#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_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	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
MPL	4352	broad.mit.edu	37	1	43804269	43804269	+	Missense_Mutation	SNP	G	G	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr1:43804269G>A	ENST00000372470.3	+	3	311	c.269G>A	c.(268-270)cGa>cAa	p.R90Q	MPL_ENST00000413998.2_Missense_Mutation_p.R90Q	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	90					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	TTTGGAACCCGATACGTGTGC	0.572			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)	uc001ciw.2			yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	Mis	"""myeloproliferative leukemia virus oncogene, thrombopoietin receptor"""	yes	congenital amegakaryocytic thrombocytopenia	L		MPD	MPD		0				haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1)	363						c.(268-270)CGA>CAA		myeloproliferative leukemia virus oncogene							113.0	98.0	103.0					1																	43804269		2203	4300	6503	SO:0001583	missense	4352				cell proliferation|platelet activation	integral to plasma membrane	cytokine receptor activity	g.chr1:43804269G>A	M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"""CD molecules"", ""Fibronectin type III domain containing"""	7217	protein-coding gene	gene with protein product		159530	"""myeloproliferative leukemia virus oncogene"""			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.269G>A	1.37:g.43804269G>A	ENSP00000361548:p.Arg90Gln					MPL_uc001civ.2_Missense_Mutation_p.R90Q|MPL_uc009vwr.2_Missense_Mutation_p.R83Q	p.R90Q	NM_005373	NP_005364	P40238	TPOR_HUMAN			3	314	+	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)	90			Extracellular (Potential).		Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	c.269G>A	CCDS483.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.987773	0.53934	.	.	ENSG00000117400	ENST00000372468;ENST00000372470;ENST00000413998	T;T	0.69685	-0.42;-0.42	5.59	4.68	0.58851	Fibronectin, type III (1);Growth hormone/erythropoietin receptor, ligand binding (1);Immunoglobulin-like fold (1);	0.131328	0.51477	N	0.000083	T	0.78861	0.4350	M	0.73598	2.24	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.996;0.997	T	0.69491	-0.5131	10	0.36615	T	0.2	-8.7946	10.5558	0.45117	0.0892:0.0:0.9108:0.0	.	83;90;90	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	Q	90	ENSP00000361548:R90Q;ENSP00000414004:R90Q	ENSP00000361546:R90Q	R	+	2	0	MPL	43576856	0.731000	0.28111	0.040000	0.18447	0.403000	0.30841	3.493000	0.53266	1.367000	0.46095	0.557000	0.71058	CGA		0.572	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373	
RUSC1	23623	broad.mit.edu	37	1	155291139	155291139	+	Intron	SNP	G	G	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr1:155291139G>A	ENST00000368352.5	+	2	65				RUSC1_ENST00000368347.4_5'Flank|RUSC1_ENST00000368354.3_Intron|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			TCCTCTGGGAGTAAGGGGTAG	0.647																																						uc001fki.2																			0					0						c.(139-141)TAC>TAT		hypothetical protein LOC284618							18.0	19.0	18.0					1																	155291139		1855	4090	5945	SO:0001627	intron_variant	284618							g.chr1:155291139G>A	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-86-340G>A	1.37:g.155291139G>A						RAG1AP1_uc010pey.1_Intron|C1orf104_uc001fkh.1_RNA|RUSC1_uc001fkj.2_Intron|RUSC1_uc001fkk.2_Intron|RUSC1_uc009wqn.1_5'Flank|RUSC1_uc009wqo.1_5'Flank|RUSC1_uc001fkl.2_5'Flank	p.Y47Y	NM_001039517	NP_001034606	Q66K80	RUAS1_HUMAN	Epithelial(20;1.32e-10)|all cancers(21;3.51e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		2	418	-	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		47					B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	37	c.141C>T	CCDS41410.1																																																																																				0.647	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1		
SPTA1	6708	broad.mit.edu	37	1	158617395	158617395	+	Missense_Mutation	SNP	C	C	T	rs201407861		TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr1:158617395C>T	ENST00000368147.4	-	27	4010	c.3830G>A	c.(3829-3831)cGt>cAt	p.R1277H		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1277					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.R1277L(2)|p.R1277H(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ATCCTTTGTACGCCCCTGCAG	0.557																																						uc001fst.1																			3	Substitution - Missense(3)		lung(2)|large_intestine(1)	ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8						c.(3829-3831)CGT>CAT		spectrin, alpha, erythrocytic 1		C	HIS/ARG	1,3951		0,1,1975	115.0	116.0	115.0		3830	-5.2	0.0	1		115	0,8294		0,0,4147	yes	missense	SPTA1	NM_003126.2	29	0,1,6122	TT,TC,CC		0.0,0.0253,0.0082	benign	1277/2420	158617395	1,12245	1976	4147	6123	SO:0001583	missense	6708				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	g.chr1:158617395C>T	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3830G>A	1.37:g.158617395C>T	ENSP00000357129:p.Arg1277His						p.R1277H	NM_003126	NP_003117	P02549	SPTA1_HUMAN			27	4029	-	all_hematologic(112;0.0378)		1277			Spectrin 12.		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	c.3830G>A	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	7.837	0.721030	0.15372	2.53E-4	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52295	0.67;0.67	4.43	-5.2	0.02823	.	.	.	.	.	T	0.14141	0.0342	L	0.39397	1.21	0.09310	N	1	B	0.16396	0.017	B	0.18561	0.022	T	0.32929	-0.9888	9	0.49607	T	0.09	.	6.0835	0.19954	0.5503:0.2286:0.0:0.221	.	1277	P02549	SPTA1_HUMAN	H	1277	ENSP00000357130:R1277H;ENSP00000357129:R1277H	ENSP00000357129:R1277H	R	-	2	0	SPTA1	156884019	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.152000	0.16302	-1.269000	0.02436	0.563000	0.77884	CGT		0.557	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CEP350	9857	broad.mit.edu	37	1	179989186	179989186	+	Silent	SNP	C	C	G			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr1:179989186C>G	ENST00000367607.3	+	12	2695	c.2277C>G	c.(2275-2277)ctC>ctG	p.L759L		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	759					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						GAAGTTTACTCTCCCATCTCT	0.403																																						uc001gnt.2																			0				ovary(4)	4						c.(2275-2277)CTC>CTG		centrosome-associated protein 350							137.0	139.0	139.0					1																	179989186		2203	4300	6503	SO:0001819	synonymous_variant	9857					centrosome|nucleus|spindle		g.chr1:179989186C>G	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.2277C>G	1.37:g.179989186C>G						CEP350_uc009wxl.2_Silent_p.L758L|CEP350_uc001gnu.2_Silent_p.L593L	p.L759L	NM_014810	NP_055625	Q5VT06	CE350_HUMAN			12	2660	+			759					O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	c.2277C>G	CCDS1336.1																																																																																				0.403	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
OR5F1	338674	broad.mit.edu	37	11	55761884	55761884	+	Missense_Mutation	SNP	T	T	G			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr11:55761884T>G	ENST00000278409.1	-	1	217	c.218A>C	c.(217-219)aAc>aCc	p.N73T		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	73					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					GGTAGTTGAGTTACAAACGTC	0.443																																						uc010riv.1																			0				ovary(1)|pancreas(1)	2						c.(217-219)AAC>ACC		olfactory receptor, family 5, subfamily F,							63.0	60.0	61.0					11																	55761884		2201	4296	6497	SO:0001583	missense	338674				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55761884T>G	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.218A>C	11.37:g.55761884T>G	ENSP00000278409:p.Asn73Thr						p.N73T	NM_003697	NP_003688	O95221	OR5F1_HUMAN			1	218	-	Esophageal squamous(21;0.00448)		73			Helical; Name=2; (Potential).		Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	c.218A>C	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	T	1.759	-0.487347	0.04352	.	.	ENSG00000149133	ENST00000278409	T	0.01335	5.0	3.03	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	N	0.02751	-0.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48559	-0.9025	9	0.87932	D	0	.	2.7854	0.05372	0.2237:0.131:0.0:0.6453	.	73	O95221	OR5F1_HUMAN	T	73	ENSP00000278409:N73T	ENSP00000278409:N73T	N	-	2	0	OR5F1	55518460	0.000000	0.05858	0.079000	0.20413	0.051000	0.14879	-0.011000	0.12721	1.167000	0.42706	0.247000	0.18012	AAC		0.443	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
RFX4	5992	broad.mit.edu	37	12	107048021	107048021	+	Nonsense_Mutation	SNP	T	T	G			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr12:107048021T>G	ENST00000392842.1	+	4	621	c.207T>G	c.(205-207)taT>taG	p.Y69*	RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Nonsense_Mutation_p.Y78*	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	69					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						AGGAGAACTATGAGATTGCAG	0.488																																						uc001tlr.2																			0				upper_aerodigestive_tract(1)	1						c.(205-207)TAT>TAG		regulatory factor X4 isoform c							111.0	111.0	111.0					12																	107048021		2203	4300	6503	SO:0001587	stop_gained	5992				transcription, DNA-dependent	nucleus	DNA binding	g.chr12:107048021T>G	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.207T>G	12.37:g.107048021T>G	ENSP00000376585:p.Tyr69*					RFX4_uc010swv.1_RNA|RFX4_uc001tls.2_Nonsense_Mutation_p.Y78*|RFX4_uc001tlt.2_Nonsense_Mutation_p.Y78*	p.Y69*	NM_213594	NP_998759	Q33E94	RFX4_HUMAN			4	273	+			69			|RFX-type winged-helix.		A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Nonsense_Mutation	SNP	ENST00000392842.1	37	c.207T>G	CCDS9106.1	.	.	.	.	.	.	.	.	.	.	T	36	5.736301	0.96865	.	.	ENSG00000111783	ENST00000392842;ENST00000357881;ENST00000266774;ENST00000551640	.	.	.	5.84	-5.04	0.02964	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.1156	17.3848	0.87413	0.0:0.6303:0.0:0.3697	.	.	.	.	X	69;78;78;14	.	ENSP00000266774:Y78X	Y	+	3	2	RFX4	105572151	0.004000	0.15560	0.898000	0.35279	0.992000	0.81027	-1.296000	0.02762	-1.162000	0.02797	-0.408000	0.06270	TAT		0.488	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
NEIL1	79661	broad.mit.edu	37	15	75641495	75641495	+	Silent	SNP	C	C	T			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr15:75641495C>T	ENST00000564784.1	+	3	878	c.249C>T	c.(247-249)ggC>ggT	p.G83G	NEIL1_ENST00000569035.1_Silent_p.G83G|NEIL1_ENST00000355059.4_Silent_p.G83G|NEIL1_ENST00000567959.1_Intron			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	83			G -> D (in dbSNP:rs5745906). {ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						GCATGTCCGGCTCTTTTCAGC	0.687								Base excision repair (BER), DNA glycosylases																														uc002bad.2																			0				ovary(1)	1						c.(247-249)GGC>GGT	BER_DNA_glycosylases	nei endonuclease VIII-like 1							36.0	33.0	34.0					15																	75641495		2197	4294	6491	SO:0001819	synonymous_variant	79661				base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress	cytoplasm|nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding	g.chr15:75641495C>T	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.249C>T	15.37:g.75641495C>T						NEIL1_uc002bae.2_Silent_p.G169G	p.G83G	NM_024608	NP_078884	Q96FI4	NEIL1_HUMAN			2	755	+			83					D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Silent	SNP	ENST00000564784.1	37	c.249C>T	CCDS10278.1																																																																																				0.687	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
CAMKK1	84254	broad.mit.edu	37	17	3779538	3779538	+	Silent	SNP	G	G	A	rs560406629	byFrequency	TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr17:3779538G>A	ENST00000348335.2	-	10	1123	c.975C>T	c.(973-975)tcC>tcT	p.S325S	CAMKK1_ENST00000381769.2_Silent_p.S352S|CAMKK1_ENST00000381771.2_Silent_p.S363S|CAMKK1_ENST00000158166.5_Silent_p.S363S	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	325	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		AGCTCTGGCCGGAATCAGAAA	0.622													G|||	3	0.000599042	0.0	0.0	5008	,	,		15341	0.0		0.0	False		,,,				2504	0.0031					uc002fwt.2																			0				ovary(1)	1						c.(973-975)TCC>TCT		calcium/calmodulin-dependent protein kinase 1							48.0	44.0	46.0					17																	3779538		2203	4300	6503	SO:0001819	synonymous_variant	84254				synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity	g.chr17:3779538G>A	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.975C>T	17.37:g.3779538G>A						CAMKK1_uc002fwu.2_Silent_p.S325S|CAMKK1_uc002fwv.2_Silent_p.S363S	p.S325S	NM_172206	NP_757343	Q8N5S9	KKCC1_HUMAN		LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)	10	1069	-			325			Protein kinase.		Q9BQH3	Silent	SNP	ENST00000348335.2	37	c.975C>T	CCDS11038.1																																																																																				0.622	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	
NF1	4763	broad.mit.edu	37	17	29560133	29560133	+	Frame_Shift_Del	DEL	C	C	-	rs199474732		TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr17:29560133delC	ENST00000358273.4	+	27	3993	c.3610delC	c.(3610-3612)cggfs	p.R1204fs	NF1_ENST00000356175.3_Frame_Shift_Del_p.R1204fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1204			R -> G (in NF1; dbSNP:rs199474732). {ECO:0000269|PubMed:10336779}.|R -> W (in NF1; dbSNP:rs199474732). {ECO:0000269|PubMed:10607834}.		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.R1204W(1)|p.G1190fs*1(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ATTGGCTGATCGGTTTGAGAG	0.453			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												uc002hgg.2			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	D|Mis|N|F|S|O	neurofibromatosis type 1 gene			O		neurofibroma|glioma	neurofibroma|glioma		14	Whole gene deletion(8)|Unknown(4)|Substitution - Missense(1)|Deletion - Frameshift(1)	p.?(2)|p.R1204W(1)	soft_tissue(8)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)|ovary(1)	soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330	GRCh37	CM000027|CM973234	NF1	M		c.(3610-3612)CGGfs		neurofibromin isoform 1							131.0	113.0	119.0					17																	29560133		2203	4300	6503	SO:0001589	frameshift_variant	4763	Neurofibromatosis_type_1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29560133delC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3610delC	17.37:g.29560133delC	ENSP00000351015:p.Arg1204fs	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_uc002hgh.2_Frame_Shift_Del_p.R1204fs|NF1_uc010csn.1_Frame_Shift_Del_p.R1064fs|NF1_uc002hgi.1_Frame_Shift_Del_p.R237fs	p.R1204fs	NM_001042492	NP_001035957	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	27	3943	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	1204		R -> W (in NF1).|R -> G (in NF1).			O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	c.3610delC	CCDS42292.1																																																																																				0.453	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
NF1	4763	broad.mit.edu	37	17	29661945	29661945	+	Nonsense_Mutation	SNP	C	C	T	rs137854552		TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr17:29661945C>T	ENST00000358273.4	+	40	6285	c.5902C>T	c.(5902-5904)Cga>Tga	p.R1968*	NF1_ENST00000356175.3_Nonsense_Mutation_p.R1947*|NF1_ENST00000444181.2_5'Flank|NF1_ENST00000417592.2_5'Flank|NF1_ENST00000581113.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1968					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.R1968*(3)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TGATGCCAAACGACAAAGAGT	0.368			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												uc002hgg.2			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	D|Mis|N|F|S|O	neurofibromatosis type 1 gene			O		neurofibroma|glioma	neurofibroma|glioma		14	Whole gene deletion(8)|Substitution - Nonsense(3)|Unknown(3)	p.R1968*(2)	soft_tissue(8)|central_nervous_system(3)|autonomic_ganglia(2)|lung(1)	soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330	GRCh37	CM900173	NF1	M	rs137854552	c.(5902-5904)CGA>TGA		neurofibromin isoform 1							131.0	119.0	123.0					17																	29661945		2203	4300	6503	SO:0001587	stop_gained	4763	Neurofibromatosis_type_1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29661945C>T		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5902C>T	17.37:g.29661945C>T	ENSP00000351015:p.Arg1968*	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_uc002hgh.2_Nonsense_Mutation_p.R1947*|NF1_uc010cso.2_Nonsense_Mutation_p.R156*|NF1_uc010wbt.1_5'Flank|NF1_uc010wbu.1_5'Flank	p.R1968*	NM_001042492	NP_001035957	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	40	6235	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	1968					O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	c.5902C>T	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	49	15.179225	0.99825	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.48	4.42	0.53409	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.975	0.71264	0.1858:0.8142:0.0:0.0	.	.	.	.	X	1968;1947;1613	.	ENSP00000348498:R1947X	R	+	1	2	NF1	26686071	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.867000	0.48428	1.079000	0.41038	0.557000	0.71058	CGA		0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs200214744|rs565505867	byFrequency	TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr17:39274291T>C	ENST00000391413.2	-	1	315	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.M93V(4)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.662																																						uc002hvz.2																			4	Substitution - Missense(4)		endometrium(3)|kidney(1)		0						c.(277-279)ATG>GTG		keratin associated protein 4-11							6.0	10.0	8.0					17																	39274291		651	1556	2207	SO:0001583	missense	653240					keratin filament		g.chr17:39274291T>C	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.277A>G	17.37:g.39274291T>C	ENSP00000375232:p.Met93Val						p.M93V	NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	316	-		Breast(137;0.000496)	93			14.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.277A>G	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.073	-1.199029	0.01581	.	.	ENSG00000212721	ENST00000391413	T	0.00580	6.43	4.25	-4.9	0.03094	.	.	.	.	.	T	0.00109	0.0003	N	0.00040	-2.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	9	0.02654	T	1	.	0.4739	0.00536	0.3479:0.2455:0.1203:0.2863	.	93	Q9BYQ6	KR411_HUMAN	V	93	ENSP00000375232:M93V	ENSP00000375232:M93V	M	-	1	0	KRTAP4-11	36527817	.	.	0.012000	0.15200	0.010000	0.07245	.	.	-1.319000	0.02286	-1.132000	0.01976	ATG		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
ETV4	2118	broad.mit.edu	37	17	41610118	41610118	+	Silent	SNP	A	A	C			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr17:41610118A>C	ENST00000319349.5	-	8	1033	c.735T>G	c.(733-735)ggT>ggG	p.G245G	ETV4_ENST00000538265.1_Silent_p.G206G|ETV4_ENST00000586826.1_5'Flank|ETV4_ENST00000591713.1_Silent_p.G245G|ETV4_ENST00000545954.1_Silent_p.G206G|ETV4_ENST00000545089.1_Silent_p.G191G|ETV4_ENST00000393664.2_Silent_p.G245G	NM_001079675.2	NP_001073143.1	P43268	ETV4_HUMAN	ets variant 4	245					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|motor neuron axon guidance (GO:0008045)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)		EWSR1/ETV4(6)|CANT1/ETV4(3)|TMPRSS2/ETV4(13)|DDX5_ENST00000540698/ETV4(2)|KLK2/ETV4(2)	ovary(2)|upper_aerodigestive_tract(1)	3		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		CATTGACCCCACCCTGGTCCA	0.617			T	"""EWSR1, TMPRSS2, DDX5, KLK2, CANT1"""	"""Ewing sarcoma, Prostate carcinoma"""																																Esophageal Squamous(116;1540 1611 12927 31103 34118)	uc002idw.2				Dom	yes		17	17q21	2118	T	"""ets variant gene 4 (E1A enhancer binding protein, E1AF)"""			"""M, E"""	EWSR1|TMPRSS2|DDX5|KLK2|CANT1		Ewing sarcoma|Prostate carcinoma	EWSR1/ETV4(6)	0				bone(4)|soft_tissue(2)|ovary(1)	7						c.(733-735)GGT>GGG		ets variant gene 4 (E1A enhancer binding							46.0	49.0	48.0					17																	41610118		2203	4300	6503	SO:0001819	synonymous_variant	2118				positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr17:41610118A>C	U18018	CCDS11465.1, CCDS58553.1, CCDS59292.1	17q21	2014-04-30	2008-09-12			ENSG00000175832			3493	protein-coding gene	gene with protein product	"""E1A enhancer binding protein"""	600711	"""ets variant gene 4 (E1A enhancer-binding protein, E1AF)"""			8530053, 1547944	Standard	NM_001986		Approved	E1A-F, E1AF, PEA3	uc002idw.3	P43268		ENST00000319349.5:c.735T>G	17.37:g.41610118A>C						ETV4_uc002idv.2_5'Flank|ETV4_uc010wih.1_Silent_p.G191G|ETV4_uc010czh.2_Silent_p.G244G|ETV4_uc010wii.1_Silent_p.G206G|ETV4_uc002idx.2_Silent_p.G245G|ETV4_uc010wij.1_Silent_p.G206G	p.G245G	NM_001986	NP_001977	P43268	ETV4_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.0798)	8	863	-		Breast(137;0.00908)	245					A8K314|B7Z5J3|B7Z9J6|Q96AW9	Silent	SNP	ENST00000319349.5	37	c.735T>G	CCDS11465.1																																																																																				0.617	ETV4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453489.1	NM_001986	
HOXB8	3218	broad.mit.edu	37	17	46692020	46692020	+	Missense_Mutation	SNP	C	C	G			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr17:46692020C>G	ENST00000239144.4	-	1	281	c.47G>C	c.(46-48)gGg>gCg	p.G16A	HOXB8_ENST00000576562.1_Missense_Mutation_p.G16A|HOXB7_ENST00000567101.2_Intron	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	16					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(8)|urinary_tract(2)	11						CAGGGACTCCCCGGTTTTGTA	0.587																																						uc002inw.2																			0					0						c.(46-48)GGG>GCG		homeobox B8							9.0	10.0	10.0					17																	46692020		2189	4271	6460	SO:0001583	missense	3218					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr17:46692020C>G		CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"""Homeoboxes / ANTP class : HOXL subclass"""	5119	protein-coding gene	gene with protein product		142963	"""homeo box B8"""	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.47G>C	17.37:g.46692020C>G	ENSP00000239144:p.Gly16Ala						p.G16A	NM_024016	NP_076921	P17481	HXB8_HUMAN			1	282	-			16					Q9H1I2	Missense_Mutation	SNP	ENST00000239144.4	37	c.47G>C	CCDS11533.1	.	.	.	.	.	.	.	.	.	.	c	15.23	2.771684	0.49680	.	.	ENSG00000120068	ENST00000239144	T	0.42131	0.98	2.86	2.86	0.33363	.	0.000000	0.64402	U	0.000020	T	0.55721	0.1938	L	0.49778	1.585	0.50171	D	0.999856	D	0.76494	0.999	D	0.78314	0.991	T	0.56727	-0.7931	10	0.42905	T	0.14	.	13.7619	0.62971	0.0:1.0:0.0:0.0	.	16	P17481	HXB8_HUMAN	A	16	ENSP00000239144:G16A	ENSP00000239144:G16A	G	-	2	0	HOXB8	44047019	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.156000	0.77453	1.443000	0.47586	0.290000	0.19541	GGG		0.587	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3		
MUC16	94025	broad.mit.edu	37	19	9062384	9062384	+	Silent	SNP	G	G	T			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr19:9062384G>T	ENST00000397910.4	-	3	25265	c.25062C>A	c.(25060-25062)acC>acA	p.T8354T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8356	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCCTCACGTTGGTCACTGCTG	0.488																																						uc002mkp.2																			0				lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						c.(25060-25062)ACC>ACA		mucin 16							199.0	195.0	196.0					19																	9062384		2115	4229	6344	SO:0001819	synonymous_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9062384G>T	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.25062C>A	19.37:g.9062384G>T							p.T8354T	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			3	25266	-			8356			Ser-rich.|Thr-rich.|Extracellular (Potential).		Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	c.25062C>A	CCDS54212.1																																																																																				0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF653	115950	broad.mit.edu	37	19	11594572	11594572	+	Silent	SNP	G	G	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr19:11594572G>A	ENST00000293771.5	-	9	1909	c.1773C>T	c.(1771-1773)tgC>tgT	p.C591C	ELAVL3_ENST00000359227.3_5'Flank|ELAVL3_ENST00000592218.1_5'Flank|CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	591					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						AGCGCTTCCCGCAGCGATCGC	0.612																																					Pancreas(83;980 1446 4542 6441 43352)	uc002mrz.1																			0					0						c.(1771-1773)TGC>TGT		zinc finger protein 653							202.0	151.0	168.0					19																	11594572		2203	4300	6503	SO:0001819	synonymous_variant	115950				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:11594572G>A	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1773C>T	19.37:g.11594572G>A						ELAVL3_uc002mrx.1_5'Flank|ELAVL3_uc002mry.1_5'Flank	p.C591C	NM_138783	NP_620138	Q96CK0	ZN653_HUMAN			9	1826	-			591			C2H2-type 5.		Q96AS7	Silent	SNP	ENST00000293771.5	37	c.1773C>T	CCDS12261.1																																																																																				0.612	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
WASH2P	375260	broad.mit.edu	37	2	114357720	114357720	+	RNA	SNP	A	A	G			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr2:114357720A>G	ENST00000538033.2	+	0	2800							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										CAGCTTGTCCAGGACAGGGTG	0.567																																						uc010yxx.1																			0					0						c.(217-219)CCT>CCC		SubName: Full=DEAD/H box polypeptide 11 like 2;																																						84771							g.chr2:114357720A>G			2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556		"""WAS protein homologs"""	33145	pseudogene	pseudogene			"""family with sequence similarity 39, member B"""	FAM39B		18159949	Standard	NR_024077		Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822		2.37:g.114357720A>G							p.P73P							3	546	-									Silent	SNP	ENST00000538033.2	37	c.219T>C																																																																																					0.567	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	pseudogene	OTTHUMT00000467782.1	NM_198943	
FAM83D	81610	broad.mit.edu	37	20	37580810	37580811	+	Frame_Shift_Ins	INS	-	-	T			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr20:37580810_37580811insT	ENST00000217429.4	+	4	1536_1537	c.1495_1496insT	c.(1495-1497)gtafs	p.V499fs		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	469					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.V499I(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				AAAAATGTCTGTATCGAGATCT	0.485																																						uc002xjg.2																			1	Substitution - Missense(1)		large_intestine(1)	ovary(3)	3						c.(1495-1497)GTAfs		hypothetical protein LOC81610																																				SO:0001589	frameshift_variant	81610				cell division|mitosis	cytoplasm|spindle pole		g.chr20:37580810_37580811insT	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 129"""	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.1496dupT	20.37:g.37580811_37580811dupT	ENSP00000217429:p.Val499fs						p.V499fs	NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN			4	1536_1537	+		Myeloproliferative disorder(115;0.00878)	469			Ser-rich.		B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Frame_Shift_Ins	INS	ENST00000217429.4	37	c.1495_1496insT	CCDS42872.1																																																																																				0.485	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1		
PCK1	5105	broad.mit.edu	37	20	56140691	56140691	+	Missense_Mutation	SNP	A	A	C			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr20:56140691A>C	ENST00000319441.4	+	10	1864	c.1700A>C	c.(1699-1701)aAa>aCa	p.K567T	PCK1_ENST00000543666.1_Missense_Mutation_p.K250T	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	567					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CTGAACCTGAAAGGCCTGGGG	0.532																																						uc002xyn.3																			0				skin(1)	1						c.(1699-1701)AAA>ACA		cytosolic phosphoenolpyruvate carboxykinase 1							81.0	76.0	77.0					20																	56140691		2203	4300	6503	SO:0001583	missense	5105				gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity	g.chr20:56140691A>C		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1700A>C	20.37:g.56140691A>C	ENSP00000319814:p.Lys567Thr					PCK1_uc010zzm.1_Missense_Mutation_p.K250T	p.K567T	NM_002591	NP_002582	P35558	PCKGC_HUMAN	BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)		10	1863	+	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		567					A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	c.1700A>C	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	A	8.585	0.883146	0.17467	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666	T;T	0.04234	3.67;3.67	5.69	3.44	0.39384	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.360617	0.35262	N	0.003338	T	0.02380	0.0073	N	0.04148	-0.265	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.51841	-0.8654	10	0.17369	T	0.5	-9.601	10.0118	0.41990	0.8634:0.0:0.1366:0.0	.	250;567	B4DT64;P35558	.;PCKGC_HUMAN	T	249;567;250	ENSP00000319814:K567T;ENSP00000445767:K250T	ENSP00000319814:K567T	K	+	2	0	PCK1	55574097	1.000000	0.71417	0.873000	0.34254	0.643000	0.38383	2.106000	0.41835	0.432000	0.26286	0.533000	0.62120	AAA		0.532	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
HUNK	30811	broad.mit.edu	37	21	33331245	33331245	+	Missense_Mutation	SNP	C	C	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr21:33331245C>A	ENST00000270112.2	+	5	1197	c.837C>A	c.(835-837)gaC>gaA	p.D279E		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						AGATGGTAGACAAAGAAATGA	0.537																																						uc002yph.2																			0				stomach(1)|skin(1)	2						c.(835-837)GAC>GAA		hormonally upregulated Neu-associated kinase							134.0	122.0	126.0					21																	33331245		2203	4300	6503	SO:0001583	missense	30811				multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity	g.chr21:33331245C>A	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.837C>A	21.37:g.33331245C>A	ENSP00000270112:p.Asp279Glu						p.D279E	NM_014586	NP_055401	P57058	HUNK_HUMAN			5	1197	+			279			Protein kinase.			Missense_Mutation	SNP	ENST00000270112.2	37	c.837C>A	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290203	0.59976	.	.	ENSG00000142149	ENST00000270112	T	0.64085	-0.08	4.87	3.99	0.46301	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.110959	0.64402	D	0.000017	T	0.40839	0.1133	N	0.03224	-0.385	0.47547	D	0.999456	B	0.32862	0.387	B	0.35859	0.212	T	0.46359	-0.9197	10	0.48119	T	0.1	-25.1095	13.1148	0.59294	0.0:0.9227:0.0:0.0772	.	279	P57058	HUNK_HUMAN	E	279	ENSP00000270112:D279E	ENSP00000270112:D279E	D	+	3	2	HUNK	32253116	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.809000	0.47971	1.272000	0.44329	0.655000	0.94253	GAC		0.537	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
CAMKV	79012	broad.mit.edu	37	3	49896857	49896857	+	Missense_Mutation	SNP	G	G	T			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr3:49896857G>T	ENST00000477224.1	-	11	1878	c.1400C>A	c.(1399-1401)cCg>cAg	p.P467Q	TRAIP_ENST00000473863.1_5'Flank|CAMKV_ENST00000463537.1_Silent_p.R399R|CAMKV_ENST00000488336.1_Missense_Mutation_p.P436Q|TRAIP_ENST00000469027.1_5'Flank|CAMKV_ENST00000296471.7_Missense_Mutation_p.P439Q|CAMKV_ENST00000466940.1_Missense_Mutation_p.P393Q|CAMKV_ENST00000498324.1_5'Flank|TRAIP_ENST00000331456.2_5'Flank|CAMKV_ENST00000467248.1_Missense_Mutation_p.P392Q			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	467	Ala-rich.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TGTGCTGTCCGGCTGGGCCAT	0.652																																						uc003cxt.1																			0				ovary(2)|lung(2)|large_intestine(2)|central_nervous_system(1)	7						c.(1399-1401)CCG>CAG		CaM kinase-like vesicle-associated							69.0	70.0	70.0					3																	49896857		2203	4300	6503	SO:0001583	missense	79012					cytoplasmic vesicle membrane|plasma membrane	ATP binding|protein serine/threonine kinase activity	g.chr3:49896857G>T	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.1400C>A	3.37:g.49896857G>T	ENSP00000419195:p.Pro467Gln					TRAIP_uc003cxs.1_5'Flank|TRAIP_uc010hla.1_5'Flank|TRAIP_uc011bcx.1_5'Flank|CAMKV_uc011bcy.1_Missense_Mutation_p.P392Q|CAMKV_uc003cxv.1_Missense_Mutation_p.P439Q|CAMKV_uc003cxw.1_Missense_Mutation_p.P299Q|CAMKV_uc003cxx.1_Missense_Mutation_p.P299Q|CAMKV_uc003cxu.2_Missense_Mutation_p.P436Q|CAMKV_uc011bcz.1_Missense_Mutation_p.P399Q|CAMKV_uc011bda.1_Missense_Mutation_p.P393Q	p.P467Q	NM_024046	NP_076951	Q8NCB2	CAMKV_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	11	1593	-			467			Ala-rich.		A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Missense_Mutation	SNP	ENST00000477224.1	37	c.1400C>A	CCDS33762.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.903440	0.52333	.	.	ENSG00000164076	ENST00000296471;ENST00000488336;ENST00000477224;ENST00000467248;ENST00000466940	T;T;T;T;T	0.72615	-0.67;-0.14;-0.18;-0.42;1.66	5.33	4.46	0.54185	.	0.000000	0.42294	D	0.000740	T	0.57710	0.2072	N	0.19112	0.55	0.31439	N	0.672212	B;P;P;P;B;B;B	0.44690	0.054;0.808;0.841;0.841;0.09;0.09;0.054	B;P;B;B;B;B;B	0.44518	0.01;0.452;0.218;0.218;0.06;0.022;0.015	T	0.66023	-0.6026	10	0.72032	D	0.01	.	8.586	0.33657	0.0806:0.0:0.767:0.1524	.	393;399;467;392;439;436;467	E7ETR1;B4DMF2;B2RDF9;B4DM24;Q8NCB2-2;Q8NCB2-3;Q8NCB2	.;.;.;.;.;.;CAMKV_HUMAN	Q	439;436;467;392;393	ENSP00000296471:P439Q;ENSP00000418809:P436Q;ENSP00000419195:P467Q;ENSP00000420053:P392Q;ENSP00000420724:P393Q	ENSP00000296471:P439Q	P	-	2	0	CAMKV	49871861	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.902000	0.28459	1.470000	0.48102	0.655000	0.94253	CCG		0.652	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
CMSS1	84319	broad.mit.edu	37	3	99891168	99891168	+	Silent	SNP	G	G	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr3:99891168G>A	ENST00000421999.2	+	8	734	c.588G>A	c.(586-588)gcG>gcA	p.A196A	CMSS1_ENST00000489081.1_Silent_p.A178A	NM_032359.3	NP_115735.2	Q9BQ75	CMS1_HUMAN	cms1 ribosomal small subunit homolog (yeast)	196							poly(A) RNA binding (GO:0044822)										AGGTCCAGGCGCAGGTAAAGT	0.413																																						uc003dtl.2																			0				skin(1)	1						c.(586-588)GCG>GCA		hypothetical protein LOC84319							68.0	72.0	70.0					3																	99891168		2203	4300	6503	SO:0001819	synonymous_variant	84319						ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr3:99891168G>A		CCDS2935.1, CCDS54618.1	3q12.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000184220	ENSG00000184220			28666	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 26"""	C3orf26		12477932	Standard	NM_032359		Approved	MGC4308	uc003dtl.3	Q9BQ75	OTTHUMG00000159054	ENST00000421999.2:c.588G>A	3.37:g.99891168G>A							p.A196A	NM_032359	NP_115735	Q9BQ75	CC026_HUMAN			8	731	+			196					A8K5S7|B4DUM1|E9PHS3	Silent	SNP	ENST00000421999.2	37	c.588G>A	CCDS2935.1																																																																																				0.413	CMSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353060.1	NM_032359	
FXR1	8087	broad.mit.edu	37	3	180651171	180651172	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr3:180651171_180651172delAT	ENST00000357559.4	+	2	485_486	c.101_102delAT	c.(100-102)aatfs	p.N35fs	FXR1_ENST00000491062.1_Intron|FXR1_ENST00000305586.7_5'UTR|FXR1_ENST00000468861.1_Intron|FXR1_ENST00000480918.1_Frame_Shift_Del_p.N22fs|FXR1_ENST00000445140.2_Frame_Shift_Del_p.N35fs	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	35	Agenet-like 1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			GTTTTTGAAAATAAGTAAGTTA	0.332																																						uc003fkq.2																			0				breast(1)	1						c.(100-102)AATfs		fragile X mental retardation-related protein 1																																				SO:0001589	frameshift_variant	8087				apoptosis|cell differentiation|muscle organ development	nucleolus|polysome		g.chr3:180651171_180651172delAT	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.101_102delAT	3.37:g.180651171_180651172delAT	ENSP00000350170:p.Asn35fs					FXR1_uc003fkp.2_5'UTR|FXR1_uc003fkr.2_Frame_Shift_Del_p.N34fs|FXR1_uc011bqj.1_Intron|FXR1_uc003fks.2_5'UTR|FXR1_uc011bqk.1_Intron|FXR1_uc011bql.1_Frame_Shift_Del_p.N21fs	p.N34fs	NM_005087	NP_005078	P51114	FXR1_HUMAN	Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)		2	123_124	+	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		34					A8K9B8|Q7Z450|Q8N6R8	Frame_Shift_Del	DEL	ENST00000357559.4	37	c.101_102delAT	CCDS3238.1																																																																																				0.332	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5		
RICTOR	253260	broad.mit.edu	37	5	38950386	38950386	+	Missense_Mutation	SNP	A	A	C			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr5:38950386A>C	ENST00000357387.3	-	31	3594	c.3564T>G	c.(3562-3564)aaT>aaG	p.N1188K	RICTOR_ENST00000296782.5_Missense_Mutation_p.N1188K	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					CTGTACCAAAATTCTTGGTGA	0.358																																						uc003jlp.2																			0				ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10						c.(3562-3564)AAT>AAG		rapamycin-insensitive companion of mTOR							138.0	150.0	146.0					5																	38950386		2203	4299	6502	SO:0001583	missense	253260				actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding	g.chr5:38950386A>C		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3564T>G	5.37:g.38950386A>C	ENSP00000349959:p.Asn1188Lys					RICTOR_uc003jlo.2_Missense_Mutation_p.N1188K|RICTOR_uc010ivf.2_Missense_Mutation_p.N903K	p.N1188K	NM_152756	NP_689969	Q6R327	RICTR_HUMAN			31	3588	-	all_lung(31;0.000396)		1188						Missense_Mutation	SNP	ENST00000357387.3	37	c.3564T>G	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	A	0.573	-0.840411	0.02692	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.40225	1.04;1.04	5.86	3.48	0.39840	.	0.449544	0.30347	N	0.009829	T	0.24275	0.0588	N	0.08118	0	0.21499	N	0.999661	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.19647	-1.0299	10	0.66056	D	0.02	-4.8453	11.5657	0.50805	0.8146:0.0:0.1854:0.0	.	1188;1188	Q6R327;Q6R327-3	RICTR_HUMAN;.	K	1188	ENSP00000349959:N1188K;ENSP00000296782:N1188K	ENSP00000296782:N1188K	N	-	3	2	RICTOR	38986143	1.000000	0.71417	1.000000	0.80357	0.090000	0.18270	0.874000	0.28065	0.198000	0.20407	-1.162000	0.01777	AAT		0.358	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
SV2C	22987	broad.mit.edu	37	5	75427791	75427791	+	Silent	SNP	C	C	T			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr5:75427791C>T	ENST00000502798.2	+	2	658	c.216C>T	c.(214-216)gaC>gaT	p.D72D	SV2C_ENST00000322285.7_Silent_p.D72D	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	72					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.D72D(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CCAACGATGACGAAGGCTCAA	0.498																																						uc003kei.1																			1	Substitution - coding silent(1)		prostate(1)	skin(1)	1						c.(214-216)GAC>GAT		synaptic vesicle glycoprotein 2C							84.0	87.0	86.0					5																	75427791		2084	4235	6319	SO:0001819	synonymous_variant	22987				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity	g.chr5:75427791C>T	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.216C>T	5.37:g.75427791C>T							p.D72D	NM_014979	NP_055794	Q496J9	SV2C_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)	2	350	+		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)	72			Cytoplasmic (Potential).		Q496K1|Q9UPU8	Silent	SNP	ENST00000502798.2	37	c.216C>T	CCDS43331.1																																																																																				0.498	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
ARRDC3	57561	broad.mit.edu	37	5	90671379	90671379	+	Missense_Mutation	SNP	A	A	C			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr5:90671379A>C	ENST00000265138.3	-	4	828	c.562T>G	c.(562-564)Tca>Gca	p.S188A	ARRDC3_ENST00000503192.1_5'UTR	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	188					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		ATTGGGCCTGAGGTACAGAAC	0.398																																						uc003kjz.2																			0				ovary(1)|breast(1)	2						c.(562-564)TCA>GCA		arrestin domain containing 3							127.0	134.0	131.0					5																	90671379		2203	4300	6503	SO:0001583	missense	57561				signal transduction	cytoplasm	protein binding	g.chr5:90671379A>C	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"""alpha-arrestin 3"""	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.562T>G	5.37:g.90671379A>C	ENSP00000265138:p.Ser188Ala						p.S188A	NM_020801	NP_065852	Q96B67	ARRD3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)	4	802	-		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)	188					A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	37	c.562T>G	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.334267	0.60853	.	.	ENSG00000113369	ENST00000265138	T	0.09163	3.01	5.51	5.51	0.81932	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.37320	0.0999	M	0.90082	3.085	0.80722	D	1	D	0.57571	0.98	P	0.60012	0.867	T	0.41875	-0.9484	10	0.51188	T	0.08	-23.7899	15.6179	0.76780	1.0:0.0:0.0:0.0	.	188	Q96B67	ARRD3_HUMAN	A	188	ENSP00000265138:S188A	ENSP00000265138:S188A	S	-	1	0	ARRDC3	90707135	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.957000	0.93082	2.094000	0.63399	0.482000	0.46254	TCA		0.398	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801	
CDC23	8697	broad.mit.edu	37	5	137524677	137524677	+	Missense_Mutation	SNP	A	A	G			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr5:137524677A>G	ENST00000394886.2	-	16	1814	c.1784T>C	c.(1783-1785)gTc>gCc	p.V595A		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	595					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTATGGCGTGACAGAAGACAA	0.493																																						uc003lcl.2																			0					0						c.(1783-1785)GTC>GCC		cell division cycle protein 23							130.0	122.0	124.0					5																	137524677		2203	4300	6503	SO:0001583	missense	8697				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity	g.chr5:137524677A>G	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1724	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 8"""	603462	"""CDC23 (cell division cycle 23, yeast, homolog)"", ""cell division cycle 23 homolog (S. cerevisiae)"""			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.1784T>C	5.37:g.137524677A>G	ENSP00000378350:p.Val595Ala						p.V595A	NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)		16	1815	-			595					A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Missense_Mutation	SNP	ENST00000394886.2	37	c.1784T>C	CCDS4200.2	.	.	.	.	.	.	.	.	.	.	A	15.93	2.977722	0.53720	.	.	ENSG00000094880	ENST00000394886	T	0.45276	0.9	5.29	4.13	0.48395	.	0.119289	0.56097	N	0.000028	T	0.28101	0.0693	N	0.22421	0.69	0.80722	D	1	B	0.16396	0.017	B	0.12156	0.007	T	0.04767	-1.0928	10	0.30078	T	0.28	-10.0554	11.1024	0.48182	0.9278:0.0:0.0722:0.0	.	595	Q9UJX2	CDC23_HUMAN	A	595	ENSP00000378350:V595A	ENSP00000378350:V595A	V	-	2	0	CDC23	137552576	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.352000	0.73027	1.040000	0.40099	0.379000	0.24179	GTC		0.493	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2		
JAKMIP2	9832	broad.mit.edu	37	5	147012259	147012259	+	Missense_Mutation	SNP	C	C	T			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr5:147012259C>T	ENST00000265272.5	-	13	2227	c.1760G>A	c.(1759-1761)cGa>cAa	p.R587Q	JAKMIP2_ENST00000333010.6_Missense_Mutation_p.R545Q|JAKMIP2_ENST00000507386.1_Missense_Mutation_p.R566Q	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	587						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTAGGTTTCGAAACTCCAG	0.388																																						uc003loq.1																			0				large_intestine(1)|ovary(1)	2						c.(1759-1761)CGA>CAA		janus kinase and microtubule interacting protein							191.0	189.0	189.0					5																	147012259		2203	4300	6503	SO:0001583	missense	9832					Golgi apparatus		g.chr5:147012259C>T	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1760G>A	5.37:g.147012259C>T	ENSP00000265272:p.Arg587Gln					JAKMIP2_uc011dbx.1_Missense_Mutation_p.R545Q|JAKMIP2_uc003lor.1_Missense_Mutation_p.R566Q|uc003lop.1_Intron|JAKMIP2_uc010jgo.1_Missense_Mutation_p.R587Q	p.R587Q	NM_014790	NP_055605	Q96AA8	JKIP2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		13	2142	-			587			Potential.		A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	c.1760G>A	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	C	36	5.754512	0.96890	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.35789	1.29;1.36;1.36	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.61286	0.2335	M	0.75615	2.305	0.58432	D	0.999999	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.66847	0.947;0.947;0.947;0.947	T	0.56583	-0.7955	10	0.39692	T	0.17	.	19.891	0.96930	0.0:1.0:0.0:0.0	.	545;587;566;587	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	Q	566;587;545;566	ENSP00000421398:R566Q;ENSP00000265272:R587Q;ENSP00000328989:R545Q	ENSP00000265272:R587Q	R	-	2	0	JAKMIP2	146992452	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.245000	0.78237	2.871000	0.98454	0.655000	0.94253	CGA		0.388	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
COL12A1	1303	broad.mit.edu	37	6	75866132	75866132	+	Missense_Mutation	SNP	G	G	A	rs575168916		TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr6:75866132G>A	ENST00000322507.8	-	15	3400	c.3091C>T	c.(3091-3093)Cgc>Tgc	p.R1031C	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.R1031C|COL12A1_ENST00000483888.2_Missense_Mutation_p.R1031C	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1031	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCATGAGGGCGATAGACAACA	0.473													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18374	0.0		0.0	False		,,,				2504	0.0					uc003phs.2																			0				ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						c.(3091-3093)CGC>TGC		collagen, type XII, alpha 1 long isoform							253.0	238.0	243.0					6																	75866132		1958	4154	6112	SO:0001583	missense	1303				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength	g.chr6:75866132G>A	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3091C>T	6.37:g.75866132G>A	ENSP00000325146:p.Arg1031Cys					COL12A1_uc003pht.2_Intron	p.R1031C	NM_004370	NP_004361	Q99715	COCA1_HUMAN			15	3257	-			1031			Fibronectin type-III 7.		O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	c.3091C>T	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.396956	0.42512	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.59364	0.27;0.27;0.27	5.46	4.56	0.56223	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	T	0.68302	0.2986	M	0.79805	2.47	0.33559	D	0.59712	D	0.76494	0.999	D	0.63033	0.91	T	0.73100	-0.4089	10	0.62326	D	0.03	.	14.6483	0.68777	0.0:0.0:0.7395:0.2605	.	1031	Q99715	COCA1_HUMAN	C	1031	ENSP00000325146:R1031C;ENSP00000412864:R1031C;ENSP00000421216:R1031C	ENSP00000325146:R1031C	R	-	1	0	COL12A1	75922852	1.000000	0.71417	0.742000	0.31022	0.170000	0.22686	2.641000	0.46587	2.543000	0.85770	0.591000	0.81541	CGC		0.473	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
CASP8AP2	9994	broad.mit.edu	37	6	90578080	90578080	+	RNA	SNP	G	G	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr6:90578080G>A	ENST00000551025.1	+	0	6508									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)		GAAAGATCCAGTCACTGAAAC	0.388																																					Colon(187;1656 2025 17045 31481 39901)	uc003pnr.2																			0				ovary(2)	2						c.(5071-5073)GTC>ATC		caspase 8 associated protein 2							54.0	55.0	55.0					6																	90578080		1865	4097	5962			9994				cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity	g.chr6:90578080G>A	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.90578080G>A						CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.V1691I|CASP8AP2_uc011dzz.1_Missense_Mutation_p.V1691I	p.V1691I	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0953)	8	5267	+		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)	1691						Missense_Mutation	SNP	ENST00000551025.1	37	c.5071G>A																																																																																					0.388	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
PEX1	5189	broad.mit.edu	37	7	92147239	92147239	+	Missense_Mutation	SNP	T	T	C			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr7:92147239T>C	ENST00000248633.4	-	5	685	c.590A>G	c.(589-591)aAa>aGa	p.K197R	PEX1_ENST00000541751.1_5'Flank|PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Missense_Mutation_p.K197R	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	197					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			ATGAAGTTTTTTATATTCAGC	0.388																																						uc003uly.2																			0				ovary(1)|central_nervous_system(1)	2						c.(589-591)AAA>AGA		peroxin1							77.0	78.0	78.0					7																	92147239		2190	4295	6485	SO:0001583	missense	5189				microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding	g.chr7:92147239T>C	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.590A>G	7.37:g.92147239T>C	ENSP00000248633:p.Lys197Arg					PEX1_uc011khr.1_5'UTR|PEX1_uc010ley.2_Missense_Mutation_p.K197R|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	p.K197R	NM_000466	NP_000457	O43933	PEX1_HUMAN	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)		5	686	-	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	197					A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	37	c.590A>G	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	T	0.027	-1.364770	0.01235	.	.	ENSG00000127980	ENST00000248633;ENST00000428214;ENST00000545192	D;D	0.94687	-3.43;-3.49	5.22	3.42	0.39159	.	0.552984	0.18792	N	0.131040	D	0.84995	0.5596	N	0.19112	0.55	0.18873	N	0.999981	B	0.23735	0.09	B	0.16289	0.015	T	0.70026	-0.4985	10	0.13470	T	0.59	-9.1545	3.158	0.06510	0.1847:0.4869:0.0:0.3284	.	197	O43933	PEX1_HUMAN	R	197	ENSP00000248633:K197R;ENSP00000394413:K197R	ENSP00000248633:K197R	K	-	2	0	PEX1	91985175	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	0.277000	0.18734	0.770000	0.33336	-0.375000	0.07067	AAA		0.388	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
HRCT1	646962	broad.mit.edu	37	9	35906348	35906350	+	In_Frame_Del	DEL	CTG	CTG	-	rs370606246		TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr9:35906348_35906350delCTG	ENST00000354323.2	+	1	160_162	c.64_66delCTG	c.(64-66)ctgdel	p.L28del		NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	28						integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						TGTGGCGGTCctgctgctgctgc	0.67																																						uc003zyr.1																			0					0						c.(64-66)CTGdel		histidine rich carboxyl terminus 1				367,3839		38,291,1774						-8.3	0.0			23	737,7385		88,561,3412	no	coding	HRCT1	NM_001039792.1		126,852,5186	A1A1,A1R,RR		9.0741,8.7256,8.9552				1104,11224				SO:0001651	inframe_deletion	646962					integral to membrane		g.chr9:35906348_35906350delCTG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.64_66delCTG	9.37:g.35906357_35906359delCTG	ENSP00000346283:p.Leu28del						p.L28del	NM_001039792	NP_001034881	Q6UXD1	HRCT1_HUMAN			1	160_162	+			28			Helical; (Potential).		B7ZBJ1	In_Frame_Del	DEL	ENST00000354323.2	37	c.64_66delCTG	CCDS35012.1																																																																																				0.670	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
KIF12	113220	broad.mit.edu	37	9	116858751	116858751	+	Silent	SNP	G	G	A			TCGA-14-1043-01B-11D-1845-08	TCGA-14-1043-10A-01D-1845-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	a439c422-8728-42f5-8dda-6e9e1590478c	778e0059-412a-40b8-98b4-d3e905f5b905	g.chr9:116858751G>A	ENST00000374118.3	-	5	477	c.240C>T	c.(238-240)agC>agT	p.S80S	KIF12_ENST00000473174.1_5'UTR	NM_138424.1	NP_612433.1	Q96FN5	KIF12_HUMAN	kinesin family member 12	213	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	17						TCCTTCGACGGCTGAGAcctg	0.547																																						uc004bif.2																			0					0						c.(238-240)AGC>AGT		kinesin family member 12							82.0	63.0	70.0					9																	116858751		2203	4300	6503	SO:0001819	synonymous_variant	113220				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity	g.chr9:116858751G>A	BC010626	CCDS6801.1	9q33.1	2008-02-05			ENSG00000136883	ENSG00000136883		"""Kinesins"""	21495	protein-coding gene	gene with protein product		611278					Standard	NM_138424		Approved		uc004bif.3	Q96FN5	OTTHUMG00000020533	ENST00000374118.3:c.240C>T	9.37:g.116858751G>A						KIF12_uc004big.2_RNA	p.S80S	NM_138424	NP_612433	Q96FN5	KIF12_HUMAN			5	478	-			213			Kinesin-motor.		Q5TBE0	Silent	SNP	ENST00000374118.3	37	c.240C>T	CCDS6801.1																																																																																				0.547	KIF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053751.1	NM_138424	
