#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ANK3	288	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	61835269	61835269	+	Silent	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr10:61835269C>T	ENST00000280772.2	-	37	5561	c.5370G>A	c.(5368-5370)caG>caA	p.Q1790Q	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1790	Ser-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.Q1790H(1)|p.Q1790Q(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTCTTAGAGACTGAAAAGCTG	0.453																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(1)|kidney(1)											111.0	119.0	116.0					10																	61835269		2203	4299	6502	SO:0001819	synonymous_variant	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.5370G>A	10.37:g.61835269C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																				0.453	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4		NM_020987	
ANKRD32	84250	broad.mit.edu	37	5	94014548	94014548	+	Silent	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr5:94014548A>G	ENST00000265140.5	+	15	2282	c.1863A>G	c.(1861-1863)ggA>ggG	p.G621G		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	621						centrosome (GO:0005813)|nucleus (GO:0005634)		p.G621G(4)		NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		TATTGGCTGGAATTCTTGGAG	0.308																																																	4	Substitution - coding silent(4)	endometrium(3)|kidney(1)																																								SO:0001819	synonymous_variant	84250			AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1863A>G	5.37:g.94014548A>G		Somatic		WXS	Illumina GAIIx	Phase_I	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Silent	SNP	ENST00000265140.5	37	CCDS4071.2																																																																																				0.308	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1		NM_032290	
ATPAF2	91647	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	17929649	17929649	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr17:17929649C>T	ENST00000474627.3	-	4	560	c.406G>A	c.(406-408)Gac>Aac	p.D136N	ATPAF2_ENST00000469327.1_5'Flank|ATPAF2_ENST00000585101.1_Missense_Mutation_p.G87E	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	136					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)		p.D136N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					GTGTCGGTGTCCAGAAACTTC	0.463																																																	1	Substitution - Missense(1)	kidney(1)											229.0	180.0	196.0					17																	17929649		2203	4300	6503	SO:0001583	missense	91647			AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.406G>A	17.37:g.17929649C>T	ENSP00000417190:p.Asp136Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	37	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193801	0.58017	.	.	ENSG00000171953	ENST00000474627;ENST00000444058	T;T	0.78126	-1.15;-1.15	5.85	5.85	0.93711	ATPase assembly, ATP12, domain (1);	0.041576	0.85682	D	0.000000	D	0.82935	0.5145	L	0.36672	1.1	0.58432	D	0.999999	D	0.63880	0.993	D	0.63113	0.911	T	0.81512	-0.0899	10	0.42905	T	0.14	-3.9253	20.1616	0.98135	0.0:1.0:0.0:0.0	.	136	Q8N5M1	ATPF2_HUMAN	N	136	ENSP00000417190:D136N;ENSP00000397198:D136N	ENSP00000434980:D136N	D	-	1	0	ATPAF2	17870374	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.725000	0.84808	2.772000	0.95346	0.655000	0.94253	GAC		0.463	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3		NM_145691	
BCORL1	63035	hgsc.bcm.edu	37	X	129149054	129149054	+	Missense_Mutation	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chrX:129149054A>G	ENST00000218147.7	+	4	2503	c.2306A>G	c.(2305-2307)aAg>aGg	p.K769R	BCORL1_ENST00000303743.5_Missense_Mutation_p.K769R|BCORL1_ENST00000540052.1_Missense_Mutation_p.K769R|BCORL1_ENST00000359304.2_Missense_Mutation_p.K769R			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	769					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						TGTGGCAAAAAGGGCAGCCAG	0.607																																																	0													57.0	51.0	53.0					X																	129149054		2203	4300	6503	SO:0001583	missense	63035			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.2306A>G	X.37:g.129149054A>G	ENSP00000218147:p.Lys769Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	37	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	A	15.57	2.873390	0.51695	.	.	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	T;T;T;T;T	0.67345	-0.21;0.23;-0.26;-0.21;0.31	5.06	5.06	0.68205	.	0.000000	0.38492	N	0.001676	T	0.69637	0.3133	L	0.27053	0.805	0.44417	D	0.997339	D;D	0.71674	0.998;0.997	D;D	0.78314	0.991;0.985	T	0.65776	-0.6086	10	0.19590	T	0.45	-15.2748	13.9737	0.64257	1.0:0.0:0.0:0.0	.	769;769	Q5H9F3-2;Q5H9F3	.;BCORL_HUMAN	R	769;769;769;769;369	ENSP00000218147:K769R;ENSP00000307541:K769R;ENSP00000352253:K769R;ENSP00000437775:K769R;ENSP00000399483:K369R	ENSP00000218147:K769R	K	+	2	0	BCORL1	128976735	1.000000	0.71417	0.998000	0.56505	0.673000	0.39480	7.700000	0.84556	1.676000	0.50930	0.356000	0.21956	AAG		0.607	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1		NM_021946	
BMP2K	55589	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	79832708	79832708	+	Missense_Mutation	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr4:79832708A>G	ENST00000335016.5	+	16	3173	c.3007A>G	c.(3007-3009)Agc>Ggc	p.S1003G	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1003					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.S1003G(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						CACGCCAACTAGCACAAAGAA	0.498																																																	1	Substitution - Missense(1)	kidney(1)											69.0	68.0	68.0					4																	79832708		1943	4146	6089	SO:0001583	missense	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.3007A>G	4.37:g.79832708A>G	ENSP00000334836:p.Ser1003Gly	Somatic		WXS	Illumina HiSeq	Phase_I	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.41|11.41	1.629475|1.629475	0.28978|0.28978	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000335016|ENST00000502613	T|.	0.42900|.	0.96|.	5.41|5.41	4.23|4.23	0.50019|0.50019	.|.	0.402320|.	0.26255|.	N|.	0.025437|.	T|.	0.43456|.	0.1248|.	N|N	0.25647|0.25647	0.755|0.755	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|.	0.20174|.	-1.0283|.	10|.	0.16896|.	T|.	0.51|.	-2.3558|-2.3558	9.4132|9.4132	0.38505|0.38505	0.847:0.0:0.153:0.0|0.847:0.0:0.153:0.0	.|.	1003|.	Q9NSY1|.	BMP2K_HUMAN|.	G|W	1003|695	ENSP00000334836:S1003G|.	ENSP00000334836:S1003G|.	S|X	+|+	1|2	0|0	BMP2K|BMP2K	80051732|80051732	0.998000|0.998000	0.40836|0.40836	0.122000|0.122000	0.21767|0.21767	0.676000|0.676000	0.39594|0.39594	3.724000|3.724000	0.54962|0.54962	0.891000|0.891000	0.36235|0.36235	0.397000|0.397000	0.26171|0.26171	AGC|TAG		0.498	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			NM_017593	
CASP8AP2	9994	hgsc.bcm.edu;ucsc.edu	37	6	90577024	90577035	+	RNA	DEL	AAGACTCCAGAG	AAGACTCCAGAG	-	rs78396072|rs369180336		TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	AAGACTCCAGAG	AAGACTCCAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr6:90577024_90577035delAAGACTCCAGAG	ENST00000551025.1	+	0	5452_5463									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GTGGGAGTTAAAGACTCCAGAGAAGCAGCTGC	0.41																																					Colon(187;1656 2025 17045 31481 39901)												0																																												9994			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577024_90577035delAAGACTCCAGAG		Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Del	DEL	ENST00000551025.1	37																																																																																					0.410	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript			NM_001137667	
CELA3A	10136	hgsc.bcm.edu	37	1	22333988	22333988	+	Missense_Mutation	SNP	T	T	G	rs112024506	byFrequency	TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr1:22333988T>G	ENST00000290122.3	+	6	641	c.622T>G	c.(622-624)Tac>Gac	p.Y208D		NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	208	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGCTGGAGGGTACATCCGCTC	0.622													T|||	13	0.00259585	0.0061	0.0043	5008	,	,		20803	0.001		0.0	False		,,,				2504	0.001																0													103.0	98.0	100.0					1																	22333988		2198	4300	6498	SO:0001583	missense	10136			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.622T>G	1.37:g.22333988T>G	ENSP00000290122:p.Tyr208Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	.	.	.	.	.	.	.	.	.	.	T	4.658	0.122419	0.08931	.	.	ENSG00000142789	ENST00000290122;ENST00000400271	D;D	0.88431	-2.38;-2.38	3.7	0.527	0.17084	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.62780	0.2456	N	0.00538	-1.39	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.55198	-0.8178	9	0.02654	T	1	-8.4545	10.6282	0.45521	0.0:0.0:0.5023:0.4977	.	208	P09093	CEL3A_HUMAN	D	208;16	ENSP00000290122:Y208D;ENSP00000383130:Y16D	ENSP00000290122:Y208D	Y	+	1	0	CELA3A	22206575	0.836000	0.29430	0.002000	0.10522	0.026000	0.11368	3.363000	0.52321	-0.070000	0.12908	-0.827000	0.03088	TAC		0.622	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1		NM_005747	
COL17A1	1308	hgsc.bcm.edu	37	10	105816869	105816895	+	In_Frame_Del	DEL	GCCACCAACACCGCCACCTCCTCCACT	GCCACCAACACCGCCACCTCCTCCACT	-	rs61731082|rs375759161|rs139463731|rs150527933|rs114051272|rs566545663|rs200949191|rs567037420|rs805697	byFrequency	TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	GCCACCAACACCGCCACCTCCTCCACT	GCCACCAACACCGCCACCTCCTCCACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr10:105816869_105816895delGCCACCAACACCGCCACCTCCTCCACT	ENST00000353479.5	-	17	1593_1619	c.1303_1329delAGTGGAGGAGGTGGCGGTGTTGGTGGC	c.(1303-1329)agtggaggaggtggcggtgttggtggcdel	p.SGGGGGVGG435del	COL17A1_ENST00000369733.3_In_Frame_Del_p.SGGGGGVGG435del|COL17A1_ENST00000480127.1_5'Flank	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	435	Nonhelical region (NC16).				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		cgccgccagcgccaccaacaccgccacctcctccactgccaccacca	0.639														87	0.0173722	0.0643	0.0029	5008	,	,		20639	0.0		0.0	False		,,,				2504	0.0																0										216,4044		11,194,1925						0.7	0.0			35	3,8251		0,3,4124	no	coding	COL17A1	NM_000494.3		11,197,6049	A1A1,A1R,RR		0.0363,5.0704,1.75				219,12295				SO:0001651	inframe_deletion	1308			M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.1303_1329delAGTGGAGGAGGTGGCGGTGTTGGTGGC	10.37:g.105816869_105816895delGCCACCAACACCGCCACCTCCTCCACT	ENSP00000340937:p.Ser435_Gly443del	Somatic		WXS	Illumina HiSeq	Phase_I	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	In_Frame_Del	DEL	ENST00000353479.5	37	CCDS7554.1																																																																																				0.639	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1		NM_130778, NM_000494	
CSPG4	1464	hgsc.bcm.edu	37	15	75981842	75981854	+	Frame_Shift_Del	DEL	CCTCCAGCACCAG	CCTCCAGCACCAG	-	rs200961060|rs544453239		TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	CCTCCAGCACCAG	CCTCCAGCACCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr15:75981842_75981854delCCTCCAGCACCAG	ENST00000308508.5	-	3	1644_1656	c.1552_1564delCTGGTGCTGGAGG	c.(1552-1566)ctggtgctggaggtgfs	p.LVLEV518fs		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	518	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GTCACCGACACCTCCAGCACCAGCTGGTCGGAG	0.624																																																	0										563,3677		0,563,1557						4.2	1.0			34	65,8119		3,59,4030	no	frameshift	CSPG4	NM_001897.4		3,622,5587	A1A1,A1R,RR		0.7942,13.2783,5.0547				628,11796				SO:0001589	frameshift_variant	1464			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1552_1564delCTGGTGCTGGAGG	15.37:g.75981842_75981854delCCTCCAGCACCAG	ENSP00000312506:p.Leu518fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DW77|Q92675	Frame_Shift_Del	DEL	ENST00000308508.5	37	CCDS10284.1																																																																																				0.624	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1		NM_001897	
CUBN	8029	broad.mit.edu	37	10	16919092	16919092	+	Silent	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr10:16919092A>G	ENST00000377833.4	-	57	8975	c.8910T>C	c.(8908-8910)cgT>cgC	p.R2970R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2970	CUB 22. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.R2970R(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCACAGCGGAACGAGCTGGAA	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											62.0	48.0	53.0					10																	16919092		2203	4300	6503	SO:0001819	synonymous_variant	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8910T>C	10.37:g.16919092A>G		Somatic		WXS	Illumina GAIIx	Phase_I	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.453	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1		NM_001081	
FGD1	2245	broad.mit.edu	37	X	54475272	54475272	+	Silent	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chrX:54475272C>T	ENST00000375135.3	-	16	3136	c.2403G>A	c.(2401-2403)caG>caA	p.Q801Q		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	801					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.Q801Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGGGTGTATGCTGGCTGCAGG	0.612																																																	1	Substitution - coding silent(1)	kidney(1)											53.0	44.0	47.0					X																	54475272		2203	4300	6503	SO:0001819	synonymous_variant	2245			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3663	protein-coding gene	gene with protein product		300546	"""faciogenital dysplasia (Aarskog-Scott syndrome)"""	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.2403G>A	X.37:g.54475272C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q5H999|Q8N4D9	Silent	SNP	ENST00000375135.3	37	CCDS14359.1																																																																																				0.612	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1		NM_004463	
GLI3	2737	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	42116424	42116424	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr7:42116424G>A	ENST00000395925.3	-	4	484	c.400C>T	c.(400-402)Cct>Tct	p.P134S	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	134					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P134S(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						ATTGGTACAGGAGGATGGAAG	0.418									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																								1	Substitution - Missense(1)	kidney(1)											139.0	119.0	126.0					7																	42116424		2203	4300	6503	SO:0001583	missense	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.400C>T	7.37:g.42116424G>A	ENSP00000379258:p.Pro134Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843200	0.91197	.	.	ENSG00000106571	ENST00000395925;ENST00000448703	T;T	0.75821	-0.97;-0.97	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.86091	0.5850	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.86392	0.1736	10	0.87932	D	0	.	20.0781	0.97751	0.0:0.0:1.0:0.0	.	134	P10071	GLI3_HUMAN	S	134	ENSP00000379258:P134S;ENSP00000406135:P134S	ENSP00000379258:P134S	P	-	1	0	GLI3	42082949	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.174000	0.94824	2.817000	0.96982	0.563000	0.77884	CCT		0.418	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3		NM_000168	
GMPR	2766	hgsc.bcm.edu	37	6	16295417	16295418	+	Stop_Codon_Ins	INS	-	-	C	rs201015786	byFrequency	TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr6:16295417_16295418insC	ENST00000259727.4	+	0	1152_1153				GMPR_ENST00000544145.1_3'UTR	NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase						nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TGTTCAGCTAACCCTGGGGACA	0.599													CCC|CCC|CCCC|insertion	34	0.00678914	0.0242	0.0029	5008	,	,		17263	0.0		0.0	False		,,,				2504	0.0																0										102,4162		0,102,2030						4.7	0.9			62	2,8252		0,2,4125	no	frameshift	GMPR	NM_006877.3		0,104,6155	A1A1,A1R,RR		0.0242,2.3921,0.8308				104,12414				SO:0001567	stop_retained_variant	2766				CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.1038dupC	6.37:g.16295420_16295420dupC		Somatic		WXS	Illumina HiSeq	Phase_I	Q96HQ6	Frame_Shift_Ins	INS	ENST00000259727.4	37	CCDS4537.1																																																																																				0.599	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2			
IARS	3376	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	95012199	95012199	+	Missense_Mutation	SNP	T	T	A			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr9:95012199T>A	ENST00000375643.3	-	25	2823	c.2557A>T	c.(2557-2559)Atc>Ttc	p.I853F	IARS_ENST00000447699.2_Missense_Mutation_p.I743F|IARS_ENST00000443024.2_Missense_Mutation_p.I853F|IARS_ENST00000375629.3_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	853					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)	p.I853F(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	TCTTGATGGATAACCACAATT	0.368																																																	1	Substitution - Missense(1)	kidney(1)											122.0	130.0	127.0					9																	95012199		2203	4299	6502	SO:0001583	missense	3376			AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.2557A>T	9.37:g.95012199T>A	ENSP00000364794:p.Ile853Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.719535	0.89205	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660;ENST00000449893	T;T;T	0.11277	2.79;2.79;2.79	5.88	5.88	0.94601	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.33323	0.0859	M	0.74258	2.255	0.80722	D	1	P;B;D	0.71674	0.815;0.353;0.998	P;B;D	0.70487	0.755;0.11;0.969	T	0.02167	-1.1202	10	0.46703	T	0.11	-22.1945	15.9512	0.79840	0.0:0.0:0.0:1.0	.	363;853;698	F5H1M4;P41252;Q6P0M4	.;SYIC_HUMAN;.	F	853;853;743;853;85	ENSP00000364794:I853F;ENSP00000406448:I853F;ENSP00000415020:I743F	ENSP00000364794:I853F	I	-	1	0	IARS	94052020	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.513000	0.81739	2.250000	0.74265	0.482000	0.46254	ATC		0.368	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2		NM_002161	
IARS	3376	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	95012201	95012201	+	Missense_Mutation	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr9:95012201A>G	ENST00000375643.3	-	25	2821	c.2555T>C	c.(2554-2556)gTt>gCt	p.V852A	IARS_ENST00000447699.2_Missense_Mutation_p.V742A|IARS_ENST00000443024.2_Missense_Mutation_p.V852A|IARS_ENST00000375629.3_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	852					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)	p.V852A(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	TTGATGGATAACCACAATTTC	0.368																																																	1	Substitution - Missense(1)	kidney(1)											120.0	128.0	125.0					9																	95012201		2203	4299	6502	SO:0001583	missense	3376			AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.2555T>C	9.37:g.95012201A>G	ENSP00000364794:p.Val852Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	A	32	5.165010	0.94727	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660;ENST00000449893	T;T;T	0.13657	2.57;2.57;2.57	5.88	5.88	0.94601	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.051556	0.85682	D	0.000000	T	0.48466	0.1501	M	0.92923	3.36	0.80722	D	1	D;P;D	0.89917	1.0;0.93;0.965	D;P;P	0.85130	0.997;0.768;0.893	T	0.60586	-0.7234	10	0.72032	D	0.01	-18.0247	15.9512	0.79840	1.0:0.0:0.0:0.0	.	362;852;697	F5H1M4;P41252;Q6P0M4	.;SYIC_HUMAN;.	A	852;852;742;852;84	ENSP00000364794:V852A;ENSP00000406448:V852A;ENSP00000415020:V742A	ENSP00000364794:V852A	V	-	2	0	IARS	94052022	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	8.739000	0.91574	2.250000	0.74265	0.482000	0.46254	GTT		0.368	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2		NM_002161	
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																																	0																																												650368					11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000529482.1	37																																																																																					0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			
LGR4	55366	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	27390552	27390552	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr11:27390552G>A	ENST00000379214.4	-	18	2161	c.1718C>T	c.(1717-1719)tCc>tTc	p.S573F	LGR4_ENST00000389858.4_Missense_Mutation_p.S549F	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	573					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.S573F(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AAACAATTTGGACGAAGGCAG	0.378																																																	1	Substitution - Missense(1)	kidney(1)											79.0	78.0	78.0					11																	27390552		2202	4299	6501	SO:0001583	missense	55366			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1718C>T	11.37:g.27390552G>A	ENSP00000368516:p.Ser573Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.349799	0.41599	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	D;D	0.85773	-2.03;-2.03	5.9	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.113777	0.64402	D	0.000008	D	0.84120	0.5402	L	0.40543	1.245	0.80722	D	1	P;P	0.46784	0.812;0.884	P;P	0.48030	0.465;0.564	D	0.85321	0.1084	10	0.56958	D	0.05	.	16.2511	0.82489	0.0:0.244:0.756:0.0	.	549;573	G5E9B3;Q9BXB1	.;LGR4_HUMAN	F	573;549	ENSP00000368516:S573F;ENSP00000374508:S549F	ENSP00000368516:S573F	S	-	2	0	LGR4	27347128	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	5.621000	0.67743	2.797000	0.96272	0.650000	0.86243	TCC		0.378	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1		NM_018490	
IGLV7-46	28775	broad.mit.edu	37	22	22724315	22724315	+	RNA	SNP	G	G	C			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr22:22724315G>C	ENST00000390295.2	+	0	245									immunoglobulin lambda variable 7-46 (gene/pseudogene)																		ACTGATTTATGATACAAGCAA	0.577																																																	0													50.0	51.0	51.0					22																	22724315		1887	4114	6001			96610			Z73674		22q11.2	2012-02-08	2008-09-12		ENSG00000211649	ENSG00000211649		"""Immunoglobulins / IGL locus"""	5930	other	immunoglobulin gene			"""immunoglobulin lambda variable 7-46"""				Standard	NG_000002		Approved				OTTHUMG00000151040		22.37:g.22724315G>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000390295.2	37																																																																																					0.577	IGLV7-46-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000321099.1		NG_000002	
MAP4K3	8491	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	39519948	39519948	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr2:39519948C>A	ENST00000263881.3	-	18	1561	c.1237G>T	c.(1237-1239)Gaa>Taa	p.E413*	MAP4K3_ENST00000437545.1_Nonsense_Mutation_p.E329*|MAP4K3_ENST00000341681.5_Nonsense_Mutation_p.E392*|MAP4K3_ENST00000536018.1_5'UTR|MAP4K3_ENST00000474502.1_5'UTR	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	413					intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.E413*(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				TCATCATCTTCTAAATGTGCG	0.318																																																	1	Substitution - Nonsense(1)	kidney(1)											156.0	162.0	160.0					2																	39519948		2203	4300	6503	SO:0001587	stop_gained	8491			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1237G>T	2.37:g.39519948C>A	ENSP00000263881:p.Glu413*	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Nonsense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	C	38	7.069456	0.98040	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	.	.	.	5.42	5.42	0.78866	.	0.376422	0.32081	N	0.006615	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	19.5655	0.95391	0.0:1.0:0.0:0.0	.	.	.	.	X	413;329;392	.	ENSP00000263881:E413X	E	-	1	0	MAP4K3	39373452	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.690000	0.61731	2.691000	0.91804	0.591000	0.81541	GAA		0.318	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2		NM_003618	
MBP	4155	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	74728852	74728852	+	Missense_Mutation	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr18:74728852A>G	ENST00000397869.3	-	1	159	c.113T>C	c.(112-114)aTc>aCc	p.I38T	MBP_ENST00000528160.1_Intron|MBP_ENST00000397860.3_Missense_Mutation_p.I171T|MBP_ENST00000579129.1_Missense_Mutation_p.I171T|MBP_ENST00000526111.1_Missense_Mutation_p.I16T|MBP_ENST00000397863.1_Missense_Mutation_p.I171T|MBP_ENST00000355994.2_Missense_Mutation_p.I171T|MBP_ENST00000578193.1_Missense_Mutation_p.I38T|MBP_ENST00000487778.1_5'Flank|MBP_ENST00000359645.3_Missense_Mutation_p.I38T|MBP_ENST00000382582.3_Missense_Mutation_p.I38T|MBP_ENST00000397875.3_Missense_Mutation_p.I38T|MBP_ENST00000397865.5_Missense_Mutation_p.I38T|MBP_ENST00000397866.4_Missense_Mutation_p.I38T|MBP_ENST00000527041.1_Missense_Mutation_p.I38T|MBP_ENST00000580402.1_Missense_Mutation_p.I171T|MBP_ENST00000354542.4_Missense_Mutation_p.I38T			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)	p.I171T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	GGAGTCAAGGATGCCCGTGTC	0.582																																					NSCLC(17;72 1131 19392)												1	Substitution - Missense(1)	kidney(1)											85.0	72.0	77.0					18																	74728852		2203	4300	6503	SO:0001583	missense	4155				CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.113T>C	18.37:g.74728852A>G	ENSP00000380967:p.Ile38Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000397869.3	37		.	.	.	.	.	.	.	.	.	.	A	24.7	4.556444	0.86231	.	.	ENSG00000197971	ENST00000382582;ENST00000355994;ENST00000397875;ENST00000397866;ENST00000397865;ENST00000527041;ENST00000359645;ENST00000397869;ENST00000354542;ENST00000526111;ENST00000397868;ENST00000498683;ENST00000397863;ENST00000397860	.	.	.	5.22	5.22	0.72569	.	0.425516	0.23935	N	0.043102	T	0.69975	0.3171	L	0.47716	1.5	0.37317	D	0.909379	D;D;D;P;P;P	0.63046	0.992;0.987;0.992;0.846;0.848;0.848	D;D;P;B;P;P	0.72982	0.93;0.979;0.743;0.332;0.614;0.772	T	0.76225	-0.3037	9	0.72032	D	0.01	-17.5991	15.1357	0.72562	1.0:0.0:0.0:0.0	.	38;171;171;38;38;38	B7Z3Y6;P02686;P02686-2;P02686-6;P02686-4;P02686-3	.;MBP_HUMAN;.;.;.;.	T	38;171;38;38;38;38;38;38;38;16;38;38;171;171	.	ENSP00000346545:I38T	I	-	2	0	MBP	72857840	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.481000	0.73608	1.971000	0.57363	0.533000	0.62120	ATC		0.582	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1		NM_001025081	
NFXL1	152518	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	47850290	47850290	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr4:47850290C>T	ENST00000507489.1	-	23	2802	c.2626G>A	c.(2626-2628)Gaa>Aaa	p.E876K	NFXL1_ENST00000381538.3_Missense_Mutation_p.E876K	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	876						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E876K(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						ACTGCCACTTCATCTCTTTTC	0.373																																																	1	Substitution - Missense(1)	kidney(1)											171.0	159.0	163.0					4																	47850290		2203	4300	6503	SO:0001583	missense	152518			AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"""ovarian zinc finger protein"""						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.2626G>A	4.37:g.47850290C>T	ENSP00000422037:p.Glu876Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	37	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	C	18.85	3.711815	0.68730	.	.	ENSG00000170448	ENST00000381538;ENST00000507489	T;T	0.23348	1.91;1.91	5.9	5.9	0.94986	.	0.078336	0.53938	D	0.000058	T	0.30572	0.0769	L	0.57536	1.79	0.80722	D	1	B	0.18863	0.031	B	0.11329	0.006	T	0.03148	-1.1067	10	0.30078	T	0.28	-15.4253	19.8812	0.96900	0.0:1.0:0.0:0.0	.	876	Q6ZNB6	NFXL1_HUMAN	K	876	ENSP00000370949:E876K;ENSP00000422037:E876K	ENSP00000370949:E876K	E	-	1	0	NFXL1	47545047	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	5.827000	0.69300	2.786000	0.95864	0.650000	0.86243	GAA		0.373	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1		NM_152995	
PPARG	5468	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	12422837	12422837	+	Silent	SNP	G	G	A			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr3:12422837G>A	ENST00000287820.6	+	3	448	c.327G>A	c.(325-327)gaG>gaA	p.E109E	PPARG_ENST00000397026.2_Silent_p.E87E|PPARG_ENST00000397012.2_Silent_p.E81E|PPARG_ENST00000309576.6_Silent_p.E81E|PPARG_ENST00000397010.2_Silent_p.E81E|PPARG_ENST00000397000.1_Silent_p.E81E|PPARG_ENST00000397015.2_Silent_p.E81E|PPARG_ENST00000539812.1_Silent_p.E79E	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	109					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|brown fat cell differentiation (GO:0050873)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|cellular response to lithium ion (GO:0071285)|epithelial cell differentiation (GO:0030855)|fatty acid oxidation (GO:0019395)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|innate immune response (GO:0045087)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|lipoprotein transport (GO:0042953)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle receptor biosynthetic process (GO:0045713)|monocyte differentiation (GO:0030224)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of cell growth (GO:0030308)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ regeneration (GO:0031100)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|placenta development (GO:0001890)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood pressure (GO:0008217)|regulation of cholesterol transporter activity (GO:0060694)|regulation of transcription involved in cell fate commitment (GO:0060850)|response to caffeine (GO:0031000)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to lipid (GO:0033993)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|arachidonic acid binding (GO:0050544)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|prostaglandin receptor activity (GO:0004955)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region DNA binding (GO:0001012)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.E109E(1)	PAX8/PPARG(117)	breast(2)|endometrium(4)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20					Balsalazide(DB01014)|Bezafibrate(DB01393)|Glipizide(DB01067)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Mesalazine(DB00244)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rosiglitazone(DB00412)|Sulfasalazine(DB00795)|Telmisartan(DB00966)	TCAAAGTGGAGCCTGCATCTC	0.453			T	PAX8	follicular thyroid		"""Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"""																																	Dom	yes		3	3p25	5468	"""peroxisome proliferative activated receptor, gamma"""	yes	E	1	Substitution - coding silent(1)	kidney(1)											67.0	63.0	64.0					3																	12422837		2203	4300	6503	SO:0001819	synonymous_variant	5468			X90563	CCDS2609.1, CCDS2610.2	3p25	2013-01-16	2006-10-17		ENSG00000132170	ENSG00000132170		"""Nuclear hormone receptors"""	9236	protein-coding gene	gene with protein product		601487	"""peroxisome proliferative activated receptor, gamma"""			7862171, 9750197	Standard	NM_005037		Approved	PPARG1, PPARG2, NR1C3, PPARgamma	uc003bwx.3	P37231	OTTHUMG00000129764	ENST00000287820.6:c.327G>A	3.37:g.12422837G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Silent	SNP	ENST00000287820.6	37	CCDS2609.1																																																																																				0.453	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2		NM_005037	
PPP2R2C	5522	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	6349697	6349697	+	Silent	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr4:6349697C>T	ENST00000382599.4	-	6	882	c.666G>A	c.(664-666)acG>acA	p.T222T	PPP2R2C_ENST00000507294.1_Silent_p.T215T|PPP2R2C_ENST00000515571.1_Silent_p.T205T|PPP2R2C_ENST00000335585.5_Silent_p.T222T|PPP2R2C_ENST00000506140.1_Silent_p.T215T|PPP2R2C_ENST00000314348.8_5'UTR			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	222					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.T222T(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						TGATCACCTCCGTAAGGTCCT	0.622																																																	1	Substitution - coding silent(1)	kidney(1)											260.0	186.0	211.0					4																	6349697		2203	4300	6503	SO:0001819	synonymous_variant	5522			AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9306	protein-coding gene	gene with protein product	"""PP2A subunit B isoform gamma"""	605997	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"""			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.666G>A	4.37:g.6349697C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Silent	SNP	ENST00000382599.4	37																																																																																					0.622	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2		NM_181876	
SETBP1	26040	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	42531246	42531246	+	Silent	SNP	A	A	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr18:42531246A>G	ENST00000282030.5	+	4	2237	c.1941A>G	c.(1939-1941)aaA>aaG	p.K647K		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	647						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K593K(1)|p.K647K(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GCGAGATGAAATTTCACAAGA	0.448									Schinzel-Giedion syndrome																																								2	Substitution - coding silent(2)	kidney(2)											53.0	46.0	48.0					18																	42531246		2187	4267	6454	SO:0001819	synonymous_variant	26040	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.1941A>G	18.37:g.42531246A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																				0.448	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4		NM_001130110	
SLITRK6	84189	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	86370304	86370304	+	Silent	SNP	G	G	A			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr13:86370304G>A	ENST00000400286.2	-	2	938	c.340C>T	c.(340-342)Ctg>Ttg	p.L114L		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	114					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.L114L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		AGTTGTTTCAGGAGGCCAAGG	0.358																																																	1	Substitution - coding silent(1)	kidney(1)											126.0	117.0	120.0					13																	86370304		1840	4088	5928	SO:0001819	synonymous_variant	84189			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.340C>T	13.37:g.86370304G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Silent	SNP	ENST00000400286.2	37	CCDS41903.1																																																																																				0.358	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2		NM_032229	
SNHG14	104472715	broad.mit.edu;hgsc.bcm.edu	37	15	25331751	25331751	+	RNA	SNP	G	G	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr15:25331751G>T	ENST00000546682.1	+	0	453				SNORD116-18_ENST00000383961.1_RNA|SNORD116-19_ENST00000384729.1_RNA|SNORD116-17_ENST00000383929.1_RNA|SNHG14_ENST00000553108.1_RNA|SNORD116-20_ENST00000384529.1_lincRNA|SNORD116-20_ENST00000384507.1_lincRNA|SNHG14_ENST00000549804.2_RNA	NR_003361.1				small nucleolar RNA host gene 14 (non-protein coding)																		CGTCATCCTCGTCGAACTGAG	0.468																																																	0													263.0	236.0	244.0					15																	25331751		876	1991	2867			100033429					15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25331751G>T		Somatic		WXS	Illumina HiSeq	Phase_I		RNA	SNP	ENST00000546682.1	37																																																																																					0.468	SNHG14-022	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000408281.1			
SRGAP3	9901	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	9034602	9034602	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr3:9034602C>T	ENST00000383836.3	-	20	2973	c.2546G>A	c.(2545-2547)gGg>gAg	p.G849E	SRGAP3_ENST00000360413.3_Missense_Mutation_p.G825E	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	849					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.G849E(1)	SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GCCCATCACCCCCCCAAAGCC	0.552			T	RAF1	pilocytic astrocytoma																																			Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	1	Substitution - Missense(1)	kidney(1)											85.0	81.0	82.0					3																	9034602		2203	4300	6503	SO:0001583	missense	9901			AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2546G>A	3.37:g.9034602C>T	ENSP00000373347:p.Gly849Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390298	0.82902	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.22945	1.93;2.34	5.17	5.17	0.71159	.	0.057605	0.64402	D	0.000001	T	0.36771	0.0979	L	0.40543	1.245	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.65443	0.935;0.863	T	0.05484	-1.0882	10	0.02654	T	1	.	18.2651	0.90050	0.0:1.0:0.0:0.0	.	825;849	O43295-2;O43295	.;SRGP2_HUMAN	E	849;825	ENSP00000373347:G849E;ENSP00000353587:G825E	ENSP00000353587:G825E	G	-	2	0	SRGAP3	9009602	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.930000	0.56522	2.410000	0.81850	0.591000	0.81541	GGG		0.552	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			
TCEB1	6921	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	74858967	74858968	+	Missense_Mutation	DNP	GT	GT	TA			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G|T	G|T	G|T	T|A	G|T	G|T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr8:74858967_74858968GT>TA	ENST00000522337.1	-	5	555_556	c.236_237AC>TA	c.(235-237)tAC>tTA	p.Y79L	TCEB1_ENST00000519487.1_Missense_Mutation_p.Y79L|TCEB1_ENST00000523815.1_Missense_Mutation_p.Y79L|TCEB1_ENST00000284811.8_Missense_Mutation_p.Y79L|TCEB1_ENST00000520210.1_Missense_Mutation_p.Y63L|TCEB1_ENST00000520242.1_Missense_Mutation_p.Y79L|TCEB1_ENST00000518127.1_Missense_Mutation_p.Y79L|TCEB1_ENST00000602840.1_Intron			Q15369	ELOC_HUMAN	transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)	79					cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.Y79F(1)|p.Y79L(1)|p.Y79*(1)		endometrium(2)|kidney(3)|lung(1)|prostate(1)	7	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)			AGCGAACCTTGTACGTAAAATA	0.411																																																	3	Substitution - Missense(2)|Substitution - Nonsense(1)	kidney(3)																																								SO:0001583	missense	6921			L34587	CCDS34910.1, CCDS56539.1	8q13.3	2010-04-21	2002-08-29		ENSG00000154582	ENSG00000154582			11617	protein-coding gene	gene with protein product		600788	"""transcription elongation factor B (SIII), polypeptide 1 (15kD, elongin C)"""			7821821, 7660122	Standard	NM_005648		Approved	SIII	uc003xzx.2	Q15369	OTTHUMG00000164501	ENST00000522337.1:c.236_237delinsTA	8.37:g.74858967_74858968delinsTA	ENSP00000429906:p.Tyr79Leu	Somatic		WXS	Illumina HiSeq	Phase_I	E5RGD9|Q567Q6	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000522337.1	37	CCDS34910.1																																																																																				0.411	TCEB1-010	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000379020.1		NM_005648	
TP53BP1	7158	hgsc.bcm.edu;ucsc.edu	37	15	43712740	43712741	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr15:43712740_43712741delAG	ENST00000263801.3	-	21	4680_4681	c.4428_4429delCT	c.(4426-4431)ggcttafs	p.L1477fs	TP53BP1_ENST00000382044.4_Frame_Shift_Del_p.L1482fs|TP53BP1_ENST00000450115.2_Frame_Shift_Del_p.L1482fs|TP53BP1_ENST00000382039.3_Frame_Shift_Del_p.L1432fs	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1477					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GAGGCATCTAAGCCATCAGAAG	0.515								Other conserved DNA damage response genes																																									0																																										SO:0001589	frameshift_variant	7158			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.4428_4429delCT	15.37:g.43712740_43712741delAG	ENSP00000263801:p.Leu1477fs	Somatic		WXS	Illumina HiSeq	Phase_I	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Frame_Shift_Del	DEL	ENST00000263801.3	37	CCDS10096.1																																																																																				0.515	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			
USO1	8615	hgsc.bcm.edu;ucsc.edu	37	4	76722353	76722353	+	Splice_Site	SNP	G	G	A	rs324726	byFrequency	TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr4:76722353G>A	ENST00000538159.1	+	18	2013	c.2013G>A	c.(2011-2013)caG>caA	p.Q671Q	USO1_ENST00000514213.2_Splice_Site_p.Q647Q			O60763	USO1_HUMAN	USO1 vesicle transport factor	662					ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi vesicle docking (GO:0048211)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|mitotic cell cycle (GO:0000278)|transcytosis (GO:0045056)|vesicle fusion with Golgi apparatus (GO:0048280)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TTCGAGAGCAGGTAAGTACTA	0.338													A|||	3268	0.652556	0.3449	0.768	5008	,	,		17749	0.8859		0.7604	False		,,,				2504	0.635																0								A		1400,2288		284,832,728	78.0	70.0	72.0		1863	1.2	1.0	4	dbSNP_79	72	6089,2101		2272,1545,278	yes	coding-synonymous-near-splice	USO1	NM_003715.2		2556,2377,1006	AA,AG,GG		25.6532,37.961,36.9507		621/922	76722353	7489,4389	1844	4095	5939	SO:0001630	splice_region_variant	8615			AL832010	CCDS75144.1	4q21.1	2012-12-10	2012-12-10		ENSG00000138768	ENSG00000138768			30904	protein-coding gene	gene with protein product	"""vesicle docking protein"", ""transcytosis associated protein"""	603344	"""USO1 homolog, vesicle docking protein (yeast)"", ""USO1 vesicle docking protein homolog (yeast)"""			9478999, 9150144, 12077354, 15979508, 14736916	Standard	XM_006714395		Approved	TAP, VDP, p115	uc003hiu.3	O60763	OTTHUMG00000160952	ENST00000538159.1:c.2013+1G>A	4.37:g.76722353G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RAQ0|Q6PK63|Q86TB8|Q8N592	Missense_Mutation	SNP	ENST00000538159.1	37		1547	0.7083333333333334	167	0.3394308943089431	286	0.7900552486187845	514	0.8986013986013986	580	0.7651715039577837	A	10.02	1.235310	0.22626	0.37961	0.743468	ENSG00000138768	ENST00000441296	.	.	.	5.61	1.24	0.21308	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23404	-1.0189	3	.	.	.	.	14.5499	0.68059	0.1641:0.0:0.8359:0.0	rs324726;rs1802533;rs11566527;rs13150865;rs17000888;rs324726	.	.	.	K	338	.	.	R	+	2	0	USO1	76941377	1.000000	0.71417	0.956000	0.39512	0.876000	0.50452	2.553000	0.45837	-0.361000	0.08125	-0.360000	0.07572	AGG		0.338	USO1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_003715	Silent
YLPM1	56252	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	75230960	75230960	+	Missense_Mutation	SNP	T	T	G			TCGA-B8-5545-01A-01D-1669-08	TCGA-B8-5545-10A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	514d2342-64ba-4c9f-9866-63bdbc26fda3	887f29fa-dc06-49d0-8b25-00dbdc7016a6	g.chr14:75230960T>G	ENST00000552421.1	+	1	892	c.768T>G	c.(766-768)aaT>aaG	p.N256K	YLPM1_ENST00000238571.3_Missense_Mutation_p.N256K|YLPM1_ENST00000325680.7_Missense_Mutation_p.N256K			P49750	YLPM1_HUMAN	YLP motif containing 1	256					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.N256K(2)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CCCCTGGAAATAAGACAACTG	0.572																																																	2	Substitution - Missense(2)	kidney(2)											58.0	62.0	61.0					14																	75230960		1893	4121	6014	SO:0001583	missense	56252			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.768T>G	14.37:g.75230960T>G	ENSP00000447921:p.Asn256Lys	Somatic		WXS	Illumina HiSeq	Phase_I	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	37		.	.	.	.	.	.	.	.	.	.	T	1.537	-0.542820	0.04053	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571	T;T;T	0.21191	2.02;2.02;2.02	4.31	3.15	0.36227	.	0.527792	0.17390	N	0.175967	T	0.07548	0.0190	N	0.08118	0	0.19575	N	0.999969	B	0.11235	0.004	B	0.14023	0.01	T	0.35847	-0.9772	10	0.09843	T	0.71	-2.0835	2.6731	0.05073	0.2273:0.1257:0.0:0.647	.	256	P49750-4	.	K	256	ENSP00000447921:N256K;ENSP00000324463:N256K;ENSP00000238571:N256K	ENSP00000238571:N256K	N	+	3	2	YLPM1	74300713	0.998000	0.40836	1.000000	0.80357	0.009000	0.06853	0.717000	0.25851	1.801000	0.52704	0.533000	0.62120	AAT		0.572	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1		NM_019589	
