#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
SPEN	23013	broad.mit.edu	37	1	16261282	16261282	+	Silent	SNP	G	G	A			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA;ManualReview;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr1:16261282G>A	ENST00000375759.3	+	11	8751	c.8547G>A	c.(8545-8547)caG>caA	p.Q2849Q		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2849	Interaction with RBPSUH. {ECO:0000250}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.Q2849Q(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AATTTCAGCAGTCAGTGTCCA	0.577																																																1	Substitution - coding silent(1)	ovary(1)	1											110.0	87.0	95.0					1																	16261282		2203	4300	6503	16133869	SO:0001819	synonymous_variant	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.8547G>A	1.37:g.16261282G>A			16133869	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																				0.577	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
AIM2	9447	broad.mit.edu	37	1	159043085	159043085	+	Missense_Mutation	SNP	A	A	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr1:159043085A>T	ENST00000368130.4	-	2	493	c.205T>A	c.(205-207)Ttt>Att	p.F69I	AIM2_ENST00000411768.1_5'UTR	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	69	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)	p.F69I(1)		breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					AACTTCTGAAAAATACGAATG	0.448																																																1	Substitution - Missense(1)	ovary(1)	1											83.0	85.0	84.0					1																	159043085		2203	4300	6503	157309709	SO:0001583	missense	9447			AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.205T>A	1.37:g.159043085A>T	ENSP00000357112:p.Phe69Ile		157309709	A8K7M7|Q5T3V9|Q96FG9	Missense_Mutation	SNP	ENST00000368130.4	37	CCDS1181.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428420	0.43122	.	.	ENSG00000163568	ENST00000368130;ENST00000411768	T;T	0.54866	0.55;0.55	3.67	1.2	0.21068	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.30759	0.0775	L	0.59436	1.845	0.09310	N	1	P	0.47409	0.895	P	0.46885	0.53	T	0.12502	-1.0545	9	0.46703	T	0.11	-0.6782	3.6803	0.08308	0.6508:0.2257:0.1234:0.0	.	69	O14862	AIM2_HUMAN	I	69	ENSP00000357112:F69I;ENSP00000405197:F69I	ENSP00000357112:F69I	F	-	1	0	AIM2	157309709	0.001000	0.12720	0.001000	0.08648	0.125000	0.20455	0.140000	0.16056	0.111000	0.17947	0.459000	0.35465	TTT		0.448	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833	
AHNAK	79026	broad.mit.edu	37	11	62301009	62301009	+	Missense_Mutation	SNP	G	G	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr11:62301009G>T	ENST00000378024.4	-	5	1154	c.880C>A	c.(880-882)Cca>Aca	p.P294T	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	294					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.P294T(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCCAGAGATGGGCCCTGTACC	0.527																																																1	Substitution - Missense(1)	ovary(1)	11											111.0	100.0	104.0					11																	62301009		2202	4299	6501	62057585	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.880C>A	11.37:g.62301009G>T	ENSP00000367263:p.Pro294Thr		62057585	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.303318	0.23736	.	.	ENSG00000124942	ENST00000378024	T	0.02656	4.21	5.49	4.58	0.56647	.	0.000000	0.36665	U	0.002480	T	0.06781	0.0173	M	0.87097	2.86	0.24770	N	0.992872	P	0.49783	0.928	B	0.39840	0.311	T	0.25779	-1.0122	10	0.56958	D	0.05	-2.8195	11.5508	0.50719	0.0841:0.0:0.9159:0.0	.	294	Q09666	AHNK_HUMAN	T	294	ENSP00000367263:P294T	ENSP00000367263:P294T	P	-	1	0	AHNAK	62057585	0.001000	0.12720	0.969000	0.41365	0.784000	0.44337	-0.204000	0.09425	1.332000	0.45431	0.655000	0.94253	CCA		0.527	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
C11orf52	91894	broad.mit.edu	37	11	111796415	111796415	+	Nonsense_Mutation	SNP	C	C	T	rs202170534		TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr11:111796415C>T	ENST00000278601.5	+	3	205	c.109C>T	c.(109-111)Cag>Tag	p.Q37*	C11orf52_ENST00000527286.1_3'UTR|DIXDC1_ENST00000529225.1_5'Flank|CRYAB_ENST00000527950.1_5'Flank|RNA5SP351_ENST00000459480.1_RNA|HSPB2-C11orf52_ENST00000534100.1_3'UTR	NM_080659.2	NP_542390.2	Q96A22	CK052_HUMAN	chromosome 11 open reading frame 52	37						extracellular vesicular exosome (GO:0070062)		p.Q37*(1)		lung(2)|ovary(1)	3		all_cancers(61;8.8e-15)|all_epithelial(67;6.27e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.63e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.7e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		GCAGCCACAACAGCTGCAGCA	0.512																																																1	Substitution - Nonsense(1)	ovary(1)	11											74.0	82.0	79.0					11																	111796415		2201	4297	6498	111301625	SO:0001587	stop_gained	91894			AK057948	CCDS8353.1	11q23.1	2006-02-06	2006-02-06		ENSG00000149300	ENSG00000149300			30531	protein-coding gene	gene with protein product							Standard	NM_080659		Approved	MGC14839, FLJ25219		Q96A22	OTTHUMG00000166888	ENST00000278601.5:c.109C>T	11.37:g.111796415C>T	ENSP00000278601:p.Gln37*		111301625		Nonsense_Mutation	SNP	ENST00000278601.5	37	CCDS8353.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512607	0.27123	.	.	ENSG00000149300	ENST00000529342;ENST00000278601	.	.	.	4.38	1.08	0.20341	.	0.574067	0.15833	N	0.242382	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-0.2206	6.4554	0.21926	0.3722:0.4467:0.1811:0.0	.	.	.	.	X	37	.	ENSP00000278601:Q37X	Q	+	1	0	C11orf52	111301625	0.728000	0.28080	0.108000	0.21378	0.186000	0.23388	1.389000	0.34453	0.543000	0.28864	0.561000	0.74099	CAG		0.512	C11orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391673.1	NM_080659	
GLB1L3	112937	broad.mit.edu	37	11	134177017	134177017	+	Splice_Site	SNP	G	G	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr11:134177017G>T	ENST00000431683.2	+	10	876		c.e10-1			NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3						carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)	p.?(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		TTTGTTTTTAGAGAGATAAGC	0.398																																																1	Unknown(1)	ovary(1)	11											137.0	120.0	126.0					11																	134177017		1846	4091	5937	133682227	SO:0001630	splice_region_variant	112937				CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.877-1G>T	11.37:g.134177017G>T			133682227	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Splice_Site	SNP	ENST00000431683.2	37	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	6.643	0.487152	0.12641	.	.	ENSG00000166105	ENST00000431683	.	.	.	4.91	3.99	0.46301	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4638	0.32944	0.103:0.0:0.897:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GLB1L3	133682227	1.000000	0.71417	0.879000	0.34478	0.147000	0.21601	4.223000	0.58587	2.717000	0.92951	0.650000	0.86243	.		0.398	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416	Intron
SACS	26278	broad.mit.edu	37	13	23911439	23911439	+	Silent	SNP	G	G	A	rs145327845	byFrequency	TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA;ManualReview;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr13:23911439G>A	ENST00000382292.3	-	9	6849	c.6576C>T	c.(6574-6576)atC>atT	p.I2192I	SACS_ENST00000382298.3_Silent_p.I2192I|SACS_ENST00000402364.1_Silent_p.I1442I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2192					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.I2045I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GTTTCTCATCGATAAGACTCA	0.368													A|||	4	0.000798722	0.0023	0.0	5008	,	,		21050	0.0		0.0	False		,,,				2504	0.001															1	Substitution - coding silent(1)	ovary(1)	13						A		10,4396	822.0+/-416.4	0,10,2193	56.0	54.0	55.0		6576	2.3	1.0	13	dbSNP_134	55	0,8598		0,0,4299	no	coding-synonymous	SACS	NM_014363.4		0,10,6492	AA,AG,GG		0.0,0.227,0.0769		2192/4580	23911439	10,12994	2203	4299	6502	22809439	SO:0001819	synonymous_variant	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.6576C>T	13.37:g.23911439G>A			22809439	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																				0.368	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
TBC1D4	9882	broad.mit.edu	37	13	75869117	75869117	+	Silent	SNP	A	A	G			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr13:75869117A>G	ENST00000377636.3	-	18	3535	c.3189T>C	c.(3187-3189)caT>caC	p.H1063H	TBC1D4_ENST00000431480.2_Silent_p.H1055H|TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000425511.1_Silent_p.H227H|TBC1D4_ENST00000377625.2_Silent_p.H1000H	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1063	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.H1063H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TGTGATAGTCATGAAGGAGCC	0.388																																																1	Substitution - coding silent(1)	ovary(1)	13											83.0	82.0	82.0					13																	75869117		1880	4129	6009	74767118	SO:0001819	synonymous_variant	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3189T>C	13.37:g.75869117A>G			74767118	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																				0.388	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
VRTN	55237	broad.mit.edu	37	14	74825030	74825030	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA;Sequenom			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr14:74825030C>T	ENST00000256362.4	+	2	1785	c.1544C>T	c.(1543-1545)gCc>gTc	p.A515V		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	515					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)	p.A515V(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						CGCAGGGCTGCCCGCAGGCAG	0.667																																																1	Substitution - Missense(1)	ovary(1)	14											60.0	65.0	63.0					14																	74825030		2202	4300	6502	73894783	SO:0001583	missense	55237			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1544C>T	14.37:g.74825030C>T	ENSP00000256362:p.Ala515Val		73894783	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	37	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534710	0.85812	.	.	ENSG00000133980	ENST00000256362	T	0.61158	0.13	4.29	3.4	0.38934	.	0.000000	0.64402	U	0.000001	T	0.45316	0.1336	L	0.32530	0.975	0.42125	D	0.991448	B	0.17038	0.02	B	0.15052	0.012	T	0.45249	-0.9274	10	0.87932	D	0	-8.7487	10.6671	0.45736	0.0:0.9101:0.0:0.0899	.	515	Q9H8Y1	VRTN_HUMAN	V	515	ENSP00000256362:A515V	ENSP00000256362:A515V	A	+	2	0	VRTN	73894783	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.491000	0.73649	1.012000	0.39366	0.491000	0.48974	GCC		0.667	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228	
GABRB3	2562	broad.mit.edu	37	15	26793203	26793203	+	Missense_Mutation	SNP	C	C	T	rs373823173		TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr15:26793203C>T	ENST00000311550.5	-	9	1270	c.1159G>A	c.(1159-1161)Gat>Aat	p.D387N	GABRB3_ENST00000400188.3_Missense_Mutation_p.D316N|GABRB3_ENST00000299267.4_Missense_Mutation_p.D387N|GABRB3_ENST00000541819.2_Missense_Mutation_p.D443N|GABRB3_ENST00000545868.1_Missense_Mutation_p.D302N	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	387					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.D387N(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTCCTGGTATCGCCAATGCCG	0.478																																																1	Substitution - Missense(1)	ovary(1)	15						C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	131.0	123.0	126.0		1159,904,946,1159	5.8	0.4	15		126	0,8600		0,0,4300	no	missense,missense,missense,missense	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	23,23,23,23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign	387/474,302/389,316/403,387/474	26793203	1,13005	2203	4300	6503	24344296	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1159G>A	15.37:g.26793203C>T	ENSP00000308725:p.Asp387Asn		24344296	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273435	0.40194	2.27E-4	0.0	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.799927	0.11783	N	0.529932	D	0.87629	0.6225	M	0.69523	2.12	0.80722	D	1	P;B;B	0.49783	0.928;0.041;0.03	P;B;B	0.50109	0.631;0.017;0.027	D	0.84018	0.0352	10	0.28530	T	0.3	.	19.0872	0.93209	0.0:1.0:0.0:0.0	.	443;387;387	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	N	387;443;387;316;302	ENSP00000308725:D387N;ENSP00000442408:D443N;ENSP00000299267:D387N;ENSP00000383049:D316N;ENSP00000439169:D302N	ENSP00000299267:D387N	D	-	1	0	GABRB3	24344296	1.000000	0.71417	0.416000	0.26546	0.475000	0.33008	5.975000	0.70475	2.752000	0.94435	0.655000	0.94253	GAT		0.478	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
PDPK1	5170	broad.mit.edu	37	16	2647124	2647124	+	Splice_Site	SNP	G	G	C			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr16:2647124G>C	ENST00000342085.4	+	13	1551	c.1402G>C	c.(1402-1404)Ggt>Cgt	p.G468R	PDPK1_ENST00000268673.7_Splice_Site_p.G341R|PDPK1_ENST00000441549.3_Intron|PDPK1_ENST00000389224.3_Splice_Site_p.G441R|PDPK1_ENST00000354836.5_Splice_Site_p.G444R|CTD-3126B10.1_ENST00000562166.1_RNA	NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	468	PH.				actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)	p.G468R(1)		central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	TTGGCGTCAGGGTTTATTTGC	0.522																																																1	Substitution - Missense(1)	ovary(1)	16											74.0	70.0	71.0					16																	2647124		2198	4300	6498	2587125	SO:0001630	splice_region_variant	5170			AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992			8816	protein-coding gene	gene with protein product	"""PkB kinase"""	605213				9094314, 9445477	Standard	NM_002613		Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.1402-1G>C	16.37:g.2647124G>C			2587125	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	Missense_Mutation	SNP	ENST00000342085.4	37	CCDS10472.1	.	.	.	.	.	.	.	.	.	.	-	24.1	4.492701	0.84962	.	.	ENSG00000140992	ENST00000342085;ENST00000268673;ENST00000354836;ENST00000389224	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.01	5.01	0.66863	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.57431	0.2053	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.993	T	0.63541	-0.6614	9	.	.	.	-18.373	17.0462	0.86504	0.0:0.0:1.0:0.0	.	341;468	O15530-4;O15530	.;PDPK1_HUMAN	R	468;341;444;441	ENSP00000344220:G468R;ENSP00000268673:G341R;ENSP00000346895:G444R;ENSP00000373876:G441R	.	G	+	1	0	PDPK1	2587125	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.590000	0.98238	2.612000	0.88384	0.655000	0.94253	GGT		0.522	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250831.3		Missense_Mutation
PNPLA6	10908	broad.mit.edu	37	19	7621564	7621564	+	Silent	SNP	C	C	T	rs148831568	byFrequency	TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr19:7621564C>T	ENST00000221249.6	+	29	3551	c.3120C>T	c.(3118-3120)aaC>aaT	p.N1040N	PNPLA6_ENST00000600737.1_Silent_p.N1078N|PNPLA6_ENST00000545201.2_Silent_p.N1013N|PNPLA6_ENST00000414982.3_Silent_p.N1088N|PNPLA6_ENST00000450331.3_Silent_p.N1040N	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	1079	Patatin.				angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)	p.N1040N(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						CTTACTTCAACGTGACCACAG	0.667													C|||	5	0.000998403	0.0038	0.0	5008	,	,		14189	0.0		0.0	False		,,,				2504	0.0															2	Substitution - coding silent(2)	ovary(1)|stomach(1)	19						C	,,,,	21,4385	28.1+/-56.4	0,21,2182	83.0	68.0	73.0		3264,3039,3120,3234,3120	-5.6	1.0	19	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PNPLA6	NM_001166111.1,NM_001166112.1,NM_001166113.1,NM_001166114.1,NM_006702.4	,,,,	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	,,,,	1088/1376,1013/1301,1040/1328,1078/1366,1040/1328	7621564	22,12984	2203	4300	6503	7527564	SO:0001819	synonymous_variant	10908			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.3120C>T	19.37:g.7621564C>T			7527564	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																				0.667	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
ZNF486	90649	broad.mit.edu	37	19	20307880	20307880	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr19:20307880C>T	ENST00000335117.8	+	4	418	c.361C>T	c.(361-363)Cac>Tac	p.H121Y	CTC-260E6.6_ENST00000593655.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	121					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H112Y(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						TGGCAATTTACACTTTAAAAA	0.353																																																1	Substitution - Missense(1)	ovary(1)	19											84.0	90.0	88.0					19																	20307880		2134	4275	6409	20168880	SO:0001583	missense	90649			BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.361C>T	19.37:g.20307880C>T	ENSP00000335042:p.His121Tyr		20168880	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	.	.	.	.	.	.	.	.	.	.	c	7.142	0.582101	0.13749	.	.	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.04917	3.53	0.85	0.85	0.18980	.	.	.	.	.	T	0.04952	0.0133	L	0.35542	1.07	0.21220	N	0.999757	P	0.34615	0.459	B	0.33339	0.162	T	0.38415	-0.9662	9	0.51188	T	0.08	.	4.7959	0.13272	0.0:1.0:0.0:0.0	.	121	Q96H40	ZN486_HUMAN	Y	160;121	ENSP00000335042:H121Y	ENSP00000335042:H121Y	H	+	1	0	ZNF486	20168880	0.000000	0.05858	0.101000	0.21167	0.100000	0.18952	-0.483000	0.06536	0.192000	0.20272	0.195000	0.17529	CAC		0.353	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
EXOC6B	23233	broad.mit.edu	37	2	72727056	72727056	+	Missense_Mutation	SNP	T	T	A			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr2:72727056T>A	ENST00000272427.6	-	12	1343	c.1213A>T	c.(1213-1215)Att>Ttt	p.I405F	EXOC6B_ENST00000410104.1_Missense_Mutation_p.I405F	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	405					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)		p.I405F(1)		breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						AAAAGCACAATGAGGTTCTTC	0.328																																																1	Substitution - Missense(1)	ovary(1)	2											65.0	58.0	60.0					2																	72727056		1843	4044	5887	72580564	SO:0001583	missense	23233			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"""SEC15-like 2 (S. cerevisiae)"", ""SEC15 homolog B (S. cerevisiae)"""	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1213A>T	2.37:g.72727056T>A	ENSP00000272427:p.Ile405Phe		72580564	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	37	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.906088	0.92107	.	.	ENSG00000144036	ENST00000272427;ENST00000410104;ENST00000290144	T;T	0.52983	0.64;0.64	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.71508	0.3348	M	0.88450	2.955	0.80722	D	1	P;D	0.63880	0.675;0.993	B;D	0.68192	0.309;0.956	T	0.77683	-0.2496	10	0.87932	D	0	.	12.9966	0.58650	0.0:0.0:0.0:1.0	.	405;405	Q9Y2D4;Q9Y2D4-2	EXC6B_HUMAN;.	F	405	ENSP00000272427:I405F;ENSP00000386698:I405F	ENSP00000272427:I405F	I	-	1	0	EXOC6B	72580564	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.645000	0.83430	2.177000	0.69029	0.533000	0.62120	ATT		0.328	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570	
CNTNAP5	129684	broad.mit.edu	37	2	125262000	125262000	+	Silent	SNP	A	A	C			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr2:125262000A>C	ENST00000431078.1	+	8	1555	c.1191A>C	c.(1189-1191)acA>acC	p.T397T		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	397	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.T397T(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGTTTCGAACATGGAACAAGG	0.547																																																1	Substitution - coding silent(1)	ovary(1)	2											89.0	85.0	86.0					2																	125262000		1912	4135	6047	124978470	SO:0001819	synonymous_variant	129684			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1191A>C	2.37:g.125262000A>C			124978470	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.547	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
CHRNA1	1134	broad.mit.edu	37	2	175619076	175619076	+	Silent	SNP	C	C	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr2:175619076C>T	ENST00000261007.5	-	6	552	c.486G>A	c.(484-486)acG>acA	p.T162T	CHRNA1_ENST00000348749.5_Silent_p.T137T|CHRNA1_ENST00000409219.1_Silent_p.T137T|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_Intron|CHRNA1_ENST00000409323.1_Silent_p.T137T	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	162					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)	p.T162T(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GAGGTGTCCACGTGATGTGGC	0.478																																																1	Substitution - coding silent(1)	ovary(1)	2											163.0	140.0	148.0					2																	175619076		2203	4300	6503	175327322	SO:0001819	synonymous_variant	1134			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.486G>A	2.37:g.175619076C>T			175327322	B4DRV6|D3DPE8	Silent	SNP	ENST00000261007.5	37	CCDS33331.1																																																																																				0.478	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
CPO	130749	broad.mit.edu	37	2	207804354	207804354	+	Silent	SNP	T	T	C			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	T	T	C	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr2:207804354T>C	ENST00000272852.3	+	1	77	c.31T>C	c.(31-33)Ttg>Ctg	p.L11L		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	11						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.L11L(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		CCTTTATCTTTTGGGGATGCT	0.418																																																1	Substitution - coding silent(1)	ovary(1)	2											165.0	164.0	164.0					2																	207804354		2203	4300	6503	207512599	SO:0001819	synonymous_variant	130749				CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.31T>C	2.37:g.207804354T>C			207512599	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																				0.418	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
PLCD4	84812	broad.mit.edu	37	2	219498451	219498451	+	Missense_Mutation	SNP	G	G	A			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr2:219498451G>A	ENST00000450993.2	+	11	1912	c.1573G>A	c.(1573-1575)Gaa>Aaa	p.E525K	RP11-548H3.1_ENST00000607946.1_RNA|PLCD4_ENST00000432688.1_Missense_Mutation_p.E557K|PLCD4_ENST00000417849.1_Missense_Mutation_p.E525K	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	525	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.E525K(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		ATCTTTCTCTGAAACCAAGGC	0.512																																																1	Substitution - Missense(1)	ovary(1)	2											75.0	69.0	71.0					2																	219498451		1904	4132	6036	219206695	SO:0001583	missense	84812			AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.1573G>A	2.37:g.219498451G>A	ENSP00000388631:p.Glu525Lys		219206695	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.006357	0.93287	.	.	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.77750	-1.12;-1.12;-1.12	5.53	5.53	0.82687	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	D	0.000000	D	0.92116	0.7501	H	0.96269	3.795	0.80722	D	1	D	0.69078	0.997	D	0.71414	0.973	D	0.93903	0.7190	10	0.87932	D	0	.	19.2635	0.93977	0.0:0.0:1.0:0.0	.	525	Q9BRC7	PLCD4_HUMAN	K	525;525;525;557	ENSP00000388631:E525K;ENSP00000396942:E525K;ENSP00000396185:E557K	ENSP00000251959:E525K	E	+	1	0	PLCD4	219206695	1.000000	0.71417	0.988000	0.46212	0.577000	0.36160	9.445000	0.97587	2.882000	0.98803	0.655000	0.94253	GAA		0.512	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		
PAX3	5077	broad.mit.edu	37	2	223158470	223158470	+	Intron	SNP	G	G	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr2:223158470G>T	ENST00000350526.4	-	4	723				PAX3_ENST00000409551.3_Intron|PAX3_ENST00000392069.2_Intron|PAX3_ENST00000258387.5_Missense_Mutation_p.A198D|PAX3_ENST00000392070.2_Intron|PAX3_ENST00000336840.6_Intron|PAX3_ENST00000409828.3_3'UTR|PAX3_ENST00000344493.4_Intron	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3						apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGAGACCAGGGCCTTTCCTGA	0.488			T	"""FOXO1A, NCOA1"""	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																																Dom	yes		2	2q35	5077	paired box gene 3	yes	M	0			2											103.0	113.0	110.0					2																	223158470		2203	4300	6503	222866714	SO:0001627	intron_variant	5077				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"""Paired boxes"", ""Homeoboxes / PRD class"""	8617	protein-coding gene	gene with protein product		606597	"""Waardenburg syndrome 1"", ""paired box gene 3 (Waardenburg syndrome 1)"""	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.586+415C>A	2.37:g.223158470G>T			222866714	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	37	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	G	9.434	1.086366	0.20390	.	.	ENSG00000135903	ENST00000258387	D	0.99394	-5.82	3.71	0.806	0.18708	.	.	.	.	.	D	0.95156	0.8430	.	.	.	0.09310	N	1	B	0.34264	0.446	B	0.24974	0.057	D	0.92639	0.6123	8	0.11794	T	0.64	.	5.7922	0.18367	0.3683:0.0:0.6317:0.0	.	198	P23760-3	.	D	198	ENSP00000258387:A198D	ENSP00000258387:A198D	A	-	2	0	PAX3	222866714	0.001000	0.12720	0.001000	0.08648	0.042000	0.13812	0.211000	0.17474	0.141000	0.18875	0.650000	0.86243	GCC		0.488	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1		
CST1	1469	broad.mit.edu	37	20	23731339	23731339	+	Silent	SNP	A	A	G	rs3188296		TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	ManualReview;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr20:23731339A>G	ENST00000304749.2	-	1	235	c.165T>C	c.(163-165)taT>taC	p.Y55Y	CST1_ENST00000398402.1_Silent_p.Y55Y	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	55					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.Y55Y(1)		kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					TGGCCTTGTTATACTCGCTGA	0.572																																																1	Substitution - coding silent(1)	ovary(1)	20											172.0	140.0	151.0					20																	23731339		2203	4300	6503	23679339	SO:0001819	synonymous_variant	1469			M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.165T>C	20.37:g.23731339A>G			23679339	Q96LE6|Q9UCQ6	Silent	SNP	ENST00000304749.2	37	CCDS13160.1																																																																																				0.572	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
HYAL2	8692	broad.mit.edu	37	3	50357666	50357666	+	Silent	SNP	C	C	G			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	G	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA;Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr3:50357666C>G	ENST00000447092.1	-	1	2547	c.255G>C	c.(253-255)ctG>ctC	p.L85L	TUSC2_ENST00000462137.1_5'UTR|HYAL2_ENST00000442581.1_Silent_p.L85L|HYAL2_ENST00000395139.3_Silent_p.L85L|HYAL2_ENST00000357750.4_Silent_p.L85L			Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	85					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|defense response to virus (GO:0051607)|fusion of virus membrane with host plasma membrane (GO:0019064)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|kidney development (GO:0001822)|monocyte activation (GO:0042117)|multicellular organismal aging (GO:0010259)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|transformation of host cell by virus (GO:0019087)|viral entry into host cell (GO:0046718)	anchored component of external side of plasma membrane (GO:0031362)|anchored component of plasma membrane (GO:0046658)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|lysosome (GO:0005764)|membrane raft (GO:0045121)|microvillus (GO:0005902)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|hyaluronic acid binding (GO:0005540)|hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)|receptor signaling protein tyrosine kinase inhibitor activity (GO:0030294)|receptor tyrosine kinase binding (GO:0030971)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)	p.L85L(1)		breast(1)|endometrium(2)|kidney(1)|ovary(1)|prostate(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		AGCGTGGATACAGGCCTAGAC	0.537																																																1	Substitution - coding silent(1)	ovary(1)	3											77.0	68.0	71.0					3																	50357666		2203	4300	6503	50332670	SO:0001819	synonymous_variant	8692			AJ000099	CCDS2818.1	3p21.3	2008-07-18			ENSG00000068001	ENSG00000068001			5321	protein-coding gene	gene with protein product	"""lysosomal hyaluronidase"", ""PH-20 homolog"", ""hyaluronidase 2"""	603551				9712871, 9790770	Standard	NM_003773		Approved	LuCa-2, LUCA2	uc003czv.3	Q12891	OTTHUMG00000156876	ENST00000447092.1:c.255G>C	3.37:g.50357666C>G			50332670	B3KRZ2|O15177|Q9BW29	Silent	SNP	ENST00000447092.1	37	CCDS2818.1																																																																																				0.537	HYAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346391.1	NM_003773	
GPR149	344758	broad.mit.edu	37	3	154147152	154147152	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr3:154147152C>T	ENST00000389740.2	-	1	352	c.253G>A	c.(253-255)Gtg>Atg	p.V85M		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	85					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V85M(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AAGATGGTCACCGACAGGACG	0.478																																																1	Substitution - Missense(1)	ovary(1)	3											93.0	97.0	96.0					3																	154147152		2056	4207	6263	155629846	SO:0001583	missense	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.253G>A	3.37:g.154147152C>T	ENSP00000374390:p.Val85Met		155629846		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923976	0.34002	.	.	ENSG00000174948	ENST00000389740	T	0.75050	-0.9	5.91	4.86	0.63082	GPCR, rhodopsin-like superfamily (1);	0.279237	0.35096	N	0.003446	T	0.64338	0.2589	L	0.34521	1.04	0.19775	N	0.99995	P	0.34462	0.454	B	0.31016	0.123	T	0.62732	-0.6792	10	0.51188	T	0.08	-8.6222	15.9597	0.79918	0.0:0.9256:0.0:0.0744	.	85	Q86SP6	GP149_HUMAN	M	85	ENSP00000374390:V85M	ENSP00000374390:V85M	V	-	1	0	GPR149	155629846	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.457000	0.60088	2.793000	0.96121	0.655000	0.94253	GTG		0.478	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
LPP	4026	broad.mit.edu	37	3	188592229	188592229	+	Missense_Mutation	SNP	A	A	C	rs150544464	byFrequency	TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr3:188592229A>C	ENST00000312675.4	+	11	2047	c.1801A>C	c.(1801-1803)Atc>Ctc	p.I601L	LPP_ENST00000543006.1_Missense_Mutation_p.I601L	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	601	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.I601L(1)	HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTCTGCCCGCATCAGGGTGTT	0.512			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""																																		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	1	Substitution - Missense(1)	ovary(1)	3											121.0	110.0	114.0					3																	188592229		2203	4300	6503	190074923	SO:0001583	missense	4026			AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1801A>C	3.37:g.188592229A>C	ENSP00000318089:p.Ile601Leu		190074923	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	.	.	.	.	.	.	.	.	.	.	A	35	5.482446	0.96307	.	.	ENSG00000145012	ENST00000312675;ENST00000543006	T;T	0.59083	0.29;0.29	5.79	5.79	0.91817	Zinc finger, LIM-type (1);	0.044096	0.85682	D	0.000000	T	0.56140	0.1965	N	0.17474	0.49	0.80722	D	1	P;B	0.48016	0.904;0.053	P;B	0.58873	0.847;0.04	T	0.51252	-0.8729	10	0.12766	T	0.61	.	15.3154	0.74074	1.0:0.0:0.0:0.0	.	454;601	B7Z8W0;Q93052	.;LPP_HUMAN	L	601	ENSP00000318089:I601L;ENSP00000438891:I601L	ENSP00000318089:I601L	I	+	1	0	LPP	190074923	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.209000	0.71365	0.533000	0.62120	ATC		0.512	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
ANKRD6	22881	broad.mit.edu	37	6	90276810	90276810	+	Missense_Mutation	SNP	A	A	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr6:90276810A>T	ENST00000522441.1	+	2	756	c.115A>T	c.(115-117)Acc>Tcc	p.T39S	ANKRD6_ENST00000485637.1_Missense_Mutation_p.T39S|RP11-16C18.3_ENST00000438267.1_RNA|ANKRD6_ENST00000520886.2_Intron|ANKRD6_ENST00000447838.2_Missense_Mutation_p.T39S|ANKRD6_ENST00000339746.4_Missense_Mutation_p.T39S|ANKRD6_ENST00000520793.1_Missense_Mutation_p.T39S|RP11-16C18.3_ENST00000425588.1_RNA|ANKRD6_ENST00000369408.5_Missense_Mutation_p.T39S	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	39					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T39S(1)		NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		GGTAGCGGTTACCAAGGTAAC	0.502																																																1	Substitution - Missense(1)	ovary(1)	6											39.0	39.0	39.0					6																	90276810		1920	4128	6048	90333529	SO:0001583	missense	22881			AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.115A>T	6.37:g.90276810A>T	ENSP00000430985:p.Thr39Ser		90333529	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Missense_Mutation	SNP	ENST00000522441.1	37	CCDS56441.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.930088	0.92389	.	.	ENSG00000135299	ENST00000369408;ENST00000339746;ENST00000447838;ENST00000520458;ENST00000465722;ENST00000523798;ENST00000522441;ENST00000522779;ENST00000485637;ENST00000522705;ENST00000518150;ENST00000520793	T;T;T;T;T;T;T;T;T;T;T	0.70749	0.68;-0.51;-0.51;1.01;-0.28;1.01;-0.51;1.01;0.68;1.01;0.61	5.89	5.89	0.94794	Ankyrin repeat-containing domain (3);	0.000000	0.56097	D	0.000034	T	0.65719	0.2718	L	0.31120	0.905	0.51233	D	0.999917	D;D;D;D	0.89917	0.992;1.0;0.999;1.0	D;D;D;D	0.91635	0.987;0.998;0.997;0.999	T	0.63773	-0.6561	10	0.09843	T	0.71	-23.2216	16.3158	0.82923	1.0:0.0:0.0:0.0	.	39;39;39;39	B3KUC3;Q9Y2G4;Q9Y2G4-1;C9JJE8	.;ANKR6_HUMAN;.;.	S	39	ENSP00000358416:T39S;ENSP00000345767:T39S;ENSP00000396771:T39S;ENSP00000431061:T39S;ENSP00000429431:T39S;ENSP00000428377:T39S;ENSP00000430985:T39S;ENSP00000429337:T39S;ENSP00000430954:T39S;ENSP00000428309:T39S;ENSP00000429782:T39S	ENSP00000345767:T39S	T	+	1	0	ANKRD6	90333529	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.870000	0.92336	2.254000	0.74563	0.533000	0.62120	ACC		0.502	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
UFL1	23376	broad.mit.edu	37	6	96988491	96988491	+	Silent	SNP	T	T	C			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	T	T	C	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr6:96988491T>C	ENST00000369278.4	+	11	1305	c.1239T>C	c.(1237-1239)agT>agC	p.S413S		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	413					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)	p.S413S(1)									TTAGTACAAGTAAAAAGGATA	0.299																																																1	Substitution - coding silent(1)	ovary(1)	6											65.0	65.0	65.0					6																	96988491		2203	4295	6498	97095212	SO:0001819	synonymous_variant	23376			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1239T>C	6.37:g.96988491T>C			97095212	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																				0.299	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
PDE7B	27115	broad.mit.edu	37	6	136475307	136475307	+	Missense_Mutation	SNP	G	G	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr6:136475307G>T	ENST00000308191.6	+	7	876	c.573G>T	c.(571-573)gaG>gaT	p.E191D	RP13-143G15.4_ENST00000417643.1_RNA|RP13-143G15.4_ENST00000591521.1_RNA|RP13-143G15.4_ENST00000585946.1_RNA	NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	191	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)	p.E191D(1)		breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	ACCTGAAAGAGCCAAAGGTAA	0.512																																																1	Substitution - Missense(1)	ovary(1)	6											105.0	80.0	88.0					6																	136475307		2203	4300	6503	136517000	SO:0001583	missense	27115			AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"""Phosphodiesterases"""	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.573G>T	6.37:g.136475307G>T	ENSP00000310661:p.Glu191Asp		136517000	Q5W154	Missense_Mutation	SNP	ENST00000308191.6	37	CCDS5175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.00|19.00	3.741047|3.741047	0.69304|0.69304	.|.	.|.	ENSG00000171408|ENSG00000171408	ENST00000446774|ENST00000308191;ENST00000367787	.|T	.|0.81415	.|-1.49	5.8|5.8	2.99|2.99	0.34606|0.34606	.|Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	.|0.051744	.|0.85682	.|D	.|0.000000	T|T	0.79082|0.79082	0.4386|0.4386	L|L	0.55834|0.55834	1.745|1.745	0.52501|0.52501	D|D	0.999951|0.999951	.|P;D	.|0.59767	.|0.951;0.986	.|P;D	.|0.63793	.|0.748;0.918	T|T	0.78409|0.78409	-0.2215|-0.2215	5|10	.|0.49607	.|T	.|0.09	.|.	10.1797|10.1797	0.42961|0.42961	0.286:0.0:0.714:0.0|0.286:0.0:0.714:0.0	.|.	.|243;191	.|A1E5M1;Q9NP56	.|.;PDE7B_HUMAN	S|D	86|191;327	.|ENSP00000310661:E191D	.|ENSP00000310661:E191D	A|E	+|+	1|3	0|2	PDE7B|PDE7B	136517000|136517000	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.936000|0.936000	0.57629|0.57629	3.409000|3.409000	0.52657|0.52657	0.334000|0.334000	0.23590|0.23590	-0.136000|-0.136000	0.14681|0.14681	GCC|GAG		0.512	PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1		
CFAP69	79846	broad.mit.edu	37	7	89938625	89938625	+	Missense_Mutation	SNP	A	A	C			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr7:89938625A>C	ENST00000389297.4	+	22	2850	c.2599A>C	c.(2599-2601)Aaa>Caa	p.K867Q	C7orf63_ENST00000316089.8_Missense_Mutation_p.K821Q|C7orf63_ENST00000497910.1_Missense_Mutation_p.K849Q	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		867								p.K821Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CAGATACCATAAACGACCACA	0.289																																																1	Substitution - Missense(1)	ovary(1)	7											114.0	110.0	111.0					7																	89938625		1804	4064	5868	89776561	SO:0001583	missense	79846																														ENST00000389297.4:c.2599A>C	7.37:g.89938625A>C	ENSP00000373948:p.Lys867Gln		89776561	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.770|0.770	-0.766285|-0.766285	0.02974|0.02974	.|.	.|.	ENSG00000105792|ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577|ENST00000412839	T;T;T;T|.	0.23147|.	2.5;2.51;2.5;1.92|.	5.56|5.56	0.429|0.429	0.16506|0.16506	.|.	0.670270|.	0.13854|.	N|.	0.358184|.	T|.	0.20333|.	0.0489|.	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B;B|.	0.22983|.	0.003;0.078|.	B;B|.	0.21360|.	0.012;0.034|.	T|.	0.23261|.	-1.0193|.	10|.	0.14656|.	T|.	0.56|.	-0.3202|-0.3202	2.6887|2.6887	0.05115|0.05115	0.3919:0.1071:0.3913:0.1097|0.3919:0.1071:0.3913:0.1097	.|.	849;867|.	A5D8W1-5;A5D8W1|.	.;CG063_HUMAN|.	Q|S	867;821;849;404|95	ENSP00000373948:K867Q;ENSP00000321753:K821Q;ENSP00000419549:K849Q;ENSP00000391571:K404Q|.	ENSP00000321753:K821Q|.	K|X	+|+	1|2	0|2	C7orf63|C7orf63	89776561|89776561	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.138000|-0.138000	0.10374|0.10374	-0.169000|-0.169000	0.10834|0.10834	-1.039000|-1.039000	0.02377|0.02377	AAA|TAA		0.289	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
FAM133B	257415	broad.mit.edu	37	7	92195341	92195341	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr7:92195341C>T	ENST00000445716.1	-	10	746	c.644G>A	c.(643-645)cGa>cAa	p.R215Q	FAM133B_ENST00000438306.1_Missense_Mutation_p.R205Q|FAM133B_ENST00000427372.1_Missense_Mutation_p.R205Q	NM_152789.2	NP_690002.2	Q5BKY9	F133B_HUMAN	family with sequence similarity 133, member B	215	Lys-rich.						poly(A) RNA binding (GO:0044822)	p.R215Q(1)		endometrium(1)|large_intestine(1)|ovary(1)|upper_aerodigestive_tract(1)	4	all_cancers(62;7.39e-11)|all_epithelial(64;7.03e-10)|Breast(17;0.00201)|all_lung(186;0.0384)|Lung NSC(181;0.053)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;9.78e-06)|all cancers(6;1.67e-05)|Epithelial(20;0.113)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TGCTTTTTCTCGTTCTTCACT	0.323																																																1	Substitution - Missense(1)	ovary(1)	7											142.0	136.0	138.0					7																	92195341		1832	4082	5914	92033277	SO:0001583	missense	257415				CCDS47640.1, CCDS47641.1	7q21.2	2014-02-12	2007-04-26		ENSG00000234545	ENSG00000234545			28629	protein-coding gene	gene with protein product						12477932	Standard	NM_152789		Approved	MGC40405	uc003umc.3	Q5BKY9	OTTHUMG00000155863	ENST00000445716.1:c.644G>A	7.37:g.92195341C>T	ENSP00000398401:p.Arg215Gln		92033277	B2R994|Q05D67|Q6P5S6|Q8N0W8	Missense_Mutation	SNP	ENST00000445716.1	37	CCDS47640.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.353867	0.41700	.	.	ENSG00000234545	ENST00000438306;ENST00000445716;ENST00000427372;ENST00000494079	T;T;T	0.45668	0.89;0.9;0.89	4.68	3.76	0.43208	.	.	.	.	.	T	0.26122	0.0637	L	0.27053	0.805	0.24473	N	0.994384	B	0.23490	0.086	B	0.08055	0.003	T	0.13124	-1.0521	9	0.26408	T	0.33	-1.8205	6.4406	0.21847	0.0:0.7673:0.0:0.2327	.	215	Q5BKY9	F133B_HUMAN	Q	205;215;205;112	ENSP00000389783:R205Q;ENSP00000398401:R215Q;ENSP00000402843:R205Q	ENSP00000402843:R205Q	R	-	2	0	FAM133B	92033277	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.862000	0.27899	1.227000	0.43598	0.563000	0.77884	CGA		0.323	FAM133B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342181.2	NM_001040057	
HEPACAM2	253012	broad.mit.edu	37	7	92825177	92825177	+	Silent	SNP	T	T	C			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	T	T	C	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr7:92825177T>C	ENST00000394468.2	-	8	1316	c.1239A>G	c.(1237-1239)gaA>gaG	p.E413E	HEPACAM2_ENST00000453812.2_Silent_p.E436E|HEPACAM2_ENST00000492616.1_5'UTR|HEPACAM2_ENST00000440868.1_Missense_Mutation_p.N393S|HEPACAM2_ENST00000341723.4_Silent_p.E401E	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	413					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)		p.E401E(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						AAGCAACAAATTCATATATTC	0.388																																																1	Substitution - coding silent(1)	ovary(1)	7											118.0	116.0	116.0					7																	92825177		2203	4300	6503	92663113	SO:0001819	synonymous_variant	253012			AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.1239A>G	7.37:g.92825177T>C			92663113	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Silent	SNP	ENST00000394468.2	37	CCDS43616.1	.	.	.	.	.	.	.	.	.	.	T	13.71	2.318807	0.41096	.	.	ENSG00000188175	ENST00000440868	T	0.57107	0.42	4.89	-0.224	0.13115	.	.	.	.	.	T	0.33498	0.0865	.	.	.	0.80722	D	1	B	0.14805	0.011	B	0.12837	0.008	T	0.09335	-1.0679	8	0.16420	T	0.52	-26.2025	9.4904	0.38955	0.0:0.4015:0.0:0.5985	.	393	C9JN07	.	S	393	ENSP00000389592:N393S	ENSP00000389592:N393S	N	-	2	0	HEPACAM2	92663113	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	0.722000	0.25925	-0.112000	0.11979	0.528000	0.53228	AAT		0.388	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151	
GYG2	8908	broad.mit.edu	37	X	2774571	2774571	+	Missense_Mutation	SNP	A	A	T			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chrX:2774571A>T	ENST00000381163.3	+	7	895	c.613A>T	c.(613-615)Agg>Tgg	p.R205W	GYG2_ENST00000381161.1_3'UTR|GYG2_ENST00000542787.1_Missense_Mutation_p.R205W|GYG2-AS1_ENST00000445107.1_RNA|GYG2_ENST00000398806.3_Missense_Mutation_p.R174W|GYG2_ENST00000338623.5_Missense_Mutation_p.R205W	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	205					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)	p.R205W(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TAGTTTCTTCAGGAACTGGTC	0.453																																																1	Substitution - Missense(1)	ovary(1)	X											134.0	105.0	115.0					X																	2774571		2203	4298	6501	2784571	SO:0001583	missense	8908			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.613A>T	X.37:g.2774571A>T	ENSP00000370555:p.Arg205Trp		2784571	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.71|13.71	2.317614|2.317614	0.40996|0.40996	.|.	.|.	ENSG00000056998|ENSG00000056998	ENST00000381157|ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787	.|T;T;T;T	.|0.45276	.|0.9;0.9;0.9;0.9	3.19|3.19	3.19|3.19	0.36642|0.36642	.|.	.|0.080555	.|0.50627	.|D	.|0.000102	T|T	0.52917|0.52917	0.1764|0.1764	L|L	0.58583|0.58583	1.82|1.82	0.24669|0.24669	N|N	0.993427|0.993427	.|D;P;D;D;D;D	.|0.63046	.|0.965;0.931;0.992;0.972;0.961;0.968	.|P;P;P;D;P;D	.|0.66602	.|0.908;0.908;0.849;0.945;0.908;0.945	T|T	0.39800|0.39800	-0.9596|-0.9596	5|10	.|0.87932	.|D	.|0	.|.	6.5855|6.5855	0.22618|0.22618	0.8823:0.0:0.1177:0.0|0.8823:0.0:0.1177:0.0	.|.	.|205;205;165;174;174;205	.|O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.|.;.;.;.;.;GLYG2_HUMAN	L|W	23|174;205;205;205	.|ENSP00000381786:R174W;ENSP00000370555:R205W;ENSP00000341273:R205W;ENSP00000446092:R205W	.|ENSP00000341273:R205W	Q|R	+|+	2|1	0|2	GYG2|GYG2	2784571|2784571	1.000000|1.000000	0.71417|0.71417	0.843000|0.843000	0.33291|0.33291	0.055000|0.055000	0.15305|0.15305	5.586000|5.586000	0.67503|0.67503	1.137000|1.137000	0.42214|0.42214	0.425000|0.425000	0.28330|0.28330	CAG|AGG		0.453	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
TP53	7157	broad.mit.edu	37	17	7573984	7573985	+	Frame_Shift_Ins	INS	-	-	AGGCCTT			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	-	-	AGGCCTT	AGGCCTT	-	-	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr17:7573984_7573985insAGGCCTT	ENST00000269305.4	-	10	1231_1232	c.1042_1043insAAGGCCT	c.(1042-1044)ttgfs	p.-347fs	TP53_ENST00000420246.2_3'UTR|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Frame_Shift_Ins_p.-347fs|TP53_ENST00000455263.2_3'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.L348*(2)|p.L344fs*22(1)|p.?(1)|p.L348fs*1(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTTGAGTTCCAAGGCCTCATTC	0.589		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	14	Whole gene deletion(8)|Substitution - Nonsense(2)|Deletion - Frameshift(2)|Unknown(1)|Insertion - Frameshift(1)	bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|stomach(1)|oesophagus(1)|lung(1)|ovary(1)	17																																								7514710	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1042_1043insAAGGCCT	17.37:g.7573984_7573985insAGGCCTT	ENSP00000269305:p.Ala347fs		7514709	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.589	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
ASTN2	23245	broad.mit.edu	37	9	119249758	119249767	+	Frame_Shift_Del	DEL	TCAGCAAAAC	TCAGCAAAAC	-			TCGA-13-0751-01A-01D-0446-08	TCGA-13-0751-10A-01D-0446-08	TCAGCAAAAC	TCAGCAAAAC	-	-	TCAGCAAAAC	TCAGCAAAAC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	9f335cd1-2736-41be-a02b-cdbe4017bb3d	f7803d4b-8f86-40d9-8000-1d8301440cb3	g.chr9:119249758_119249767delTCAGCAAAAC	ENST00000313400.4	-	20	3468_3477	c.3368_3377delGTTTTGCTGA	c.(3367-3378)agttttgctgatfs	p.SFAD1123fs	ASTN2_ENST00000361477.3_Frame_Shift_Del_p.SFAD175fs|ASTN2_ENST00000373996.3_Frame_Shift_Del_p.SFAD1119fs|ASTN2_ENST00000288520.5_Frame_Shift_Del_p.SFAD224fs|ASTN2_ENST00000341734.4_Frame_Shift_Del_p.SFAD175fs|ASTN2_ENST00000361209.2_Frame_Shift_Del_p.SFAD1072fs			O75129	ASTN2_HUMAN	astrotactin 2	1123	Fibronectin type-III.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.S1072fs*12(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GAGTAAGTCATCAGCAAAACTCAGGAATTC	0.481																																																1	Deletion - Frameshift(1)	ovary(1)	9																																								118289588	SO:0001589	frameshift_variant	23245			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3368_3377delGTTTTGCTGA	9.37:g.119249758_119249767delTCAGCAAAAC	ENSP00000314038:p.Ser1123fs		118289579	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Frame_Shift_Del	DEL	ENST00000313400.4	37																																																																																					0.481	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
