.	.	.	0.41529	D	0.988445	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-1.0374	9.0538	0.36392	0.1107:0.0:0.8893:0.0	.	.	.	.	X	782;738	.	ENSP00000370889:Q782X	Q	-	1	0	DENND1C	6418577	0.000000	0.05858	0.039000	0.18376	0.096000	0.18686	0.484000	0.22308	2.251000	0.74343	0.306000	0.20318	CAA		0.597	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
CLIP3	25999	broad.mit.edu	37	19	36508837	36508837	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr19:36508837C>T	ENST00000360535.4	-	10	1467	c.1240G>A	c.(1240-1242)Gcc>Acc	p.A414T	CLIP3_ENST00000593074.1_Missense_Mutation_p.A414T|AC002116.7_ENST00000586962.1_RNA	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	414					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)	p.A414T(1)		cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCAGCCTTGGCCCCGTCACGC	0.612																																																1	Substitution - Missense(1)	ovary(1)	19											81.0	76.0	78.0					19																	36508837		2203	4300	6503	41200677	SO:0001583	missense	25999			AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"""Ankyrin repeat domain containing"""	24314	protein-coding gene	gene with protein product	"""CLIP-170-related"", ""restin-like 1"""	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.1240G>A	19.37:g.36508837C>T	ENSP00000353732:p.Ala414Thr		41200677	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	37	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	C	9.408	1.079654	0.20309	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	T	0.74106	-0.81	4.77	2.53	0.30540	Cytoskeleton-associated protein, Gly-rich domain (2);	0.441049	0.23642	N	0.046013	T	0.45478	0.1344	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15694	-1.0428	10	0.13108	T	0.6	-16.8177	3.7311	0.08493	0.1662:0.5798:0.1615:0.0925	.	414	Q96DZ5	CLIP3_HUMAN	T	414;296;390	ENSP00000353732:A414T	ENSP00000353732:A414T	A	-	1	0	CLIP3	41200677	0.078000	0.21339	0.867000	0.34043	0.754000	0.42855	0.408000	0.21065	1.243000	0.43853	0.561000	0.74099	GCC		0.612	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526	
INSIG2	51141	broad.mit.edu	37	2	118860793	118860793	+	Missense_Mutation	SNP	C	C	G			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	G	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr2:118860793C>G	ENST00000245787.4	+	3	471	c.265C>G	c.(265-267)Ccc>Gcc	p.P89A	INSIG2_ENST00000485520.1_3'UTR	NM_016133.2	NP_057217.2	Q9Y5U4	INSI2_HUMAN	insulin induced gene 2	89					cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|response to fatty acid (GO:0070542)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)		p.P89A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						GTTATTATACCCCTGCATTGA	0.383																																																1	Substitution - Missense(1)	ovary(1)	2											146.0	153.0	151.0					2																	118860793		2203	4300	6503	118577263	SO:0001583	missense	51141			AF527632	CCDS2122.1	2q14.1	2008-02-05			ENSG00000125629	ENSG00000125629			20452	protein-coding gene	gene with protein product		608660				12242332	Standard	NM_016133		Approved		uc002tlk.3	Q9Y5U4	OTTHUMG00000058518	ENST00000245787.4:c.265C>G	2.37:g.118860793C>G	ENSP00000245787:p.Pro89Ala		118577263	A8K5W8|Q8TBI8	Missense_Mutation	SNP	ENST00000245787.4	37	CCDS2122.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892624	0.91889	.	.	ENSG00000125629	ENST00000245787	.	.	.	5.49	5.49	0.81192	.	0.109104	0.64402	D	0.000005	D	0.84946	0.5585	M	0.86420	2.815	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.86183	0.1607	9	0.62326	D	0.03	.	19.5721	0.95425	0.0:1.0:0.0:0.0	.	89	Q9Y5U4	INSI2_HUMAN	A	89	.	ENSP00000245787:P89A	P	+	1	0	INSIG2	118577263	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.604000	0.82830	2.857000	0.98124	0.650000	0.86243	CCC		0.383	INSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129624.1	NM_016133	
MAP3K19	80122	broad.mit.edu	37	2	135779323	135779323	+	Missense_Mutation	SNP	T	T	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr2:135779323T>A	ENST00000375845.3	-	2	130	c.100A>T	c.(100-102)Aat>Tat	p.N34Y	MAP3K19_ENST00000392918.3_Missense_Mutation_p.N34Y|MAP3K19_ENST00000392915.1_Missense_Mutation_p.N51Y|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Missense_Mutation_p.N34Y|MAP3K19_ENST00000392917.3_Missense_Mutation_p.N34Y|MAP3K19_ENST00000358371.4_Missense_Mutation_p.N34Y	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	34							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.N34Y(1)									ATGTTTTGATTTTTGGTAACT	0.363																																																1	Substitution - Missense(1)	ovary(1)	2											157.0	141.0	147.0					2																	135779323		2203	4300	6503	135495793	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.100A>T	2.37:g.135779323T>A	ENSP00000365005:p.Asn34Tyr		135495793	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197343	0.58126	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000392915;ENST00000425952;ENST00000414343	T;T;T;T;T;T	0.71817	-0.52;-0.52;-0.55;-0.6;-0.5;1.85	4.44	4.44	0.53790	.	0.373374	0.19277	N	0.118255	T	0.77980	0.4212	L	0.57536	1.79	0.80722	D	1	P;D;D;P;D;P;D	0.64830	0.826;0.994;0.983;0.936;0.983;0.867;0.976	B;P;P;P;P;P;P	0.62740	0.365;0.906;0.804;0.568;0.847;0.466;0.556	T	0.78558	-0.2158	10	0.59425	D	0.04	.	10.0351	0.42125	0.0:0.0:0.0:1.0	.	34;34;34;34;51;34;34	B7ZMH9;Q56UN5-2;Q56UN5-3;Q56UN5-4;A8MWG7;Q56UN5-5;Q56UN5	.;.;.;.;.;.;YSK4_HUMAN	Y	34;34;34;34;34;51;6;6	ENSP00000365005:N34Y;ENSP00000351140:N34Y;ENSP00000365004:N34Y;ENSP00000376650:N34Y;ENSP00000376649:N34Y;ENSP00000376647:N51Y	ENSP00000351140:N34Y	N	-	1	0	YSK4	135495793	0.997000	0.39634	0.837000	0.33122	0.886000	0.51366	3.685000	0.54678	1.877000	0.54381	0.477000	0.44152	AAT		0.363	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
MYO3B	140469	broad.mit.edu	37	2	171248912	171248912	+	Silent	SNP	A	A	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr2:171248912A>T	ENST00000408978.4	+	16	1841	c.1698A>T	c.(1696-1698)ggA>ggT	p.G566G	MYO3B_ENST00000334231.6_Silent_p.G575G|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.G566G	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	566	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)	p.G566G(1)		breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						ATGAAACTGGAAGGGTGATGC	0.408																																																1	Substitution - coding silent(1)	ovary(1)	2											111.0	100.0	104.0					2																	171248912		1932	4144	6076	170957158	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1698A>T	2.37:g.171248912A>T			170957158	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																				0.408	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
KANSL1L	151050	broad.mit.edu	37	2	210888760	210888760	+	Silent	SNP	G	G	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr2:210888760G>C	ENST00000281772.9	-	14	2993	c.2730C>G	c.(2728-2730)acC>acG	p.T910T	KANSL1L_ENST00000418791.1_Silent_p.T868T	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	910						histone acetyltransferase complex (GO:0000123)		p.T910T(1)									CACTTACCTTGGTTTCTTGAC	0.363																																																1	Substitution - coding silent(1)	ovary(1)	2											71.0	69.0	70.0					2																	210888760		2203	4300	6503	210597005	SO:0001819	synonymous_variant	151050			AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"""KIAA1267-like"""	613833	"""chromosome 2 open reading frame 67"""	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.2730C>G	2.37:g.210888760G>C			210597005	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Silent	SNP	ENST00000281772.9	37	CCDS33370.1																																																																																				0.363	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519	
EMILIN3	90187	broad.mit.edu	37	20	39990364	39990364	+	Silent	SNP	G	G	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr20:39990364G>C	ENST00000332312.3	-	4	2037	c.1845C>G	c.(1843-1845)gcC>gcG	p.A615A		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	615						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)		p.A615A(1)		biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				GGGACGTGTTGGCAGCCAAGA	0.587																																																1	Substitution - coding silent(1)	ovary(1)	20											64.0	56.0	59.0					20																	39990364		2203	4300	6503	39423778	SO:0001819	synonymous_variant	90187			AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1845C>G	20.37:g.39990364G>C			39423778	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																				0.587	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
MASP1	5648	broad.mit.edu	37	3	186969527	186969527	+	Silent	SNP	T	T	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	T	T	C	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr3:186969527T>C	ENST00000337774.5	-	7	1295	c.906A>G	c.(904-906)ccA>ccG	p.P302P	MASP1_ENST00000495249.1_Intron|MASP1_ENST00000169293.6_Silent_p.P302P|MASP1_ENST00000392472.2_Silent_p.P189P|MASP1_ENST00000296280.6_Silent_p.P302P|MASP1_ENST00000392470.2_Silent_p.P276P	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	302	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.P302P(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		GCTGTAGCTCTGGGCACTCAT	0.498																																																1	Substitution - coding silent(1)	ovary(1)	3											108.0	103.0	105.0					3																	186969527		2203	4300	6503	188452221	SO:0001819	synonymous_variant	5648			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.906A>G	3.37:g.186969527T>C			188452221	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	37	CCDS33907.1																																																																																				0.498	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
PLEKHG4B	153478	broad.mit.edu	37	5	156195	156195	+	Nonsense_Mutation	SNP	G	G	T	rs138938524		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr5:156195G>T	ENST00000283426.6	+	8	1200	c.1150G>T	c.(1150-1152)Gag>Tag	p.E384*		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	384							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E384K(2)|p.E384*(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGAAGTCGCCGAGTTAATTGA	0.582																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	large_intestine(2)|ovary(1)	5											125.0	116.0	119.0					5																	156195		2203	4300	6503	209195	SO:0001587	stop_gained	153478			BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1150G>T	5.37:g.156195G>T	ENSP00000283426:p.Glu384*		209195		Nonsense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.351118	0.41599	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	.	.	.	3.65	0.651	0.17817	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	2.1558	0.03811	0.1172:0.1948:0.4879:0.2001	.	.	.	.	X	384;298	.	ENSP00000283426:E384X	E	+	1	0	PLEKHG4B	209195	0.997000	0.39634	0.000000	0.03702	0.006000	0.05464	5.044000	0.64214	-0.241000	0.09681	-0.373000	0.07131	GAG		0.582	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
LIFR	3977	broad.mit.edu	37	5	38523678	38523678	+	Missense_Mutation	SNP	A	A	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr5:38523678A>T	ENST00000263409.4	-	5	566	c.404T>A	c.(403-405)aTt>aAt	p.I135N	LIFR_ENST00000453190.2_Missense_Mutation_p.I135N|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	135	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.I135N(1)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					AGTATCTGGAATTAAGGCTTT	0.338			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	1	Substitution - Missense(1)	ovary(1)	5											59.0	65.0	63.0					5																	38523678		2202	4300	6502	38559435	SO:0001583	missense	3977			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.404T>A	5.37:g.38523678A>T	ENSP00000263409:p.Ile135Asn		38559435	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049015	0.75846	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.44083	0.93;0.93	5.38	5.38	0.77491	Fibronectin, type III (1);	0.798569	0.12433	N	0.469346	T	0.56077	0.1961	M	0.62723	1.935	0.39663	D	0.970645	D	0.69078	0.997	P	0.56278	0.795	T	0.58440	-0.7636	10	0.87932	D	0	-20.158	11.7852	0.52039	1.0:0.0:0.0:0.0	.	135	P42702	LIFR_HUMAN	N	135	ENSP00000263409:I135N;ENSP00000398368:I135N	ENSP00000263409:I135N	I	-	2	0	LIFR	38559435	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	4.910000	0.63321	2.021000	0.59480	0.533000	0.62120	ATT		0.338	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
SLC36A3	285641	broad.mit.edu	37	5	150657199	150657199	+	Missense_Mutation	SNP	G	G	A	rs147738288		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr5:150657199G>A	ENST00000335230.3	-	10	1579	c.1168C>T	c.(1168-1170)Cgc>Tgc	p.R390C	SLC36A3_ENST00000377713.3_Missense_Mutation_p.R431C	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	390						integral component of membrane (GO:0016021)		p.R390C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTCCAGGCGGGGGATGAGG	0.522													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18904	0.0		0.0	False		,,,				2504	0.0															1	Substitution - Missense(1)	ovary(1)	5											47.0	44.0	45.0					5																	150657199		2203	4300	6503	150637392	SO:0001583	missense	285641			AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1168C>T	5.37:g.150657199G>A	ENSP00000334750:p.Arg390Cys		150637392	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	37	CCDS4314.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.36	1.913321	0.33815	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02369	4.32;4.32	4.68	3.78	0.43462	.	0.332746	0.32055	N	0.006654	T	0.08179	0.0204	M	0.86953	2.85	0.49299	D	0.999771	B;B;B	0.24823	0.112;0.078;0.098	B;B;B	0.27887	0.084;0.054;0.035	T	0.02901	-1.1096	10	0.66056	D	0.02	-23.9064	14.3346	0.66581	0.0:0.0:0.8506:0.1493	.	431;390;375	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	C	390;431	ENSP00000334750:R390C;ENSP00000366942:R431C	ENSP00000334750:R390C	R	-	1	0	SLC36A3	150637392	0.927000	0.31430	1.000000	0.80357	0.454000	0.32378	1.561000	0.36342	1.283000	0.44513	0.650000	0.86243	CGC		0.522	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
KIAA1191	57179	broad.mit.edu	37	5	175774713	175774713	+	Missense_Mutation	SNP	A	A	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr5:175774713A>C	ENST00000298569.4	-	9	1341	c.808T>G	c.(808-810)Ttg>Gtg	p.L270V	KIAA1191_ENST00000393728.2_5'UTR|KIAA1191_ENST00000393725.2_Missense_Mutation_p.L251V|KIAA1191_ENST00000510164.1_Missense_Mutation_p.L270V|RP11-843P14.2_ENST00000508187.1_RNA	NM_020444.3	NP_065177.2	Q96A73	P33MX_HUMAN	KIAA1191	270						cytoplasm (GO:0005737)	oxidoreductase activity (GO:0016491)	p.L270V(1)		endometrium(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6	all_cancers(89;0.00575)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.101)		GGGGGCTTCAAGGCTGCTGGA	0.572																																																1	Substitution - Missense(1)	ovary(1)	5											108.0	109.0	109.0					5																	175774713		2203	4300	6503	175707319	SO:0001583	missense	57179			BC010448	CCDS4399.1, CCDS43402.1, CCDS75373.1	5q35.2	2008-02-05			ENSG00000122203	ENSG00000122203			29209	protein-coding gene	gene with protein product						10574461, 10565538	Standard	XM_005265941		Approved	FLJ21022	uc003mdy.3	Q96A73	OTTHUMG00000130656	ENST00000298569.4:c.808T>G	5.37:g.175774713A>C	ENSP00000298569:p.Leu270Val		175707319	B2RD69|B8K1S6|Q6IA24|Q8NDU3|Q9BRE5|Q9H7D5|Q9ULM9	Missense_Mutation	SNP	ENST00000298569.4	37	CCDS4399.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.398382	0.25205	.	.	ENSG00000122203	ENST00000298569;ENST00000393725;ENST00000510164	.	.	.	5.1	3.94	0.45596	.	0.244071	0.41605	D	0.000847	T	0.43500	0.1250	L	0.27053	0.805	0.80722	D	1	B	0.27068	0.167	B	0.27380	0.079	T	0.47995	-0.9073	9	0.66056	D	0.02	-11.4741	10.4896	0.44744	0.9234:0.0:0.0766:0.0	.	270	Q96A73	K1191_HUMAN	V	270;251;270	.	ENSP00000298569:L270V	L	-	1	2	KIAA1191	175707319	1.000000	0.71417	0.905000	0.35620	0.160000	0.22226	4.712000	0.61888	2.039000	0.60335	0.533000	0.62120	TTG		0.572	KIAA1191-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253146.2	NM_020444	
GCM2	9247	broad.mit.edu	37	6	10875154	10875154	+	Missense_Mutation	SNP	G	G	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr6:10875154G>C	ENST00000379491.4	-	5	742	c.595C>G	c.(595-597)Caa>Gaa	p.Q199E	SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	199					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|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 (GO:0043565)	p.Q199E(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				CTGCTGTCTTGATTTTCTTCT	0.413																																																1	Substitution - Missense(1)	ovary(1)	6											87.0	83.0	85.0					6																	10875154		2203	4300	6503	10983140	SO:0001583	missense	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"""glial cells missing (Drosophila) homolog b"""	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.595C>G	6.37:g.10875154G>C	ENSP00000368805:p.Gln199Glu		10983140	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	G	9.013	0.982936	0.18889	.	.	ENSG00000124827	ENST00000379491	T	0.67698	-0.28	5.72	5.72	0.89469	.	0.591630	0.19001	N	0.125359	T	0.47116	0.1428	L	0.56769	1.78	0.80722	D	1	P	0.35433	0.501	B	0.29785	0.107	T	0.47761	-0.9092	10	0.27785	T	0.31	-3.4057	13.3542	0.60619	0.0:0.0:0.7244:0.2755	.	199	O75603	GCM2_HUMAN	E	199	ENSP00000368805:Q199E	ENSP00000368805:Q199E	Q	-	1	0	GCM2	10983140	1.000000	0.71417	0.127000	0.21898	0.267000	0.26476	4.158000	0.58150	2.699000	0.92147	0.591000	0.81541	CAA		0.413	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1		
UBR2	23304	broad.mit.edu	37	6	42650839	42650839	+	Missense_Mutation	SNP	G	G	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr6:42650839G>T	ENST00000372899.1	+	43	5023	c.4765G>T	c.(4765-4767)Gat>Tat	p.D1589Y	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Missense_Mutation_p.D1589Y	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1589					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D1589Y(2)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AGGTGAAAGAGATGCTATAAG	0.363																																																2	Substitution - Missense(2)	ovary(1)|kidney(1)	6											94.0	92.0	92.0					6																	42650839		2203	4299	6502	42758817	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.4765G>T	6.37:g.42650839G>T	ENSP00000361990:p.Asp1589Tyr		42758817	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.231797	0.39399	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.50001	0.76;0.76	5.21	2.94	0.34122	.	0.969283	0.08554	N	0.928510	T	0.16514	0.0397	N	0.24115	0.695	0.80722	D	1	B;B	0.19583	0.037;0.0	B;B	0.25291	0.059;0.004	T	0.23833	-1.0177	10	0.32370	T	0.25	-16.8452	5.9745	0.19371	0.1479:0.3454:0.5067:0.0	.	1589;1589	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	Y	1589	ENSP00000361990:D1589Y;ENSP00000361992:D1589Y	ENSP00000361990:D1589Y	D	+	1	0	UBR2	42758817	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.160000	0.31761	1.081000	0.41110	0.591000	0.81541	GAT		0.363	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
MLIP	90523	broad.mit.edu	37	6	53989552	53989552	+	Silent	SNP	G	G	A	rs145946168	byFrequency	TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr6:53989552G>A	ENST00000274897.5	+	3	614	c.501G>A	c.(499-501)tcG>tcA	p.S167S	MLIP_ENST00000370877.2_Silent_p.S115S|MLIP_ENST00000502396.1_Silent_p.S178S|MLIP_ENST00000370876.2_Silent_p.S105S|MLIP_ENST00000511744.1_3'UTR|MLIP_ENST00000509997.1_Silent_p.S115S|MLIP_ENST00000514921.1_Silent_p.S167S|MLIP_ENST00000358276.5_Silent_p.S161S	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	167						nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)		p.S167S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						TAGCTATCTCGTCCAGTCTGG	0.552													G|||	2	0.000399361	0.0	0.0014	5008	,	,		16304	0.0		0.0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	ovary(1)	6											80.0	75.0	77.0					6																	53989552		2203	4300	6503	54097511	SO:0001819	synonymous_variant	90523			AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"""muscle-enriched A-type lamin interacting protein"""	614106	"""chromosome 6 open reading frame 142"""	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.501G>A	6.37:g.53989552G>A			54097511	B7Z2N0|D6RE05|Q96H08|Q96NF7	Silent	SNP	ENST00000274897.5	37	CCDS4954.1																																																																																				0.552	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	
PDSS2	57107	broad.mit.edu	37	6	107595389	107595389	+	Silent	SNP	A	A	C			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr6:107595389A>C	ENST00000369037.4	-	3	751	c.474T>G	c.(472-474)gcT>gcG	p.A158A	PDSS2_ENST00000369031.4_Silent_p.A158A|PDSS2_ENST00000453874.2_Silent_p.A158A	NM_020381.3	NP_065114.3	Q86YH6	DLP1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 2	158					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|regulation of body fluid levels (GO:0050878)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.A158A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)	19	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		GTACAAGGAGAGCAATATGAA	0.343																																																1	Substitution - coding silent(1)	ovary(1)	6											77.0	72.0	74.0					6																	107595389		2203	4300	6503	107702082	SO:0001819	synonymous_variant	57107			AF254956	CCDS5059.1	6q21	2006-02-14	2006-02-14	2006-02-14	ENSG00000164494	ENSG00000164494			23041	protein-coding gene	gene with protein product		610564	"""chromosome 6 open reading frame 210"""	C6orf210		16262699	Standard	NM_020381		Approved	bA59I9.3	uc003prt.2	Q86YH6	OTTHUMG00000059359	ENST00000369037.4:c.474T>G	6.37:g.107595389A>C			107702082	Q33DR4|Q4G158|Q5VU38|Q5VU39|Q9NR58	Silent	SNP	ENST00000369037.4	37	CCDS5059.1																																																																																				0.343	PDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131954.1	NM_020381	
RELN	5649	broad.mit.edu	37	7	103301822	103301822	+	Splice_Site	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr7:103301822C>T	ENST00000428762.1	-	12	1601		c.e12+1		RELN_ENST00000424685.2_Splice_Site|RELN_ENST00000343529.5_Splice_Site	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin						associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.?(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AATGTACTTACCCATCACAAA	0.428																																					NSCLC(146;835 1944 15585 22231 52158)											1	Unknown(1)	ovary(1)	7											139.0	103.0	115.0					7																	103301822		2203	4300	6503	103089058	SO:0001630	splice_region_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.1441+1G>A	7.37:g.103301822C>T			103089058	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Splice_Site	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658599	0.47467	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9384	0.92595	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RELN	103089058	1.000000	0.71417	1.000000	0.80357	0.127000	0.20565	7.421000	0.80204	2.477000	0.83638	0.467000	0.42956	.		0.428	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	Intron
RHOBTB2	23221	broad.mit.edu	37	8	22864559	22864559	+	Silent	SNP	C	C	T	rs547602967		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr8:22864559C>T	ENST00000251822.6	+	5	1338	c.801C>T	c.(799-801)gaC>gaT	p.D267D	RP11-875O11.1_ENST00000523884.1_RNA|RHOBTB2_ENST00000519685.1_Silent_p.D289D|RP11-875O11.1_ENST00000502083.2_RNA|RHOBTB2_ENST00000522948.1_Silent_p.D274D	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	267	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.D267D(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		TCTGCGCGGACGTCATCCTGG	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16413	0.0		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	ovary(1)	8											87.0	87.0	87.0					8																	22864559		2203	4300	6503	22920504	SO:0001819	synonymous_variant	23221			AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"""BTB/POZ domain containing"""	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.801C>T	8.37:g.22864559C>T			22920504	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Silent	SNP	ENST00000251822.6	37	CCDS6034.1																																																																																				0.642	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2		
KCNK9	51305	broad.mit.edu	37	8	140630763	140630763	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr8:140630763G>A	ENST00000520439.1	-	2	926	c.863C>T	c.(862-864)gCg>gTg	p.A288V	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_Missense_Mutation_p.A288V	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	288					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.A288V(1)		NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CGGGACGTCCGCCTTGTACCT	0.667																																																1	Substitution - Missense(1)	ovary(1)	8											48.0	53.0	51.0					8																	140630763		2203	4300	6503	140699945	SO:0001583	missense	51305			AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.863C>T	8.37:g.140630763G>A	ENSP00000430676:p.Ala288Val		140699945	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	37	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676779	0.47886	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.17528	2.27;2.27;2.27	5.53	3.67	0.42095	.	1.078660	0.07116	N	0.843000	T	0.22282	0.0537	M	0.63843	1.955	0.26385	N	0.976664	B	0.26876	0.162	B	0.25759	0.063	T	0.42258	-0.9462	10	0.15066	T	0.55	.	14.9469	0.71039	0.0:0.2816:0.7184:0.0	.	288	Q9NPC2	KCNK9_HUMAN	V	288	ENSP00000429847:A288V;ENSP00000302166:A288V;ENSP00000430676:A288V	ENSP00000302166:A288V	A	-	2	0	KCNK9	140699945	0.997000	0.39634	0.905000	0.35620	0.886000	0.51366	3.277000	0.51654	0.624000	0.30286	0.591000	0.81541	GCG		0.667	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601	
TRPM3	80036	broad.mit.edu	37	9	73151501	73151501	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr9:73151501G>A	ENST00000377110.3	-	25	4735	c.4492C>T	c.(4492-4494)Cgt>Tgt	p.R1498C	TRPM3_ENST00000360823.2_Missense_Mutation_p.R1360C|TRPM3_ENST00000396280.5_Missense_Mutation_p.R1347C|TRPM3_ENST00000377106.1_Missense_Mutation_p.R1370C|TRPM3_ENST00000377105.1_Missense_Mutation_p.R1357C|TRPM3_ENST00000358082.3_Missense_Mutation_p.R1360C|TRPM3_ENST00000396292.4_Missense_Mutation_p.R1370C|TRPM3_ENST00000357533.2_Missense_Mutation_p.R1502C|TRPM3_ENST00000408909.2_Missense_Mutation_p.R1357C|TRPM3_ENST00000396285.1_Missense_Mutation_p.R1357C|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000423814.3_Missense_Mutation_p.R1525C			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1523					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.R1370C(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CTTTTGGAACGCTCAATGGTG	0.498																																																1	Substitution - Missense(1)	ovary(1)	9											97.0	105.0	103.0					9																	73151501		2203	4300	6503	72341321	SO:0001583	missense	80036			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4492C>T	9.37:g.73151501G>A	ENSP00000366314:p.Arg1498Cys		72341321	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	37	CCDS43835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.18|18.18	3.566397|3.566397	0.65651|0.65651	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	.|T;T;T;T;T;T;T;T;T;T	.|0.62232	.|0.15;0.06;0.06;0.04;0.15;0.04;0.05;0.06;0.06;0.14	6.02|6.02	5.13|5.13	0.70059|0.70059	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69178|0.69178	0.3082|0.3082	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|B;D;D;B;B;D;B	.|0.89917	.|0.045;1.0;0.999;0.027;0.045;0.996;0.027	.|B;D;P;B;B;P;B	.|0.70227	.|0.016;0.968;0.858;0.007;0.016;0.788;0.007	T|T	0.72484|0.72484	-0.4279|-0.4279	5|10	.|0.59425	.|D	.|0.04	-5.5052|-5.5052	15.4941|15.4941	0.75634|0.75634	0.0663:0.0:0.9337:0.0|0.0663:0.0:0.9337:0.0	.|.	.|1498;1488;1502;1360;1357;1470;1357	.|Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|.;.;.;.;.;.;.	V|C	1346|1498;1370;1360;1357;1502;1357;1357;1370;1360;1525	.|ENSP00000366314:R1498C;ENSP00000366310:R1370C;ENSP00000354066:R1360C;ENSP00000366309:R1357C;ENSP00000350140:R1502C;ENSP00000386127:R1357C;ENSP00000379581:R1357C;ENSP00000379587:R1370C;ENSP00000350791:R1360C;ENSP00000389542:R1525C	.|ENSP00000350140:R1502C	A|R	-|-	2|1	0|0	TRPM3|TRPM3	72341321|72341321	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.177000|6.177000	0.71961|0.71961	1.561000|1.561000	0.49584|0.49584	0.655000|0.655000	0.94253|0.94253	GCG|CGT		0.498	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
GNA14	9630	broad.mit.edu	37	9	80039058	80039058	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr9:80039058C>T	ENST00000341700.6	-	7	1418	c.905G>A	c.(904-906)aGa>aAa	p.R302K	GNA14_ENST00000464095.1_5'UTR	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	302					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R302K(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						GATAAAGTCTCTGGCAGCTCT	0.408																																																1	Substitution - Missense(1)	ovary(1)	9											141.0	133.0	136.0					9																	80039058		2203	4300	6503	79228878	SO:0001583	missense	9630			AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.905G>A	9.37:g.80039058C>T	ENSP00000365807:p.Arg302Lys		79228878	B1ALW3	Missense_Mutation	SNP	ENST00000341700.6	37	CCDS6657.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.251015	0.39797	.	.	ENSG00000156049	ENST00000341700	D	0.87809	-2.3	6.07	6.07	0.98685	.	0.090958	0.85682	D	0.000000	T	0.79046	0.4380	N	0.17838	0.53	0.33830	D	0.630088	B	0.06786	0.001	B	0.15870	0.014	T	0.77443	-0.2586	10	0.30854	T	0.27	.	14.418	0.67163	0.0:0.9293:0.0:0.0707	.	302	O95837	GNA14_HUMAN	K	302	ENSP00000365807:R302K	ENSP00000365807:R302K	R	-	2	0	GNA14	79228878	0.439000	0.25610	1.000000	0.80357	0.997000	0.91878	0.864000	0.27926	2.884000	0.98904	0.655000	0.94253	AGA		0.408	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
ZNF189	7743	broad.mit.edu	37	9	104170904	104170904	+	Missense_Mutation	SNP	A	A	G			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr9:104170904A>G	ENST00000339664.2	+	3	983	c.854A>G	c.(853-855)gAg>gGg	p.E285G	ZNF189_ENST00000259395.4_Missense_Mutation_p.E243G|ZNF189_ENST00000374861.3_Missense_Mutation_p.E271G	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	285					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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.E285G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				CACACTGGTGAGAAACCTTAT	0.403																																																1	Substitution - Missense(1)	ovary(1)	9											161.0	165.0	164.0					9																	104170904		2203	4300	6503	103210725	SO:0001583	missense	7743			AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.854A>G	9.37:g.104170904A>G	ENSP00000342019:p.Glu285Gly		103210725	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.330275	0.60743	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.27557	1.66;1.66;1.66	4.79	4.79	0.61399	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000144	T	0.53126	0.1777	M	0.73217	2.22	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.985;0.997	D;D;D	0.79108	0.992;0.927;0.956	T	0.56450	-0.7977	10	0.72032	D	0.01	.	12.9471	0.58379	1.0:0.0:0.0:0.0	.	270;271;285	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	G	271;285;243	ENSP00000363995:E271G;ENSP00000342019:E285G;ENSP00000259395:E243G	ENSP00000259395:E243G	E	+	2	0	ZNF189	103210725	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.139000	0.94554	2.371000	0.80710	0.533000	0.62120	GAG		0.403	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
KAL1	3730	broad.mit.edu	37	X	8553413	8553413	+	Missense_Mutation	SNP	T	T	A			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chrX:8553413T>A	ENST00000262648.3	-	6	900	c.751A>T	c.(751-753)Act>Tct	p.T251S		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	251	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T251S(1)		breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						CTTATGTCAGTCAGTTGAACT	0.493																																																1	Substitution - Missense(1)	ovary(1)	X											190.0	133.0	152.0					X																	8553413		2203	4300	6503	8513413	SO:0001583	missense	3730				CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.751A>T	X.37:g.8553413T>A	ENSP00000262648:p.Thr251Ser		8513413	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.766736	0.00651	.	.	ENSG00000011201	ENST00000262648	T	0.57752	0.38	3.74	1.0	0.19881	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.564801	0.19436	N	0.114318	T	0.18383	0.0441	N	0.04203	-0.255	0.21386	N	0.999701	B	0.09022	0.002	B	0.14023	0.01	T	0.19451	-1.0305	10	0.02654	T	1	.	0.7211	0.00941	0.4532:0.1296:0.1376:0.2795	.	251	P23352	KALM_HUMAN	S	251	ENSP00000262648:T251S	ENSP00000262648:T251S	T	-	1	0	KAL1	8513413	0.999000	0.42202	0.019000	0.16419	0.322000	0.28314	1.282000	0.33226	0.258000	0.21686	0.481000	0.45027	ACT		0.493	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
MAP3K15	389840	broad.mit.edu	37	X	19380952	19380952	+	Missense_Mutation	SNP	C	C	G			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	G	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chrX:19380952C>G	ENST00000338883.4	-	26	3582	c.3583G>C	c.(3583-3585)Gtt>Ctt	p.V1195L	MAP3K15_ENST00000469203.2_Missense_Mutation_p.V1027L|MAP3K15_ENST00000359173.3_Missense_Mutation_p.V630L|MAP3K15_ENST00000518578.1_5'UTR	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1195							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.V670L(1)		NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					TCTTTTTCAACTAGGTGTTCC	0.333																																																1	Substitution - Missense(1)	ovary(1)	X											95.0	93.0	94.0					X																	19380952		2202	4300	6502	19290873	SO:0001583	missense	389840			AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3583G>C	X.37:g.19380952C>G	ENSP00000345629:p.Val1195Leu		19290873	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	37		.	.	.	.	.	.	.	.	.	.	C	11.15	1.552974	0.27739	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.72394	-0.62;-0.65;-0.62	5.91	-2.09	0.07232	.	0.093226	0.42964	U	0.000633	T	0.51483	0.1677	L	0.44542	1.39	0.26929	N	0.966517	B;B	0.21606	0.058;0.008	B;B	0.25987	0.065;0.01	T	0.34527	-0.9825	10	0.20519	T	0.43	.	2.2048	0.03933	0.1075:0.3252:0.3105:0.2568	.	670;1195	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	L	1195;630;1027	ENSP00000345629:V1195L;ENSP00000352093:V630L;ENSP00000428356:V1027L	ENSP00000345629:V1195L	V	-	1	0	MAP3K15	19290873	0.249000	0.23941	0.015000	0.15790	0.978000	0.69477	0.146000	0.16180	-1.030000	0.03312	0.600000	0.82982	GTT		0.333	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671	
FAM47C	442444	broad.mit.edu	37	X	37026705	37026705	+	Silent	SNP	C	C	T	rs149618786	byFrequency	TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chrX:37026705C>T	ENST00000358047.3	+	1	274	c.222C>T	c.(220-222)gaC>gaT	p.D74D		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	74								p.D74D(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GTCGCCGTGACGAGTTTTTAC	0.527																																																1	Substitution - coding silent(1)	ovary(1)	X						C		2,3831		0,2,0,1629,571	78.0	71.0	74.0		222	-1.0	0.0	X	dbSNP_134	74	5,6723		0,2,3,2426,1869	no	coding-synonymous	FAM47C	NM_001013736.2		0,4,3,4055,2440	TT,TC,T,CC,C		0.0743,0.0522,0.0663		74/1036	37026705	7,10554	2202	4300	6502	36936626	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.222C>T	X.37:g.37026705C>T			36936626	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				0.527	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
UPF3B	65109	broad.mit.edu	37	X	118975082	118975082	+	Missense_Mutation	SNP	C	C	T	rs142862074	byFrequency	TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chrX:118975082C>T	ENST00000276201.2	-	7	833	c.764G>A	c.(763-765)aGa>aAa	p.R255K	UPF3B_ENST00000478840.1_5'UTR|UPF3B_ENST00000345865.2_Missense_Mutation_p.R255K	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	255	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R255K(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						TTCTGGAATTCTGTCTATCTT	0.328													C|||	10	0.00264901	0.0076	0.0	3775	,	,		13206	0.0		0.0	False		,,,				2504	0.0															1	Substitution - Missense(1)	ovary(1)	X						C	LYS/ARG,LYS/ARG	32,3803		0,23,9,1609,562	298.0	227.0	251.0		764,764	4.6	1.0	X	dbSNP_134	251	0,6727		0,0,0,2428,1871	yes	missense,missense	UPF3B	NM_023010.3,NM_080632.2	26,26	0,23,9,4037,2433	TT,TC,T,CC,C		0.0,0.8344,0.303	benign,benign	255/471,255/484	118975082	32,10530	2203	4299	6502	118859110	SO:0001583	missense	65109			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"""mental retardation, X-linked 62"""	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.764G>A	X.37:g.118975082C>T	ENSP00000276201:p.Arg255Lys		118859110	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	1	6.027727546714888E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.492	0.862186	0.17178	0.008344	0.0	ENSG00000125351	ENST00000276201;ENST00000345865	T;T	0.75589	-0.92;-0.95	4.64	4.64	0.57946	.	0.149111	0.64402	D	0.000008	T	0.46132	0.1377	L	0.27053	0.805	0.41114	D	0.985767	B;B	0.23128	0.08;0.064	B;B	0.16289	0.015;0.013	T	0.47649	-0.9101	10	0.02654	T	1	.	9.4954	0.38984	0.0:0.8978:0.0:0.1022	.	255;255	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	K	255	ENSP00000276201:R255K;ENSP00000245418:R255K	ENSP00000276201:R255K	R	-	2	0	UPF3B	118859110	1.000000	0.71417	0.996000	0.52242	0.839000	0.47603	2.267000	0.43329	2.059000	0.61396	0.538000	0.68166	AGA		0.328	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		
PSG9	5678	broad.mit.edu	37	19	43771977	43771978	+	Frame_Shift_Ins	INS	-	-	C	rs147964831	byFrequency	TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	-	-	C	C	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr19:43771977_43771978insC	ENST00000270077.3	-	2	484_485	c.388_389insG	c.(388-390)gagfs	p.E130fs	PSG9_ENST00000593948.1_Frame_Shift_Ins_p.E130fs|PSG9_ENST00000596730.1_Frame_Shift_Ins_p.E130fs|PSG9_ENST00000418820.2_Frame_Shift_Ins_p.E130fs|PSG9_ENST00000291752.5_Frame_Shift_Ins_p.E130fs|PSG9_ENST00000244293.7_Frame_Shift_Ins_p.E130fs|PSG9_ENST00000443718.3_Frame_Shift_Ins_p.E130fs	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	130	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.E130fs*3(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				TTCTCTAGTCTCATCACCTCGC	0.465																																																1	Insertion - Frameshift(1)	ovary(1)	19																																								48463818	SO:0001589	frameshift_variant	5678			M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.389dupG	19.37:g.43771978_43771978dupC	ENSP00000270077:p.Glu130fs		48463817	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Frame_Shift_Ins	INS	ENST00000270077.3	37	CCDS12618.1																																																																																				0.465	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
SAP130	79595	broad.mit.edu	37	2	128753991	128754003	+	Frame_Shift_Del	DEL	GGCTACTCCTCTC	GGCTACTCCTCTC	-	rs147076612|rs370299555|rs374338478		TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	GGCTACTCCTCTC	GGCTACTCCTCTC	-	-	GGCTACTCCTCTC	GGCTACTCCTCTC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr2:128753991_128754003delGGCTACTCCTCTC	ENST00000259235.3	-	11	1483_1495	c.1354_1366delGAGAGGAGTAGCC	c.(1354-1368)gagaggagtagcctgfs	p.ERSSL452fs	SAP130_ENST00000259234.6_Frame_Shift_Del_p.ERSSL426fs|SAP130_ENST00000357702.5_Frame_Shift_Del_p.ERSSL452fs	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	452					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.E452fs*1(1)		NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		ATGGGAATCAGGCTACTCCTCTCGGCAGGGTAG	0.549																																																1	Deletion - Frameshift(1)	ovary(1)	2																																								128470473	SO:0001589	frameshift_variant	79595			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.1354_1366delGAGAGGAGTAGCC	2.37:g.128753991_128754003delGGCTACTCCTCTC	ENSP00000259235:p.Glu452fs		128470461	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Frame_Shift_Del	DEL	ENST00000259235.3	37	CCDS2153.1																																																																																				0.549	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
COL6A6	131873	broad.mit.edu	37	3	130284412	130284430	+	Frame_Shift_Del	DEL	ACACACAGTCTCTGTCTTT	ACACACAGTCTCTGTCTTT	-			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	ACACACAGTCTCTGTCTTT	ACACACAGTCTCTGTCTTT	-	-	ACACACAGTCTCTGTCTTT	ACACACAGTCTCTGTCTTT	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr3:130284412_130284430delACACACAGTCTCTGTCTTT	ENST00000358511.6	+	3	1267_1285	c.1236_1254delACACACAGTCTCTGTCTTT	c.(1234-1254)acacacacagtctctgtctttfs	p.THTVSVF412fs	COL6A6_ENST00000453409.2_Frame_Shift_Del_p.THTVSVF412fs	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	412	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.H413fs*37(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						ACCAAATAACACACACAGTCTCTGTCTTTTCAGAGAGGA	0.434																																																1	Deletion - Frameshift(1)	ovary(1)	3																																								131767120	SO:0001589	frameshift_variant	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1236_1254delACACACAGTCTCTGTCTTT	3.37:g.130284412_130284430delACACACAGTCTCTGTCTTT	ENSP00000351310:p.Thr412fs		131767102	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Frame_Shift_Del	DEL	ENST00000358511.6	37	CCDS46911.1																																																																																				0.434	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
ARHGAP18	93663	broad.mit.edu	37	6	129959599	129959599	+	Frame_Shift_Del	DEL	T	T	-			TCGA-24-2254-01A-01W-0722-08	TCGA-24-2254-10A-01W-0722-08	T	T	-	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	596d98c4-3af6-494f-b6ea-b8cd1ddabc8e	32aad8d8-ed00-4b3e-bc11-e624973eedf1	g.chr6:129959599delT	ENST00000368149.2	-	3	580	c.492delA	c.(490-492)aaafs	p.K164fs		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18									p.K164fs*54(1)		NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		TCTGGTACTGTTTGTTTTTTT	0.413																																																1	Deletion - Frameshift(1)	ovary(1)	6											223.0	220.0	221.0					6																	129959599		2203	4300	6503	130001292	SO:0001589	frameshift_variant	93663			AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"""Rho GTPase activating proteins"""	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.492delA	6.37:g.129959599delT	ENSP00000357131:p.Lys164fs		130001292		Frame_Shift_Del	DEL	ENST00000368149.2	37	CCDS34535.1																																																																																				0.413	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515	
