#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
HKDC1	80201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	71007297	71007297	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr10:71007297C>T	ENST00000354624.5	+	9	1346	c.1213C>T	c.(1213-1215)Cgg>Tgg	p.R405W	HKDC1_ENST00000488706.1_3'UTR|HKDC1_ENST00000395086.2_Missense_Mutation_p.R405W	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	405	Hexokinase type-2 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GAAGGTGGAACGGCTCCGGAC	0.612																																																0													68.0	61.0	64.0					10																	71007297		2203	4300	6503	SO:0001583	missense	80201				CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1213C>T	10.37:g.71007297C>T	ENSP00000346643:p.Arg405Trp		B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.229215	0.39399	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.96619	-4.07;-4.07	4.84	1.81	0.25067	Hexokinase, C-terminal (1);	0.256080	0.35262	N	0.003330	D	0.97448	0.9165	M	0.76838	2.35	0.23449	N	0.99766	D	0.89917	1.0	D	0.63381	0.914	D	0.93864	0.7156	10	0.72032	D	0.01	-21.3789	15.1686	0.72850	0.6461:0.3539:0.0:0.0	.	405	Q2TB90	HKDC1_HUMAN	W	405	ENSP00000346643:R405W;ENSP00000378521:R405W	ENSP00000346643:R405W	R	+	1	2	HKDC1	70677303	0.001000	0.12720	0.274000	0.24659	0.487000	0.33371	-0.138000	0.10374	0.192000	0.20272	-0.314000	0.08810	CGG		0.612	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		17	40	17	40
ACTA2	59	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	90708581	90708581	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr10:90708581A>G	ENST00000458208.1	-	2	581	c.107T>C	c.(106-108)aTt>aCt	p.I36T	ACTA2_ENST00000224784.6_Missense_Mutation_p.I36T|STAMBPL1_ENST00000371927.3_Intron|ACTA2_ENST00000480297.1_5'UTR	NM_001141945.1	NP_001135417.1	P62736	ACTA_HUMAN	actin, alpha 2, smooth muscle, aorta	36					glomerular mesangial cell development (GO:0072144)|muscle contraction (GO:0006936)|regulation of blood pressure (GO:0008217)|response to virus (GO:0009615)|vascular smooth muscle contraction (GO:0014829)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|smooth muscle contractile fiber (GO:0030485)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(2)	17		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)		ACGTCCCACAATGGATGGGAA	0.502																																																0													127.0	122.0	123.0					10																	90708581		2203	4300	6503	SO:0001583	missense	59			X13839	CCDS7392.1	10q23.31	2014-09-17			ENSG00000107796	ENSG00000107796			130	protein-coding gene	gene with protein product		102620				2398629	Standard	NM_001141945		Approved	ACTSA	uc001kfp.3	P62736	OTTHUMG00000018700	ENST00000458208.1:c.107T>C	10.37:g.90708581A>G	ENSP00000402373:p.Ile36Thr		B2R8A4|P03996|P04108|Q6FI19	Missense_Mutation	SNP	ENST00000458208.1	37	CCDS7392.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425237	0.62733	.	.	ENSG00000107796	ENST00000224784;ENST00000458208;ENST00000415557;ENST00000458159	D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000001	D	0.96787	0.8951	M	0.92026	3.265	0.58432	D	0.999995	D;P	0.69078	0.997;0.752	D;D	0.87578	0.998;0.995	D	0.97599	1.0122	10	0.87932	D	0	.	14.7882	0.69819	1.0:0.0:0.0:0.0	.	36;36	B7Z6I1;P62736	.;ACTA_HUMAN	T	36	ENSP00000224784:I36T;ENSP00000402373:I36T;ENSP00000396730:I36T;ENSP00000398239:I36T	ENSP00000224784:I36T	I	-	2	0	ACTA2	90698561	1.000000	0.71417	0.910000	0.35882	0.966000	0.64601	9.339000	0.96797	2.171000	0.68590	0.528000	0.53228	ATT		0.502	ACTA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049264.1	NM_001613		57	58	57	58
MEN1	4221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	64573758	64573758	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr11:64573758C>T	ENST00000337652.1	-	7	1513	c.1010G>A	c.(1009-1011)cGc>cAc	p.R337H	MEN1_ENST00000377326.3_Missense_Mutation_p.R332H|MEN1_ENST00000377313.1_Missense_Mutation_p.R337H|MEN1_ENST00000312049.6_Missense_Mutation_p.R332H|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000443283.1_Missense_Mutation_p.R337H|MEN1_ENST00000394376.1_Missense_Mutation_p.R337H|MEN1_ENST00000394374.2_Missense_Mutation_p.R337H|MEN1_ENST00000377321.1_Missense_Mutation_p.R297H|MEN1_ENST00000315422.4_Missense_Mutation_p.R332H|MEN1_ENST00000377316.2_Missense_Mutation_p.R332H	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	337	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						CCGCACATTGCGGTTGCGACA	0.602			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated		OREG0004014	type=REGULATORY REGION|Gene=MEN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	0													211.0	183.0	192.0					11																	64573758		2201	4297	6498	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1010G>A	11.37:g.64573758C>T	ENSP00000337088:p.Arg337His	1077	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991942	0.74703	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873	D;D;D;D;D;D;D;D;D;D;D	0.99454	-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92	3.92	3.92	0.45320	.	0.139807	0.41712	U	0.000830	D	0.98729	0.9573	L	0.43152	1.355	0.41578	D	0.988725	D;D;D	0.76494	0.999;0.991;0.999	P;P;P	0.60012	0.791;0.796;0.867	D	0.97955	1.0334	10	0.46703	T	0.11	-14.869	7.8854	0.29646	0.0:0.8839:0.0:0.1161	.	332;297;337	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	H	332;297;332;332;332;337;337;337;337;337;332	ENSP00000366533:R332H;ENSP00000366538:R297H;ENSP00000366543:R332H;ENSP00000308975:R332H;ENSP00000323747:R332H;ENSP00000337088:R337H;ENSP00000377901:R337H;ENSP00000377899:R337H;ENSP00000396940:R337H;ENSP00000366530:R337H;ENSP00000413944:R332H	ENSP00000308975:R332H	R	-	2	0	MEN1	64330334	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	2.274000	0.43390	1.927000	0.55829	0.456000	0.33151	CGC		0.602	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			47	68	47	68
MTUS2	23281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	29600879	29600879	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr13:29600879G>A	ENST00000431530.3	+	1	2132	c.2074G>A	c.(2074-2076)Gag>Aag	p.E692K		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	682	Mediates interaction with MAPRE1.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						TCCCCACGAAGAGAAGGCAGC	0.587																																																0													54.0	57.0	56.0					13																	29600879		1959	4130	6089	SO:0001583	missense	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2074G>A	13.37:g.29600879G>A	ENSP00000392057:p.Glu692Lys		A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	13.66	2.304953	0.40795	.	.	ENSG00000132938	ENST00000431530	T	0.14266	2.52	6.17	5.32	0.75619	.	0.317898	0.27143	N	0.020728	T	0.16214	0.0390	L	0.57536	1.79	0.80722	D	1	P	0.42296	0.775	B	0.39660	0.306	T	0.00740	-1.1586	9	.	.	.	.	13.279	0.60205	0.0:0.32:0.68:0.0	.	682	Q5JR59	MTUS2_HUMAN	K	692	ENSP00000392057:E692K	.	E	+	1	0	MTUS2	28498879	1.000000	0.71417	0.994000	0.49952	0.009000	0.06853	4.664000	0.61540	2.941000	0.99782	0.655000	0.94253	GAG		0.587	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		16	21	16	21
AKAP6	9472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	33293788	33293788	+	Missense_Mutation	SNP	G	G	A	rs140237441	byFrequency	TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr14:33293788G>A	ENST00000280979.4	+	13	6939	c.6769G>A	c.(6769-6771)Gga>Aga	p.G2257R	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2257					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.G2257R(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GGAAAGTTCCGGAAAACCAGG	0.438																																					Melanoma(49;821 1200 7288 13647 42351)											1	Substitution - Missense(1)	endometrium(1)						G	ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	65.0	66.0	66.0		6769	2.7	0.0	14	dbSNP_134	66	0,8600		0,0,4300	yes	missense	AKAP6	NM_004274.4	125	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	2257/2320	33293788	3,13003	2203	4300	6503	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6769G>A	14.37:g.33293788G>A	ENSP00000280979:p.Gly2257Arg		A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	8.440	0.850628	0.17034	6.81E-4	0.0	ENSG00000151320	ENST00000280979	T	0.05258	3.47	5.73	2.7	0.31948	.	0.464952	0.21793	N	0.069024	T	0.04497	0.0123	L	0.29908	0.895	0.09310	N	1	B	0.17268	0.021	B	0.06405	0.002	T	0.45614	-0.9249	10	0.15499	T	0.54	0.0147	8.4575	0.32908	0.2597:0.0:0.7403:0.0	.	2257	Q13023	AKAP6_HUMAN	R	2257	ENSP00000280979:G2257R	ENSP00000280979:G2257R	G	+	1	0	AKAP6	32363539	0.987000	0.35691	0.002000	0.10522	0.207000	0.24258	1.506000	0.35747	0.251000	0.21505	0.591000	0.81541	GGA		0.438	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		27	35	27	35
CCDC175	729665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	59970667	59970667	+	IGR	SNP	G	G	A			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr14:59970667G>A	ENST00000537690.2	-	0	2616				JKAMP_ENST00000554271.1_Silent_p.V285V|JKAMP_ENST00000261247.9_Silent_p.V271V|JKAMP_ENST00000425728.2_Silent_p.V265V|JKAMP_ENST00000356057.5_Silent_p.V279V|RP11-701B16.2_ENST00000554253.1_RNA	NM_001164399.1	NP_001157871.1	P0C221	CC175_HUMAN	coiled-coil domain containing 175																		TTTCCAGAGTGGATAAACTTG	0.398																																																0													137.0	130.0	132.0					14																	59970667		1833	4085	5918	SO:0001628	intergenic_variant	51528				CCDS53898.1	14q23.1	2012-09-24	2012-09-24	2012-09-24	ENSG00000151838	ENSG00000151838			19847	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 38"""	C14orf38			Standard	NM_001164399		Approved		uc021rtw.1	P0C221			14.37:g.59970667G>A			G3V5J7	Silent	SNP	ENST00000537690.2	37	CCDS53898.1																																																																																				0.398	CCDC175-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471273.1	NM_001164399		25	35	25	35
RYR3	6263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	33822854	33822854	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr15:33822854C>G	ENST00000389232.4	+	4	411	c.341C>G	c.(340-342)tCt>tGt	p.S114C	RYR3_ENST00000415757.3_Missense_Mutation_p.S114C	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	114	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTGAGGCACTCTTTCAGCGGA	0.512																																																0													69.0	66.0	67.0					15																	33822854		1962	4159	6121	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.341C>G	15.37:g.33822854C>G	ENSP00000373884:p.Ser114Cys		O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.588993	0.66105	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.91180	-2.8;-2.8	5.76	5.76	0.90799	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);MIR motif (2);	0.000000	0.85682	D	0.000000	D	0.92169	0.7517	L	0.38531	1.155	0.53688	D	0.999971	B;D	0.89917	0.024;1.0	B;D	0.75020	0.011;0.985	D	0.91078	0.4897	10	0.38643	T	0.18	.	14.3701	0.66833	0.0:0.8519:0.1481:0.0	.	114;114	Q15413-2;Q15413	.;RYR3_HUMAN	C	114	ENSP00000373884:S114C;ENSP00000399610:S114C	ENSP00000354735:S114C	S	+	2	0	RYR3	31610146	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	5.634000	0.67833	2.713000	0.92767	0.655000	0.94253	TCT		0.512	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			7	11	7	11
MFAP1	4236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	44109449	44109449	+	Missense_Mutation	SNP	T	T	C	rs202057440		TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr15:44109449T>C	ENST00000267812.3	-	2	509	c.277A>G	c.(277-279)Att>Gtt	p.I93V		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	93					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		TCTTCACTAATACGGTTCTGT	0.398													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19222	0.0		0.0	False		,,,				2504	0.0															0													149.0	145.0	146.0					15																	44109449		2198	4298	6496	SO:0001583	missense	4236				CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.277A>G	15.37:g.44109449T>C	ENSP00000267812:p.Ile93Val		Q86TG6	Missense_Mutation	SNP	ENST00000267812.3	37	CCDS10105.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	13.27	2.188150	0.38609	.	.	ENSG00000140259	ENST00000267812	.	.	.	4.9	4.9	0.64082	.	0.207698	0.51477	D	0.000095	T	0.36580	0.0972	N	0.05230	-0.09	0.37242	D	0.906166	B	0.02656	0.0	B	0.01281	0.0	T	0.31166	-0.9953	9	0.28530	T	0.3	-5.5202	14.917	0.70805	0.0:0.0:0.0:1.0	.	93	P55081	MFAP1_HUMAN	V	93	.	ENSP00000267812:I93V	I	-	1	0	MFAP1	41896741	0.996000	0.38824	0.994000	0.49952	0.989000	0.77384	2.845000	0.48254	2.137000	0.66172	0.533000	0.62120	ATT		0.398	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		33	65	33	65
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	78422352	78422352	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr1:78422352C>T	ENST00000370768.2	-	17	1691	c.1610G>A	c.(1609-1611)tGg>tAg	p.W537*	FUBP1_ENST00000370767.1_Nonsense_Mutation_p.W537*|FUBP1_ENST00000436586.2_Nonsense_Mutation_p.W558*	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	537	Pro-rich.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						ATAAGCAGCCCAAGCTGCTGA	0.458			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0													143.0	137.0	139.0					1																	78422352		2203	4300	6503	SO:0001587	stop_gained	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1610G>A	1.37:g.78422352C>T	ENSP00000359804:p.Trp537*		Q12828	Nonsense_Mutation	SNP	ENST00000370768.2	37	CCDS683.1	.	.	.	.	.	.	.	.	.	.	C	38	6.819066	0.97861	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.0616	19.9659	0.97266	0.0:1.0:0.0:0.0	.	.	.	.	X	536;537;537;522;558	.	ENSP00000294623:W536X	W	-	2	0	FUBP1	78194940	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.625000	0.83145	2.711000	0.92665	0.650000	0.86243	TGG		0.458	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		23	6	23	6
TAGLN2	8407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	159890149	159890149	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr1:159890149T>C	ENST00000368097.4	-	2	461	c.151A>G	c.(151-153)Aac>Gac	p.N51D	TAGLN2_ENST00000478033.1_5'UTR|TAGLN2_ENST00000320307.4_Missense_Mutation_p.N51D|TAGLN2_ENST00000368096.1_Missense_Mutation_p.N72D	NM_001277223.1|NM_003564.1	NP_001264152.1|NP_003555.1	P37802	TAGL2_HUMAN	transgelin 2	51	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)				endometrium(1)|large_intestine(2)|lung(6)	9	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTCTGGAAGTTCTCGCGTCCA	0.587																																																0													58.0	60.0	59.0					1																	159890149		2203	4300	6503	SO:0001583	missense	8407			D21261	CCDS1189.1, CCDS60314.1	1q21-q25	2008-07-18			ENSG00000158710	ENSG00000158710			11554	protein-coding gene	gene with protein product	"""SM22-alpha homolog"""	604634				9693045	Standard	NM_001277223		Approved	KIAA0120, HA1756	uc031pqu.1	P37802	OTTHUMG00000022793	ENST00000368097.4:c.151A>G	1.37:g.159890149T>C	ENSP00000357077:p.Asn51Asp		E9KL39|Q5JRQ6|Q5JRQ7|Q6FGI1|Q9BUH5|Q9H4P0	Missense_Mutation	SNP	ENST00000368097.4	37	CCDS1189.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.092043	0.36952	.	.	ENSG00000158710	ENST00000368097;ENST00000368096;ENST00000320307;ENST00000397334	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	4.92	3.77	0.43336	Calponin homology domain (5);	0.372528	0.21941	U	0.066870	T	0.18882	0.0453	N	0.21448	0.665	0.39515	D	0.968416	P;B	0.36199	0.543;0.001	B;B	0.34180	0.177;0.01	T	0.03630	-1.1018	9	.	.	.	-8.3296	10.263	0.43438	0.0:0.0:0.1669:0.8331	.	51;51	B7Z5A2;P37802	.;TAGL2_HUMAN	D	51;72;51;51	ENSP00000357077:N51D;ENSP00000357076:N72D;ENSP00000357075:N51D;ENSP00000412429:N51D	.	N	-	1	0	TAGLN2	158156773	0.562000	0.26586	0.992000	0.48379	0.924000	0.55760	0.968000	0.29357	0.812000	0.34326	0.459000	0.35465	AAC		0.587	TAGLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059105.1	NM_003564		46	5	46	5
SULF2	55959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	46305256	46305256	+	Silent	SNP	C	C	A	rs372325728		TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr20:46305256C>A	ENST00000359930.4	-	10	2213	c.1362G>T	c.(1360-1362)gcG>gcT	p.A454A	CTD-2653D5.1_ENST00000526566.2_RNA|SULF2_ENST00000484875.1_Silent_p.A454A|SULF2_ENST00000361612.4_Silent_p.A454A|SULF2_ENST00000467815.1_Silent_p.A454A	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	454					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GCTGCTCACACGCCGTCTGGT	0.612																																																0													99.0	59.0	73.0					20																	46305256		2202	4299	6501	SO:0001819	synonymous_variant	55959			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1362G>T	20.37:g.46305256C>A			E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Silent	SNP	ENST00000359930.4	37	CCDS13408.1																																																																																				0.612	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		6	5	6	5
LSM14B	149986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	60701373	60701373	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr20:60701373C>G	ENST00000279068.6	+	3	465	c.305C>G	c.(304-306)tCt>tGt	p.S102C	LSM14B_ENST00000253001.4_Missense_Mutation_p.S102C|LSM14B_ENST00000370915.1_Missense_Mutation_p.S102C	NM_144703.2	NP_653304.2	Q9BX40	LS14B_HUMAN	LSM14B, SCD6 homolog B (S. cerevisiae)	102					multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)	ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|lung(4)	8	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			TCCCTGGGTTCTGCCTCCGCC	0.657																																																0													71.0	76.0	74.0					20																	60701373		2147	4241	6388	SO:0001583	missense	149986			AF172328	CCDS46626.1	20q13.33	2010-01-27	2006-12-21	2006-01-24	ENSG00000149657	ENSG00000149657			15887	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 40"", ""family with sequence similarity 61, member B"", ""LSM14 homolog B (SCD6, S. cerevisiae)"""	C20orf40, FAM61B			Standard	NM_144703		Approved	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B	uc010gjy.1	Q9BX40	OTTHUMG00000032901	ENST00000279068.6:c.305C>G	20.37:g.60701373C>G	ENSP00000279068:p.Ser102Cys		Q6PFW8|Q96LH8	Missense_Mutation	SNP	ENST00000279068.6	37	CCDS46626.1	.	.	.	.	.	.	.	.	.	.	C	19.66	3.869102	0.72065	.	.	ENSG00000149657	ENST00000370915;ENST00000279068;ENST00000253001;ENST00000400318;ENST00000279069	T;T;T	0.50001	0.8;0.76;0.79	5.42	4.47	0.54385	.	0.203473	0.42682	D	0.000663	T	0.66297	0.2775	M	0.64997	1.995	0.42261	D	0.992011	P;D;D	0.89917	0.948;1.0;0.999	P;D;D	0.81914	0.514;0.995;0.98	T	0.71101	-0.4690	10	0.72032	D	0.01	.	16.2584	0.82528	0.0:0.8672:0.1328:0.0	.	102;128;102	Q9BX40;Q5TBQ0;Q9BX40-2	LS14B_HUMAN;.;.	C	102;102;102;128;102	ENSP00000279068:S102C;ENSP00000253001:S102C;ENSP00000383172:S128C	ENSP00000253001:S102C	S	+	2	0	LSM14B	60134768	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.420000	0.44679	1.266000	0.44231	0.511000	0.50034	TCT		0.657	LSM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079996.4	NM_144703		17	18	17	18
HELZ2	85441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	62200696	62200696	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr20:62200696T>C	ENST00000467148.1	-	4	962	c.893A>G	c.(892-894)aAc>aGc	p.N298S	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	298					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CACGTGGCGGTTGCCAGTGTG	0.697																																																0													19.0	21.0	20.0					20																	62200696		2187	4294	6481	SO:0001583	missense	85441			AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.893A>G	20.37:g.62200696T>C	ENSP00000417401:p.Asn298Ser		Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.373054	0.42105	.	.	ENSG00000130589	ENST00000467148	T	0.22134	1.97	4.5	4.5	0.54988	.	0.111771	0.64402	D	0.000018	T	0.33235	0.0856	L	0.55481	1.735	0.31922	N	0.613338	D	0.69078	0.997	P	0.60541	0.876	T	0.38200	-0.9672	10	0.41790	T	0.15	-8.3518	8.5496	0.33444	0.0:0.0881:0.0:0.9119	.	298	Q9BYK8	PR285_HUMAN	S	298	ENSP00000417401:N298S	ENSP00000417401:N298S	N	-	2	0	RP4-697K14.7	61671140	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	1.722000	0.38042	1.681000	0.50988	0.460000	0.39030	AAC		0.697	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		6	8	6	8
TAF1B	9014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	10016065	10016065	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr2:10016065A>G	ENST00000263663.5	+	7	813	c.625A>G	c.(625-627)Atg>Gtg	p.M209V	TAF1B_ENST00000396242.3_Intron	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	209	N-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AATCGTGAAGATGACCATGCC	0.413																																																0													239.0	202.0	215.0					2																	10016065		2203	4300	6503	SO:0001583	missense	9014			L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.625A>G	2.37:g.10016065A>G	ENSP00000263663:p.Met209Val		B4DI42|F8WD72|Q15574|Q8WVC3	Missense_Mutation	SNP	ENST00000263663.5	37	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.685087	0.47991	.	.	ENSG00000115750	ENST00000263663	T	0.03468	3.92	5.82	5.82	0.92795	.	0.037618	0.85682	D	0.000000	T	0.16171	0.0389	M	0.71581	2.175	0.80722	D	1	D;D	0.69078	0.997;0.99	D;D	0.72982	0.97;0.979	T	0.00216	-1.1910	9	.	.	.	-29.7323	13.7071	0.62646	1.0:0.0:0.0:0.0	.	209;209	Q53T94;Q53T94-2	TAF1B_HUMAN;.	V	209	ENSP00000263663:M209V	.	M	+	1	0	TAF1B	9933516	1.000000	0.71417	1.000000	0.80357	0.350000	0.29205	5.604000	0.67626	2.222000	0.72286	0.533000	0.62120	ATG		0.413	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		54	70	54	70
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			19	39	19	39
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	52621372	52621372	+	Silent	SNP	G	G	C			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr3:52621372G>C	ENST00000296302.7	-	19	3121	c.3120C>G	c.(3118-3120)gtC>gtG	p.V1040V	PBRM1_ENST00000356770.4_Silent_p.V1008V|PBRM1_ENST00000409114.3_Silent_p.V1055V|PBRM1_ENST00000394830.3_Silent_p.V1015V|PBRM1_ENST00000409767.1_Silent_p.V1055V|PBRM1_ENST00000410007.1_Silent_p.V1015V|PBRM1_ENST00000337303.4_Silent_p.V1040V|PBRM1_ENST00000409057.1_Silent_p.V1040V			Q86U86	PB1_HUMAN	polybromo 1	1040	BAH 1. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTCTTACCTTGACAAACATGA	0.318			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																		Rec	yes		3	3p21	55193	polybromo 1		E	0													103.0	107.0	106.0					3																	52621372		2203	4300	6503	SO:0001819	synonymous_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3120C>G	3.37:g.52621372G>C			A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																					0.318	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		30	41	30	41
FSTL5	56884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	162841556	162841556	+	Splice_Site	SNP	C	C	T			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr4:162841556C>T	ENST00000306100.5	-	4	845	c.409G>A	c.(409-411)Gga>Aga	p.G137R	FSTL5_ENST00000427802.2_Splice_Site_p.G136R|FSTL5_ENST00000536695.1_Splice_Site_p.G136R|FSTL5_ENST00000379164.4_Splice_Site_p.G136R	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	137						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CTTCATTTACCTTTAAAGAAG	0.378																																																0													108.0	100.0	103.0					4																	162841556		2203	4300	6503	SO:0001630	splice_region_variant	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.409+1G>A	4.37:g.162841556C>T			E9PCP6|Q9NSW7|Q9ULF7	Splice_Site	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831930	0.91036	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.72394	-0.63;-0.61;-0.65;-0.61	5.86	5.86	0.93980	.	0.107329	0.64402	D	0.000005	T	0.77738	0.4175	M	0.66939	2.045	0.80722	D	1	D;P;P	0.53619	0.961;0.799;0.933	P;B;P	0.50405	0.64;0.297;0.542	T	0.76192	-0.3049	9	.	.	.	.	19.5509	0.95319	0.0:1.0:0.0:0.0	.	136;136;137	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	R	137;136;136;136	ENSP00000305334:G137R;ENSP00000368462:G136R;ENSP00000389270:G136R;ENSP00000440409:G136R	.	G	-	1	0	FSTL5	163061006	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.445000	0.80570	2.937000	0.99478	0.650000	0.86243	GGA		0.378	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	Missense_Mutation	20	33	20	33
HSPA5	3309	hgsc.bcm.edu;broad.mit.edu	37	9	128001229	128001229	+	Silent	SNP	C	C	T			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr9:128001229C>T	ENST00000324460.6	-	5	1190	c.987G>A	c.(985-987)gaG>gaA	p.E329E	RP11-65N13.8_ENST00000468244.1_RNA	NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	329					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	CCATGTTGAGCTCTTCAAATT	0.418										Prostate(1;0.17)																																						0													52.0	52.0	52.0					9																	128001229		2201	4299	6500	SO:0001819	synonymous_variant	3309				CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"""Heat shock proteins / HSP70"""	5238	protein-coding gene	gene with protein product		138120	"""heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"""	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.987G>A	9.37:g.128001229C>T			B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Silent	SNP	ENST00000324460.6	37	CCDS6863.1																																																																																				0.418	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1			4	66	4	66
ANGPTL2	23452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	129853996	129853996	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr9:129853996T>C	ENST00000373425.3	-	4	1852	c.1235A>G	c.(1234-1236)aAc>aGc	p.N412S	RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000259351.5_Intron|ANGPTL2_ENST00000373417.1_Missense_Mutation_p.N110S|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	412	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CTGCTTGCCGTTGTGCCATGT	0.537																																																0													209.0	202.0	204.0					9																	129853996		2203	4300	6503	SO:0001583	missense	23452			AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.1235A>G	9.37:g.129853996T>C	ENSP00000362524:p.Asn412Ser		Q5JT58|Q8NCH7	Missense_Mutation	SNP	ENST00000373425.3	37	CCDS6868.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.786262	0.70337	.	.	ENSG00000136859	ENST00000373425;ENST00000373417	T;T	0.79033	-1.23;-1.23	5.2	5.2	0.72013	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.84813	0.5555	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83710	0.0187	10	0.34782	T	0.22	.	15.3682	0.74541	0.0:0.0:0.0:1.0	.	412	Q9UKU9	ANGL2_HUMAN	S	412;110	ENSP00000362524:N412S;ENSP00000362516:N110S	ENSP00000362516:N110S	N	-	2	0	ANGPTL2	128893817	1.000000	0.71417	0.945000	0.38365	0.982000	0.71751	6.234000	0.72326	2.082000	0.62665	0.533000	0.62120	AAC		0.537	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		114	132	114	132
MED14	9282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	40572233	40572233	+	Silent	SNP	T	T	C			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chrX:40572233T>C	ENST00000324817.1	-	6	832	c.714A>G	c.(712-714)ggA>ggG	p.G238G		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	238	Interaction with STAT2.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CAGGGTCATCTCCCATCACAG	0.383																																																0													98.0	79.0	85.0					X																	40572233		2203	4300	6503	SO:0001819	synonymous_variant	9282			AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.714A>G	X.37:g.40572233T>C			Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																				0.383	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		15	6	15	6
PAX4	5078	broad.mit.edu;ucsc.edu	37	7	127255106	127255106	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr7:127255106C>T	ENST00000341640.2	-	2	369	c.164G>A	c.(163-165)cGc>cAc	p.R55H	PAX4_ENST00000463946.1_Missense_Mutation_p.R53H|PAX4_ENST00000338516.3_Missense_Mutation_p.R63H|PAX4_ENST00000378740.2_Missense_Mutation_p.R55H	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	63	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GACACCTGTGCGGTAGTAACG	0.572																																					Ovarian(113;737 1605 7858 27720 34092)											0													94.0	88.0	90.0					7																	127255106		2203	4300	6503	SO:0001583	missense	5078				CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"""Paired boxes"", ""Homeoboxes / PRD class"""	8618	protein-coding gene	gene with protein product		167413	"""paired box gene 4"""				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.164G>A	7.37:g.127255106C>T	ENSP00000339906:p.Arg55His		O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482891	0.84747	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740;ENST00000463946	D;D;D	0.99338	-5.76;-5.76;-5.76	5.73	5.73	0.89815	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.052608	0.85682	D	0.000000	D	0.98998	0.9658	L	0.55481	1.735	0.44677	D	0.997666	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.73380	0.949;0.973;0.98;0.974	D	0.98452	1.0592	10	0.87932	D	0	.	10.7773	0.46356	0.0:0.9144:0.0:0.0856	.	55;53;63;53	O43316-4;Q1W386;O43316;G3V4Q1	.;.;PAX4_HUMAN;.	H	55;63;63;53	ENSP00000339906:R55H;ENSP00000344297:R63H;ENSP00000451923:R53H	ENSP00000344297:R63H	R	-	2	0	PAX4	127042342	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.413000	0.44618	2.693000	0.91896	0.655000	0.94253	CGC		0.572	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			44	44	44	44
CCDC175	729665	broad.mit.edu;ucsc.edu	37	14	59970666	59970666	+	IGR	SNP	T	T	A			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr14:59970666T>A	ENST00000537690.2	-	0	2616				JKAMP_ENST00000554271.1_Missense_Mutation_p.V285E|JKAMP_ENST00000261247.9_Missense_Mutation_p.V271E|JKAMP_ENST00000425728.2_Missense_Mutation_p.V265E|JKAMP_ENST00000356057.5_Missense_Mutation_p.V279E|RP11-701B16.2_ENST00000554253.1_RNA	NM_001164399.1	NP_001157871.1	P0C221	CC175_HUMAN	coiled-coil domain containing 175																		ATTTCCAGAGTGGATAAACTT	0.398																																																0													136.0	129.0	131.0					14																	59970666		1832	4084	5916	SO:0001628	intergenic_variant	51528				CCDS53898.1	14q23.1	2012-09-24	2012-09-24	2012-09-24	ENSG00000151838	ENSG00000151838			19847	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 38"""	C14orf38			Standard	NM_001164399		Approved		uc021rtw.1	P0C221			14.37:g.59970666T>A			G3V5J7	Missense_Mutation	SNP	ENST00000537690.2	37	CCDS53898.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.732979	0.69189	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000554271;ENST00000356057	.	.	.	5.62	5.62	0.85841	.	0.129137	0.53938	D	0.000055	T	0.48519	0.1504	L	0.29908	0.895	0.58432	D	0.999999	B;B;B;B;B	0.30211	0.273;0.231;0.078;0.231;0.078	B;B;B;B;B	0.29176	0.099;0.06;0.06;0.06;0.037	T	0.51371	-0.8714	9	0.72032	D	0.01	-7.0037	15.8181	0.78621	0.0:0.0:0.0:1.0	.	286;285;265;279;271	Q9P055;G3V2M4;Q9P055-3;Q9P055-5;Q9P055-4	JKAMP_HUMAN;.;.;.;.	E	271;265;285;279	.	ENSP00000261247:V271E	V	+	2	0	JKAMP	59040419	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.106000	0.71511	2.139000	0.66308	0.533000	0.62120	GTG		0.398	CCDC175-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471273.1	NM_001164399		24	33	24	33
PCDH10	57575	broad.mit.edu;hgsc.bcm.edu	37	4	134071550	134071553	+	Frame_Shift_Del	DEL	CAAA	CAAA	-			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr4:134071550_134071553delCAAA	ENST00000264360.5	+	1	1081_1084	c.255_258delCAAA	c.(253-258)tgcaaafs	p.CK85fs	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	85	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C85*(1)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		AACAAATCTGCAAACAGAGCCCCT	0.549																																																1	Substitution - Nonsense(1)	kidney(1)																																								SO:0001589	frameshift_variant	57575			AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"""Cadherins / Protocadherins : Non-clustered"""	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.255_258delCAAA	4.37:g.134071550_134071553delCAAA	ENSP00000264360:p.Cys85fs		Q4W5F6|Q96SF0	Frame_Shift_Del	DEL	ENST00000264360.5	37	CCDS34063.1																																																																																				0.549	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		30	71	30	71
PIK3R1	5295	broad.mit.edu;hgsc.bcm.edu	37	5	67589586	67589591	+	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	rs17852841		TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr5:67589586_67589591delATGAAT	ENST00000521381.1	+	11	1965_1970	c.1349_1354delATGAAT	c.(1348-1356)catgaatat>cat	p.EY451del	PIK3R1_ENST00000274335.5_In_Frame_Del_p.EY451del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.EY451del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.EY451del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.EY88del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.EY181del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.EY151del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	451			E -> K (in dbSNP:rs17852841). {ECO:0000269|PubMed:15489334}.		B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.H450_E451del(2)|p.G446_Y452>VI(1)|p.Y152N(1)|p.0?(1)|p.?(1)|p.Y452N(1)|p.Y182N(1)|p.E451_Y452del(1)|p.N453_T454insN(1)|p.E451_Y452delEY(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAAAAATTACATGAATATAACACTCA	0.277			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	11	Deletion - In frame(4)|Substitution - Missense(3)|Insertion - In frame(1)|Unknown(1)|Whole gene deletion(1)|Complex - deletion inframe(1)	endometrium(5)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|lung(1)																																								SO:0001651	inframe_deletion	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1349_1354delATGAAT	5.37:g.67589586_67589591delATGAAT	ENSP00000428056:p.Glu451_Tyr452del		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	ENST00000521381.1	37	CCDS3993.1																																																																																				0.277	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		21	27	21	27
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42798786	42798787	+	Frame_Shift_Ins	INS	-	-	A			TCGA-CS-5394-01A-01D-1468-08	TCGA-CS-5394-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e67f766-3799-4ce1-8c9c-d966d96302bf	ed3dfb55-5905-4bb2-a497-276c2d8b43d2	g.chr19:42798786_42798787insA	ENST00000575354.2	+	19	4398_4399	c.4358_4359insA	c.(4357-4362)ctagagfs	p.E1454fs	CIC_ENST00000572681.2_Frame_Shift_Ins_p.E2360fs|CIC_ENST00000160740.3_Frame_Shift_Ins_p.E1452fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1454					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CTTGGGGAGCTAGAGTATGACA	0.644			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4359dupA	19.37:g.42798787_42798787dupA	ENSP00000458663:p.Glu1454fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Ins	INS	ENST00000575354.2	37	CCDS12601.1																																																																																				0.644	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			25	14	25	14
