#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
LILRA2	11027	broad.mit.edu	37	19	55086935	55086935	+	Missense_Mutation	SNP	G	G	A	rs368237647		TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr19:55086935G>A	ENST00000251377.3	+	6	1001	c.868G>A	c.(868-870)Ggg>Agg	p.G290R	LILRA2_ENST00000391738.3_Missense_Mutation_p.G290R|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Missense_Mutation_p.G290R|LILRA2_ENST00000391737.1_Missense_Mutation_p.G278R			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	290	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.G290W(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CCCCTCCCACGGGGGCCAGTA	0.657																																						ENST00000251377.3																			1	Substitution - Missense(1)	p.G290W(1)	lung(1)	breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50						c.(868-870)Ggg>Agg		leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2		G	ARG/GLY,ARG/GLY	0,4406		0,0,2203	49.0	50.0	50.0		868,868	-0.9	0.0	19		50	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	125,125	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,	290/484,290/467	55086935	1,13003	2203	4299	6502	SO:0001583	missense	0							g.chr19:55086935G>A	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.868G>A	19.37:g.55086935G>A	ENSP00000251377:p.Gly290Arg		Somatic				LILRB1_ENST00000418536.2_Intron|LILRA2_ENST00000391737.1_Missense_Mutation_p.G278R|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000391738.3_Missense_Mutation_p.G290R|LILRA2_ENST00000251376.3_Missense_Mutation_p.G290R|LILRB1_ENST00000448689.1_Intron	p.G290R			WXS	Illumina GAIIx	Phase_I				GBM - Glioblastoma multiforme(193;0.0963)	6	1001	+								O75020	Missense_Mutation	SNP	ENST00000251377.3	37	c.868G>A	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.443974	0.25987	0.0	1.16E-4	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	2.8	-0.934	0.10428	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.218720	0.06017	N	0.650667	T	0.12944	0.0314	L	0.33753	1.03	0.09310	N	1	P;P;P;P	0.49559	0.925;0.692;0.692;0.514	P;B;B;B	0.46299	0.511;0.344;0.344;0.231	T	0.26395	-1.0104	10	0.52906	T	0.07	.	5.3337	0.15945	0.4728:0.0:0.5272:0.0	.	290;278;290;290	E9PDF4;A8MZH0;Q8N149;Q8N149-2	.;.;LIRA2_HUMAN;.	R	290;290;290;290;278	ENSP00000388131:G290R;ENSP00000251377:G290R;ENSP00000375618:G290R;ENSP00000251376:G290R;ENSP00000375617:G278R	ENSP00000251376:G290R	G	+	1	0	LILRA2	59778747	0.000000	0.05858	0.001000	0.08648	0.179000	0.23085	-1.676000	0.01946	-0.239000	0.09710	0.400000	0.26472	GGG		0.657	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			30	34	0	0	0	1	0	30	34				
APLF	200558	broad.mit.edu	37	2	68753323	68753323	+	Silent	SNP	A	A	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr2:68753323A>T	ENST00000303795.4	+	6	924	c.753A>T	c.(751-753)acA>acT	p.T251T		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	251					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AACAAGACACAGGAGAAGAGT	0.338																																						ENST00000303795.4																			0				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						c.(751-753)acA>acT		aprataxin and PNKP like factor							108.0	112.0	110.0					2																	68753323		2203	4300	6503	SO:0001819	synonymous_variant	200558				double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding	g.chr2:68753323A>T	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.753A>T	2.37:g.68753323A>T			Somatic					p.T251T	NM_173545.2	NP_775816.1	WXS	Illumina GAIIx	Phase_I	Q8IW19	APLF_HUMAN			6	924	+			251					A8K476|Q53P47|Q53PB9|Q53QU0	Silent	SNP	ENST00000303795.4	37	c.753A>T	CCDS1888.1																																																																																				0.338	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		3	52	0	0	0	1	0	3	52				
MUC4	4585	broad.mit.edu	37	3	195515449	195515449	+	Missense_Mutation	SNP	A	A	G	rs200672669	byFrequency	TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr3:195515449A>G	ENST00000463781.3	-	2	3461	c.3002T>C	c.(3001-3003)gTa>gCa	p.V1001A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V1001A|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	425	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V1001A(1)|p.V1001E(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGC	0.587													.|||	123	0.0245607	0.0401	0.013	5008	,	,		21572	0.002		0.0199	False		,,,				2504	0.0399					ENST00000463781.3																			2	Substitution - Missense(2)	p.V1001A(1)|p.V1001E(1)	prostate(1)|endometrium(1)	NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						c.(3001-3003)gTa>gCa		mucin 4, cell surface associated		A	,,ALA/VAL	193,4193		2,189,2002	45.0	36.0	39.0		,,3002	-2.5	0.0	3		39	152,8362		0,152,4105	no	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,64	2,341,6107	GG,GA,AA		1.7853,4.4004,2.6744	,,benign	,,1001/5413	195515449	345,12555	2193	4257	6450	SO:0001583	missense	4585				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity	g.chr3:195515449A>G	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3002T>C	3.37:g.195515449A>G	ENSP00000417498:p.Val1001Ala		Somatic				MUC4_ENST00000475231.1_Missense_Mutation_p.V1001A|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	p.V1001A	NM_018406.6	NP_060876.5	WXS	Illumina GAIIx	Phase_I	Q99102	MUC4_HUMAN	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)	2	3461	-	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	1006			Ser-rich.		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	c.3002T>C	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	4.034	0.003800	0.07866	0.044004	0.017853	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.25;1.24	1.24	-2.48	0.06423	.	.	.	.	.	T	0.03390	0.0098	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.20472	-1.0274	8	.	.	.	.	2.7997	0.05411	0.2821:0.0:0.4902:0.2277	.	1001	E7ESK3	.	A	1001	ENSP00000417498:V1001A;ENSP00000420243:V1001A	.	V	-	2	0	MUC4	196999844	.	.	0.000000	0.03702	0.127000	0.20565	.	.	-0.712000	0.04988	0.055000	0.15244	GTA		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406		4	0	0	0	0	1	0	4	0				
DNAH8	1769	broad.mit.edu	37	6	38828378	38828378	+	Missense_Mutation	SNP	G	G	A			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr6:38828378G>A	ENST00000359357.3	+	41	5707	c.5453G>A	c.(5452-5454)cGt>cAt	p.R1818H	DNAH8_ENST00000441566.1_Missense_Mutation_p.R1818H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R2035H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1818	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGTACTGATCGTCTTGTTATC	0.289																																						ENST00000359357.3																			0				NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						c.(5452-5454)cGt>cAt		dynein, axonemal, heavy chain 8							97.0	98.0	98.0					6																	38828378		2203	4299	6502	SO:0001583	missense	1769							g.chr6:38828378G>A	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.5453G>A	6.37:g.38828378G>A	ENSP00000352312:p.Arg1818His		Somatic				DNAH8_ENST00000449981.2_Missense_Mutation_p.R2035H|DNAH8_ENST00000441566.1_Missense_Mutation_p.R1818H	p.R1818H			WXS	Illumina GAIIx	Phase_I					41	5707	+								O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37	c.5453G>A		.	.	.	.	.	.	.	.	.	.	G	32	5.178752	0.94846	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.15017	2.46;2.46;2.46	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.49150	0.1540	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64024	-0.6504	10	0.87932	D	0	.	19.177	0.93605	0.0:0.0:1.0:0.0	.	1818	Q96JB1	DYH8_HUMAN	H	2023;2023;1818;1818	ENSP00000333363:R2023H;ENSP00000352312:R1818H;ENSP00000402294:R1818H	ENSP00000333363:R2023H	R	+	2	0	DNAH8	38936356	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.869000	0.99810	2.525000	0.85131	0.650000	0.86243	CGT		0.289	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		7	65	0	0	0	1	0	7	65				
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.2_ENST00000585980.1_RNA|AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4				Dom	yes		19	19p13.3	2767	Mis	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""			E			uveal melanoma		82	Substitution - Missense(82)	p.Q209L(80)|p.Q209P(2)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg		guanine nucleotide binding protein (G protein), alpha 11 (Gq class)							104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767				activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256			4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	Standard	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		Somatic				AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	p.Q209L	NM_002067.2	NP_002058.2	WXS	Illumina GAIIx	Phase_I	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209					O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2	NM_002067		26	42	0	0	0	1	0	26	42				
SHANK1	50944	broad.mit.edu	37	19	51220008	51220008	+	Missense_Mutation	SNP	G	G	A			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr19:51220008G>A	ENST00000293441.1	-	1	187	c.169C>T	c.(169-171)Ctc>Ttc	p.L57F	SHANK1_ENST00000359082.3_Missense_Mutation_p.L57F|SHANK1_ENST00000391814.1_Missense_Mutation_p.L57F	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	57					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CGGCCCTGGAGGCCTCTAACA	0.672																																						ENST00000293441.1																			0				breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64						c.(169-171)Ctc>Ttc		SH3 and multiple ankyrin repeat domains 1							51.0	46.0	48.0					19																	51220008		2203	4300	6503	SO:0001583	missense	50944				cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding	g.chr19:51220008G>A	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15474	protein-coding gene	gene with protein product	"""somatostatin receptor-interacting protein"""	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.169C>T	19.37:g.51220008G>A	ENSP00000293441:p.Leu57Phe		Somatic				SHANK1_ENST00000359082.3_Missense_Mutation_p.L57F|SHANK1_ENST00000391814.1_Missense_Mutation_p.L57F	p.L57F	NM_016148.2	NP_057232.2	WXS	Illumina GAIIx	Phase_I	Q9Y566	SHAN1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)	1	187	-		all_neural(266;0.057)	57					A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	c.169C>T	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.048774	0.36181	.	.	ENSG00000161681	ENST00000293441;ENST00000359082;ENST00000391814	T;T;T	0.40476	1.14;1.13;1.03	3.18	2.12	0.27331	.	1.696560	0.05419	U	0.543844	T	0.25975	0.0633	N	0.08118	0	0.29684	N	0.841484	B	0.12630	0.006	B	0.08055	0.003	T	0.27536	-1.0071	10	0.54805	T	0.06	.	8.3835	0.32486	0.1257:0.0:0.8743:0.0	.	57	Q9Y566	SHAN1_HUMAN	F	57	ENSP00000293441:L57F;ENSP00000351984:L57F;ENSP00000375690:L57F	ENSP00000293441:L57F	L	-	1	0	SHANK1	55911820	1.000000	0.71417	0.999000	0.59377	0.757000	0.42996	3.299000	0.51826	0.461000	0.27071	0.282000	0.19409	CTC		0.672	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		3	31	0	0	0	1	0	3	31				
TSC22D4	81628	broad.mit.edu	37	7	100074941	100074941	+	Missense_Mutation	SNP	G	G	A			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr7:100074941G>A	ENST00000300181.2	-	2	1475	c.721C>T	c.(721-723)Cgg>Tgg	p.R241W	TSC22D4_ENST00000496728.1_5'UTR|TSC22D4_ENST00000393991.1_Missense_Mutation_p.R2W	NM_030935.3	NP_112197.1	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	241					negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATCCGCAGCCGCATGTCTACA	0.652																																						ENST00000300181.2																			0				breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8						c.(721-723)Cgg>Tgg		TSC22 domain family, member 4							61.0	65.0	64.0					7																	100074941		2203	4300	6503	SO:0001583	missense	81628				negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding transcription factor activity	g.chr7:100074941G>A	BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925			21696	protein-coding gene	gene with protein product		611914					Standard	NM_030935		Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000300181.2:c.721C>T	7.37:g.100074941G>A	ENSP00000300181:p.Arg241Trp		Somatic				TSC22D4_ENST00000393991.1_Missense_Mutation_p.R2W|TSC22D4_ENST00000496728.1_5'UTR	p.R241W	NM_030935.3	NP_112197.1	WXS	Illumina GAIIx	Phase_I	Q9Y3Q8	T22D4_HUMAN			2	1475	-	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		241					A4D2C3|A8MWR6|D6W5V9	Missense_Mutation	SNP	ENST00000300181.2	37	c.721C>T	CCDS5695.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802794	0.31869	.	.	ENSG00000166925	ENST00000300181;ENST00000393991	.	.	.	4.33	3.35	0.38373	.	0.358712	0.20599	N	0.089183	T	0.19886	0.0478	N	0.14661	0.345	0.21290	N	0.99974	D;D	0.60160	0.987;0.978	P;B	0.47705	0.555;0.249	T	0.04664	-1.0935	9	0.42905	T	0.14	-4.8287	6.3839	0.21550	0.136:0.0:0.864:0.0	.	241;241	Q8IV54;Q9Y3Q8	.;T22D4_HUMAN	W	241;2	.	ENSP00000300181:R241W	R	-	1	2	TSC22D4	99912877	0.739000	0.28196	0.608000	0.28969	0.589000	0.36550	1.724000	0.38064	2.255000	0.74692	0.549000	0.68633	CGG		0.652	TSC22D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316970.1	NM_030935		4	49	0	0	0	1	0	4	49				
COL14A1	7373	broad.mit.edu	37	8	121224799	121224799	+	Missense_Mutation	SNP	C	C	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr8:121224799C>T	ENST00000297848.3	+	13	1850	c.1580C>T	c.(1579-1581)aCg>aTg	p.T527M	COL14A1_ENST00000247781.3_Missense_Mutation_p.T432M|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_Missense_Mutation_p.T527M|COL14A1_ENST00000309791.4_Missense_Mutation_p.T527M	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			GATCCTGTTACGGGACAAGAA	0.443																																						ENST00000297848.3																			0				NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119						c.(1579-1581)aCg>aTg		collagen, type XIV, alpha 1							111.0	101.0	104.0					8																	121224799		2203	4300	6503	SO:0001583	missense	7373				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging	g.chr8:121224799C>T		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1580C>T	8.37:g.121224799C>T	ENSP00000297848:p.Thr527Met		Somatic				COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Missense_Mutation_p.T527M|COL14A1_ENST00000247781.3_Missense_Mutation_p.T432M|COL14A1_ENST00000537875.1_Missense_Mutation_p.T527M	p.T527M	NM_021110.1	NP_066933.1	WXS	Illumina GAIIx	Phase_I	Q05707	COEA1_HUMAN	OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)		13	1850	+	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		527			Fibronectin type-III 3.			Missense_Mutation	SNP	ENST00000297848.3	37	c.1580C>T	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.591516	0.86953	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T;T	0.05139	3.49;3.49;3.49;3.49;3.49	6.17	6.17	0.99709	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.053628	0.64402	D	0.000001	T	0.30947	0.0781	M	0.86268	2.805	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;P	0.65233	0.933;0.825	T	0.01071	-1.1461	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	527;527	Q05707-2;Q05707	.;COEA1_HUMAN	M	527;527;527;432;340	ENSP00000443974:T527M;ENSP00000311809:T527M;ENSP00000297848:T527M;ENSP00000247781:T432M;ENSP00000409461:T340M	ENSP00000247781:T432M	T	+	2	0	COL14A1	121293980	1.000000	0.71417	0.912000	0.35992	0.952000	0.60782	7.247000	0.78257	2.941000	0.99782	0.655000	0.94253	ACG		0.443	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		96	20	0	0	0	1	0	96	20				
ARSJ	79642	broad.mit.edu	37	4	114823726	114823726	+	Missense_Mutation	SNP	G	G	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr4:114823726G>T	ENST00000315366.7	-	2	2370	c.1504C>A	c.(1504-1506)Cca>Aca	p.P502T	ARSJ_ENST00000541197.1_Missense_Mutation_p.P502T	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	502					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		CTCTCATATGGGTCGGCTGTG	0.512																																						ENST00000315366.7																			0				endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21						c.(1504-1506)Cca>Aca		arylsulfatase family, member J							77.0	74.0	75.0					4																	114823726		1929	4132	6061	SO:0001583	missense	79642					extracellular region	arylsulfatase activity|metal ion binding	g.chr4:114823726G>T		CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"""Arylsulfatase family"""	26286	protein-coding gene	gene with protein product		610010	"""arylsulfatase J"""			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.1504C>A	4.37:g.114823726G>T	ENSP00000320219:p.Pro502Thr		Somatic				ARSJ_ENST00000541197.1_Missense_Mutation_p.P502T	p.P502T	NM_024590.3	NP_078866.3	WXS	Illumina GAIIx	Phase_I	Q5FYB0	ARSJ_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00194)	2	2370	-		Ovarian(17;0.0035)|Hepatocellular(203;0.217)	502					A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Missense_Mutation	SNP	ENST00000315366.7	37	c.1504C>A	CCDS43264.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.046908	0.75846	.	.	ENSG00000180801	ENST00000315366;ENST00000541197;ENST00000545965	D;D	0.98234	-4.81;-4.81	5.41	5.41	0.78517	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.369476	0.27526	N	0.018969	D	0.99360	0.9775	H	0.96547	3.84	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98730	1.0712	10	0.72032	D	0.01	.	19.2114	0.93757	0.0:0.0:1.0:0.0	.	502;502	Q1HA39;Q5FYB0	.;ARSJ_HUMAN	T	502;502;71	ENSP00000320219:P502T;ENSP00000438836:P502T	ENSP00000320219:P502T	P	-	1	0	ARSJ	115043175	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	9.697000	0.98697	2.544000	0.85801	0.655000	0.94253	CCA		0.512	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590		20	25	1	0	1.96292e-10	1	2.11392e-10	20	25				
MTOR	2475	broad.mit.edu	37	1	11169412	11169412	+	Missense_Mutation	SNP	A	A	C			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr1:11169412A>C	ENST00000361445.4	-	56	7539	c.7463T>G	c.(7462-7464)gTg>gGg	p.V2488G	MTOR_ENST00000376838.1_Missense_Mutation_p.V693G	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2488	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)			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)	CTCTGGTTTCACCAAACCGTC	0.393																																						ENST00000361445.4																			0				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						c.(7462-7464)gTg>gGg		mechanistic target of rapamycin (serine/threonine kinase)							134.0	123.0	127.0					1																	11169412		2203	4300	6503	SO:0001583	missense	2475				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity	g.chr1:11169412A>C	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.7463T>G	1.37:g.11169412A>C	ENSP00000354558:p.Val2488Gly		Somatic				MTOR_ENST00000376838.1_Missense_Mutation_p.V693G	p.V2488G	NM_004958.3	NP_004949.1	WXS	Illumina GAIIx	Phase_I	P42345	MTOR_HUMAN			56	7539	-			2488			PI3K/PI4K.		Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	c.7463T>G	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428641	0.43122	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	T;T;T	0.23552	3.21;2.96;1.9	5.82	5.82	0.92795	Phosphatidylinositol 3-/4-kinase, catalytic (1);	0.056274	0.64402	D	0.000001	T	0.13200	0.0320	N	0.04297	-0.235	0.80722	D	1	B	0.20671	0.047	B	0.18263	0.021	T	0.17137	-1.0379	10	0.24483	T	0.36	-21.7174	13.9151	0.63893	1.0:0.0:0.0:0.0	.	2488	P42345	MTOR_HUMAN	G	2488;693;144	ENSP00000354558:V2488G;ENSP00000366034:V693G;ENSP00000398745:V144G	ENSP00000354558:V2488G	V	-	2	0	MTOR	11091999	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.690000	0.91272	2.223000	0.72356	0.482000	0.46254	GTG		0.393	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		49	7	0	0	0	1	0	49	7				
REC114	283677	broad.mit.edu	37	15	73852150	73852150	+	Nonsense_Mutation	SNP	G	G	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr15:73852150G>T	ENST00000331090.6	+	6	722	c.694G>T	c.(694-696)Gaa>Taa	p.E232*	C15orf60_ENST00000560581.1_Nonsense_Mutation_p.E204*	NM_001042367.1	NP_001035826.1	Q7Z4M0	RE114_HUMAN		232					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)					endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						ATGGGGTGCAGAAGAGTTAGG	0.478																																						ENST00000331090.6																			0				endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						c.(694-696)Gaa>Taa		chromosome 15 open reading frame 60							91.0	89.0	89.0					15																	73852150		1850	4085	5935	SO:0001587	stop_gained	283677							g.chr15:73852150G>T																												ENST00000331090.6:c.694G>T	15.37:g.73852150G>T	ENSP00000328423:p.Glu232*		Somatic				C15orf60_ENST00000560581.1_Nonsense_Mutation_p.E204*	p.E232*	NM_001042367.1	NP_001035826.1	WXS	Illumina GAIIx	Phase_I	Q7Z4M0	CO060_HUMAN			6	722	+			232						Nonsense_Mutation	SNP	ENST00000331090.6	37	c.694G>T	CCDS45296.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.530040	0.27387	.	.	ENSG00000183324	ENST00000331090	.	.	.	6.02	6.02	0.97574	.	0.694289	0.14214	N	0.333848	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-5.7041	15.7463	0.77944	0.0:0.1456:0.8544:0.0	.	.	.	.	X	232	.	ENSP00000328423:E232X	E	+	1	0	C15orf60	71639203	0.924000	0.31332	0.008000	0.14137	0.431000	0.31685	3.797000	0.55514	2.857000	0.98124	0.650000	0.86243	GAA		0.478	C15orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419069.1			6	65	1	0	0.00198382	1	0.00198382	6	65				
PPP4R1	9989	broad.mit.edu	37	18	9550172	9550172	+	Missense_Mutation	SNP	C	C	A			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr18:9550172C>A	ENST00000400556.3	-	18	2498	c.2425G>T	c.(2425-2427)Gtg>Ttg	p.V809L	PPP4R1_ENST00000400555.3_Missense_Mutation_p.V792L	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	809					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						AGCTTCTTCACCATCTCGCTG	0.483																																					Melanoma(188;1232 2082 5061 11948 35994)	ENST00000400556.3																			0				large_intestine(1)|skin(2)	3						c.(2425-2427)Gtg>Ttg		protein phosphatase 4, regulatory subunit 1							72.0	80.0	77.0					18																	9550172		2074	4215	6289	SO:0001583	missense	9989				protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity	g.chr18:9550172C>A	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2425G>T	18.37:g.9550172C>A	ENSP00000383402:p.Val809Leu		Somatic				PPP4R1_ENST00000400555.3_Missense_Mutation_p.V792L	p.V809L	NM_001042388.2	NP_001035847.1	WXS	Illumina GAIIx	Phase_I	Q8TF05	PP4R1_HUMAN			18	2498	-			809					Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	37	c.2425G>T	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	C	8.003	0.755744	0.15846	.	.	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.28069	1.63;1.63	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.229234	0.38492	N	0.001671	T	0.14442	0.0349	N	0.02865	-0.47	0.53688	D	0.999975	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.10450	0.004;0.003;0.005	T	0.17715	-1.0360	9	.	.	.	-29.6409	15.5022	0.75709	0.0:0.8622:0.1378:0.0	.	792;809;792	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	L	809;792	ENSP00000383402:V809L;ENSP00000383401:V792L	.	V	-	1	0	PPP4R1	9540172	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.728000	0.47319	2.804000	0.96469	0.655000	0.94253	GTG		0.483	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		18	31	1	0	2.70639e-06	1	2.80663e-06	18	31				
LSM1	27257	broad.mit.edu	37	8	38021245	38021245	+	Missense_Mutation	SNP	C	C	G			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr8:38021245C>G	ENST00000311351.4	-	4	740	c.345G>C	c.(343-345)caG>caC	p.Q115H	RP11-90P5.7_ENST00000521915.1_RNA|LSM1_ENST00000520755.1_3'UTR|RP11-90P5.2_ENST00000520598.1_RNA|LSM1_ENST00000522515.1_5'UTR	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated	115					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					CCTTCAGGGCCTGCACTTTCA	0.488																																						ENST00000311351.4																			0				kidney(2)|large_intestine(3)|lung(2)	7						c.(343-345)caG>caC		LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)							160.0	133.0	142.0					8																	38021245		2203	4300	6503	SO:0001583	missense	27257				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|mRNA processing|RNA splicing, via transesterification reactions	cytosol|nucleus|ribonucleoprotein complex	protein binding|RNA binding	g.chr8:38021245C>G	AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"""LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"""			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.345G>C	8.37:g.38021245C>G	ENSP00000310596:p.Gln115His		Somatic				RP11-90P5.2_ENST00000520598.1_RNA|LSM1_ENST00000522515.1_5'UTR|LSM1_ENST00000520755.1_3'UTR	p.Q115H	NM_014462.2	NP_055277.1	WXS	Illumina GAIIx	Phase_I	O15116	LSM1_HUMAN			4	740	-	Colorectal(12;0.000442)		115					B2R5E6	Missense_Mutation	SNP	ENST00000311351.4	37	c.345G>C	CCDS6103.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.413204	0.42817	.	.	ENSG00000175324	ENST00000311351	.	.	.	5.91	2.64	0.31445	.	0.053094	0.85682	D	0.000000	T	0.46795	0.1411	L	0.48362	1.52	0.80722	D	1	P	0.37038	0.579	B	0.34418	0.182	T	0.48445	-0.9035	9	0.62326	D	0.03	-10.3867	9.8378	0.40980	0.0:0.6306:0.0:0.3694	.	115	O15116	LSM1_HUMAN	H	115	.	ENSP00000310596:Q115H	Q	-	3	2	LSM1	38140402	1.000000	0.71417	0.963000	0.40424	0.817000	0.46193	1.652000	0.37313	0.791000	0.33826	0.650000	0.86243	CAG		0.488	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462		21	26	0	0	0	1	0	21	26				
GMEB2	26205	broad.mit.edu	37	20	62236098	62236098	+	Nonsense_Mutation	SNP	A	A	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr20:62236098A>T	ENST00000266068.1	-	2	705	c.227T>A	c.(226-228)tTa>tAa	p.L76*	GMEB2_ENST00000370077.1_Nonsense_Mutation_p.L76*|GMEB2_ENST00000370069.1_Nonsense_Mutation_p.L25*			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	76					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			CTTCCTACCTAACACGGCTTC	0.572																																						ENST00000266068.1																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18						c.(226-228)tTa>tAa		glucocorticoid modulatory element binding protein 2							74.0	72.0	73.0					20																	62236098		2203	4300	6503	SO:0001587	stop_gained	26205				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding	g.chr20:62236098A>T	AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.227T>A	20.37:g.62236098A>T	ENSP00000266068:p.Leu76*		Somatic				GMEB2_ENST00000370077.1_Nonsense_Mutation_p.L76*|GMEB2_ENST00000370069.1_Nonsense_Mutation_p.L25*	p.L76*			WXS	Illumina GAIIx	Phase_I	Q9UKD1	GMEB2_HUMAN	Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)		2	705	-	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		76					E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Nonsense_Mutation	SNP	ENST00000266068.1	37	c.227T>A	CCDS13528.1	.	.	.	.	.	.	.	.	.	.	A	38	6.668376	0.97747	.	.	ENSG00000101216	ENST00000370069;ENST00000370077;ENST00000266068	.	.	.	4.87	4.87	0.63330	.	0.090745	0.46758	D	0.000270	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-8.4045	14.1277	0.65233	1.0:0.0:0.0:0.0	.	.	.	.	X	25;76;76	.	ENSP00000266068:L76X	L	-	2	0	GMEB2	61706542	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	5.709000	0.68384	1.822000	0.53115	0.379000	0.24179	TTA		0.572	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384		9	50	0	0	0	1	0	9	50				
MTOR	2475	broad.mit.edu	37	1	11169374	11169374	+	Missense_Mutation	SNP	T	T	A			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr1:11169374T>A	ENST00000361445.4	-	56	7577	c.7501A>T	c.(7501-7503)Att>Ttt	p.I2501F	MTOR_ENST00000376838.1_Missense_Mutation_p.I706F	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2501	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)			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)	ACCCTGTTAATAATCTGGATA	0.413																																						ENST00000361445.4																			0				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						c.(7501-7503)Att>Ttt		mechanistic target of rapamycin (serine/threonine kinase)							177.0	156.0	163.0					1																	11169374		2203	4300	6503	SO:0001583	missense	2475				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity	g.chr1:11169374T>A	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.7501A>T	1.37:g.11169374T>A	ENSP00000354558:p.Ile2501Phe		Somatic				MTOR_ENST00000376838.1_Missense_Mutation_p.I706F	p.I2501F	NM_004958.3	NP_004949.1	WXS	Illumina GAIIx	Phase_I	P42345	MTOR_HUMAN			56	7577	-			2501			PI3K/PI4K.		Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	c.7501A>T	CCDS127.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.180381	0.78677	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	T;T;T	0.28454	3.1;2.84;1.61	5.82	5.82	0.92795	Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.85197	2.74	0.80722	D	1	D	0.62365	0.991	P	0.54924	0.764	T	0.61178	-0.7115	10	0.72032	D	0.01	-1.8424	13.9151	0.63893	0.0:0.0:0.0:1.0	.	2501	P42345	MTOR_HUMAN	F	2501;706;157	ENSP00000354558:I2501F;ENSP00000366034:I706F;ENSP00000398745:I157F	ENSP00000354558:I2501F	I	-	1	0	MTOR	11091961	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.466000	0.80914	2.223000	0.72356	0.482000	0.46254	ATT		0.413	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		9	57	0	0	0	1	0	9	57				
ZNF733P	643955	broad.mit.edu	37	7	62752443	62752443	+	RNA	SNP	G	G	C	rs372167638		TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr7:62752443G>C	ENST00000331425.6	-	0	992					NR_003952.1				zinc finger protein 733, pseudogene																		CTTATGTCTAGTAAGGTTTGA	0.438																																						ENST00000331425.6																			0																																																			0							g.chr7:62752443G>C			7q11.21	2012-04-20	2012-04-20	2012-04-20	ENSG00000185037	ENSG00000185037			32473	pseudogene	pseudogene			"""zinc finger protein 733"""	ZNF733			Standard	NR_003952		Approved		uc011kdj.2		OTTHUMG00000156270		7.37:g.62752443G>C			Somatic						NR_003952.1		WXS	Illumina GAIIx	Phase_I					0	992	-									RNA	SNP	ENST00000331425.6	37																																																																																						0.438	ZNF733P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000343679.1			4	38	0	0	0	1	0	4	38				
IGHV4-61	28391	broad.mit.edu	37	14	107095454	107095454	+	RNA	SNP	A	A	G	rs199512044	byFrequency	TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr14:107095454A>G	ENST00000390630.2	-	0	147				RNA5SP389_ENST00000362610.1_RNA					immunoglobulin heavy variable 4-61																		AGAGACCCACAGTGAGCCCTG	0.617																																						ENST00000390630.2																			0																				19.0	36.0	31.0					14																	107095454		1772	4034	5806			0							g.chr14:107095454A>G	M29811		14q32.33	2012-02-08			ENSG00000211970	ENSG00000211970		"""Immunoglobulins / IGH locus"""	5655	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151976		14.37:g.107095454A>G			Somatic								WXS	Illumina GAIIx	Phase_I					0	147	-									RNA	SNP	ENST00000390630.2	37																																																																																						0.617	IGHV4-61-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000324623.1	NG_001019		3	13	0	0	0	1	0	3	13				
POU4F1	5457	broad.mit.edu	37	13	79175838	79175838	+	Silent	SNP	C	C	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr13:79175838C>T	ENST00000377208.5	-	2	1183	c.972G>A	c.(970-972)gcG>gcA	p.A324A	RP11-52L5.6_ENST00000607269.1_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606124.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	324	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	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 distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		TGGGCTTGAGCGCGATCATGT	0.637																																					Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	ENST00000377208.5																			0				central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16						c.(970-972)gcG>gcA		POU class 4 homeobox 1							38.0	36.0	37.0					13																	79175838		2203	4300	6503	SO:0001819	synonymous_variant	5457				axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr13:79175838C>T	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"""Homeoboxes / POU class"""	9218	protein-coding gene	gene with protein product		601632	"""POU domain class 4, transcription factor 1"""	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.972G>A	13.37:g.79175838C>T			Somatic				RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607220.1_RNA	p.A324A	NM_006237.3	NP_006228.3	WXS	Illumina GAIIx	Phase_I	Q01851	PO4F1_HUMAN		GBM - Glioblastoma multiforme(99;0.129)	2	1183	-		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)	324			POU-specific.		Q14986|Q15318|Q5T227	Silent	SNP	ENST00000377208.5	37	c.972G>A	CCDS31996.1																																																																																				0.637	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3			3	22	0	0	0	1	0	3	22				
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	A	G			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr17:62968690A>G	ENST00000430983.1	-	0	1554					NR_026903.1				archaelysin family metallopeptidase 2 pseudogene 1																		AAAATTCCACAAGTCTCTTGG	0.373																																						ENST00000430983.1																			0																																																			0							g.chr17:62968690A>G	AK056627		17q24.1	2012-10-16	2010-04-08		ENSG00000214174	ENSG00000214174			26491	pseudogene	pseudogene							Standard	NR_026903		Approved	FLJ32065	uc002jfb.3		OTTHUMG00000132075		17.37:g.62968690A>G			Somatic						NR_026903.1		WXS	Illumina GAIIx	Phase_I					0	1554	-									RNA	SNP	ENST00000430983.1	37																																																																																						0.373	AMZ2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255102.1	NM_153032		3	90	0	0	0	1	0	3	90				
EDEM2	55741	broad.mit.edu	37	20	33722607	33722607	+	Silent	SNP	C	C	T			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr20:33722607C>T	ENST00000374492.3	-	6	741	c.636G>A	c.(634-636)ccG>ccA	p.P212P	EDEM2_ENST00000540582.1_Silent_p.P171P|EDEM2_ENST00000542871.1_Intron|EDEM2_ENST00000541621.1_5'UTR|EDEM2_ENST00000374491.3_Silent_p.P175P	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	212					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CTTCGAACACCGGGTCACCAG	0.582																																					Esophageal Squamous(51;906 1021 24535 36410 39145)	ENST00000540582.1																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22						c.(511-513)ccG>ccA		ER degradation enhancer, mannosidase alpha-like 2							93.0	80.0	85.0					20																	33722607		2203	4300	6503	SO:0001819	synonymous_variant	55741				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding	g.chr20:33722607C>T	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.636G>A	20.37:g.33722607C>T			Somatic				EDEM2_ENST00000542871.1_Intron|EDEM2_ENST00000374492.3_Silent_p.P212P|EDEM2_ENST00000374491.3_Silent_p.P175P|EDEM2_ENST00000541621.1_5'UTR	p.P171P			WXS	Illumina GAIIx	Phase_I	Q9BV94	EDEM2_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.00936)		10	1234	-			212					B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Silent	SNP	ENST00000374492.3	37	c.513G>A	CCDS13247.1																																																																																				0.582	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217		3	50	0	0	0	1	0	3	50				
TOX	9760	broad.mit.edu	37	8	59750796	59750798	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr8:59750796_59750798delCTT	ENST00000361421.1	-	5	986_988	c.766_768delAAG	c.(766-768)aagdel	p.K256del		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	256						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				CATTGGGATCCTTCTTCTTCTTC	0.453																																					Pancreas(161;610 1969 17913 21374 22725)	ENST00000361421.1																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33						c.(766-768)aagdel		thymocyte selection-associated high mobility group box																																				SO:0001651	inframe_deletion	9760					nucleus	DNA binding	g.chr8:59750796_59750798delCTT		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.766_768delAAG	8.37:g.59750805_59750807delCTT	ENSP00000354842:p.Lys256del		Somatic					p.K256del	NM_014729.2	NP_055544.1	WXS	Illumina GAIIx	Phase_I	O94900	TOX_HUMAN			5	986_988	-		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)	256					Q96AV5	In_Frame_Del	DEL	ENST00000361421.1	37	c.766_768delAAG	CCDS34897.1																																																																																				0.453	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		9	357						9	357	---	---	---	---
MIR7162	102466227	broad.mit.edu	37	15	62538522	62538523	+	RNA	INS	-	-	GA	rs3055695|rs540111016|rs370506651	byFrequency	TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr15:62538522_62538523insGA	ENST00000570077.1	-	0	693_694				AC126323.1_ENST00000408214.1_RNA																							GGGGGCTCCGGGTAGGGGTTCA	0.609																																						ENST00000570077.1																			0																																																			0							g.chr15:62538522_62538523insGA																													15.37:g.62538522_62538523insGA			Somatic								WXS	Illumina GAIIx	Phase_I					0	693_694	-									RNA	INS	ENST00000570077.1	37																																																																																						0.609	hsa-mir-7162.1-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000422143.1			3	3						3	3	---	---	---	---
CTC-559E9.6	0	broad.mit.edu	37	19	19944579	19944580	+	RNA	INS	-	-	T	rs200238177|rs372322378		TCGA-RZ-AB0B-01A-11D-A39W-08	TCGA-RZ-AB0B-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b4a5e52a-4422-40bc-b6a4-b8403051345e	3cd31965-60cf-4ffc-a130-e5b3aa8f124c	g.chr19:19944579_19944580insT	ENST00000591884.1	+	0	520																											GATGTTTAATCttttttttttt	0.376																																						ENST00000591884.1																			0																																																			0							g.chr19:19944579_19944580insT																													19.37:g.19944590_19944590dupT			Somatic								WXS	Illumina GAIIx	Phase_I					0	520	+									RNA	INS	ENST00000591884.1	37																																																																																						0.376	CTC-559E9.6-003	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000460786.1			3	5						3	5	---	---	---	---
