#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_IsAdjacentToRepeatRegion	i_IsMicroSat	i_MUTSIG_Published_Results	i_Mutation_Status	i_NumberOfSatRepeats	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_is_in_m2pon	i_refseq_mrna_id	i_secondary_variant_classification	i_site
ACTRT2	140625	broad.mit.edu	37	1	2938408	2938410	+	In_Frame_Del	DEL	AGA	AGA	-	rs4013154|rs201580305	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AGA	AGA	-	-	AGA	AGA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:2938408_2938410delAGA	ENST00000378404.2	+	1	363_365	c.158_160delAGA	c.(157-162)cagaag>cag	p.K55del		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	55				Missing (in Ref. 5; AAH29499). {ECO:0000305}.		cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		GAGGCCAACCAGAAGAAGTACTT	0.611														563	0.11242	0.0106	0.2176	5008	,	,		17049	0.1925		0.1581	False		,,,				2504	0.046					ENST00000378404.2		NA																	0				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26						c.(157-162)cagaag>cag		actin-related protein T2				152,4114		9,134,1990						4.1	0.8		dbSNP_108	43	1412,6842		109,1194,2824	no	coding	ACTRT2	NM_080431.4		118,1328,4814	A1A1,A1R,RR		17.1069,3.5631,12.492				1564,10956				SO:0001651	inframe_deletion	140625					cytoplasm|cytoskeleton		g.chr1:2938408_2938410delAGA	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.158_160delAGA	1.37:g.2938411_2938413delAGA	ENSP00000367658:p.Lys55del	False	False		Somatic	2					p.K55del	NM_080431.4	NP_536356.3	WXS	Illumina HiSeq	Phase_I	Q8TDY3	ACTT2_HUMAN		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)	1	363_365	+	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)	55	Missing (in Ref. 5; AAH29499).				B1AN52|Q8NHS6|Q8TDG1	In_Frame_Del	DEL	ENST00000378404.2	37	c.158_160delAGA	CCDS45.1																																																																																				0.611	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	0	NM_080431		1:2938408
MUC5B	727897	broad.mit.edu	37	11	1271219	1271221	+	In_Frame_Del	DEL	CCA	CCA	-	rs61430934|rs199629887	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CCA	CCA	-	-	CCA	CCA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:1271219_1271221delCCA	ENST00000529681.1	+	31	13167_13169	c.13109_13111delCCA	c.(13108-13113)gccacc>gcc	p.T4373del	MUC5B_ENST00000447027.1_In_Frame_Del_p.T4376del|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4373	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.			Missing (in Ref. 4; CAA96577). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACCACGAAGGCCACCACGACAAG	0.635														328	0.0654952	0.0242	0.1095	5008	,	,		19711	0.0496		0.0805	False		,,,				2504	0.091					ENST00000529681.1		NA																	0				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137						c.(13108-13113)gccacc>gcc		mucin 5B, oligomeric mucus/gel-forming				85,4011		5,75,1968						-0.1	0.0		dbSNP_129	110	576,7474		25,526,3474	no	coding	MUC5B	NM_002458.2		30,601,5442	A1A1,A1R,RR		7.1553,2.0752,5.4421				661,11485				SO:0001651	inframe_deletion	727897				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding	g.chr11:1271219_1271221delCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13109_13111delCCA	11.37:g.1271222_1271224delCCA	ENSP00000436812:p.Thr4373del	False	False		Somatic	2				MUC5B_ENST00000447027.1_In_Frame_Del_p.T4376del	p.T4373del	NM_002458.2	NP_002449.2	WXS	Illumina HiSeq	Phase_I	Q9HC84	MUC5B_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	31	13167_13169	+		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	4373	Missing (in Ref. 4; CAA96577).		23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	In_Frame_Del	DEL	ENST00000529681.1	37	c.13109_13111delCCA	CCDS44515.2																																																																																				0.635	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	0	XM_001126093		11:1271219
OR52D1	390066	broad.mit.edu	37	11	5510540	5510541	+	Frame_Shift_Ins	INS	-	-	GGCT	rs146317894|rs576495879|rs190320444|rs36066208|rs377247106	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:5510540_5510541insGGCT	ENST00000322641.5	+	1	626_627	c.604_605insGGCT	c.(604-606)gggfs	p.-203fs	AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1						detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TATTGTCTATGGGCTAACTGTG	0.49														471	0.0940495	0.0212	0.1715	5008	,	,		23752	0.0754		0.1779	False		,,,				2504	0.0706					ENST00000322641.5		NA																	0				central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22						c.(604-606)gggfs		olfactory receptor, family 52, subfamily D, member 1				221,4041		4,213,1914						5.5	1.0		dbSNP_130	269	1217,7035		95,1027,3004	no	frameshift	OR52D1	NM_001005163.2		99,1240,4918	A1A1,A1R,RR		14.7479,5.1854,11.4911				1438,11076				SO:0001589	frameshift_variant	390066				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:5510540_5510541insGGCT	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.605_608dupGGCT	11.37:g.5510541_5510544dupGGCT	ENSP00000326232:p.Leu203fs	True	False		Somatic	1				HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	p.-203fs	NM_001005163.2	NP_001005163.1	WXS	Illumina HiSeq	Phase_I	Q9H346	O52D1_HUMAN		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	1	626_627	+		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)	NA					B9EGY9|Q6IFI6	Frame_Shift_Ins	INS	ENST00000322641.5	37	c.604_605insGGCT	CCDS31384.1																																																																																				0.490	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	0	NM_001005163		11:5510540
RBM4	5936	broad.mit.edu	37	11	66411364	66411384	+	In_Frame_Del	DEL	GCTGCTGCTGCAGCAGCAGCC	GCTGCTGCTGCAGCAGCAGCC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	GCTGCTGCTGCAGCAGCAGCC	GCTGCTGCTGCAGCAGCAGCC	-	-	GCTGCTGCTGCAGCAGCAGCC	GCTGCTGCTGCAGCAGCAGCC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:66411364_66411384delGCTGCTGCTGCAGCAGCAGCC	ENST00000409406.1	+	2	1633_1653	c.856_876delGCTGCTGCTGCAGCAGCAGCC	c.(856-876)gctgctgctgcagcagcagccdel	p.AAAAAAA286del	RBM4_ENST00000506523.2_Intron|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000408993.2_In_Frame_Del_p.AAAAAAA286del|RBM14-RBM4_ENST00000500635.2_Intron|RBM14-RBM4_ENST00000412278.2_In_Frame_Del_p.AAAAAAA261del|RBM4_ENST00000514361.3_In_Frame_Del_p.AAAAAAA261del|RBM4_ENST00000396053.4_Intron|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000503028.2_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000515838.2_3'UTR|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000310092.7_In_Frame_Del_p.AAAAAAA286del			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	286	Interaction with TNPO3.|Poly-Ala.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		tgctgccacagctgctgctgcagcagcagccgctgctgctg	0.615																																						ENST00000412278.2		NA																	0					NA						c.(781-801)gctgctgctgcagcagcagccdel																																						SO:0001651	inframe_deletion	0							g.chr11:66411364_66411384delGCTGCTGCTGCAGCAGCAGCC	U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.856_876delGCTGCTGCTGCAGCAGCAGCC	11.37:g.66411364_66411384delGCTGCTGCTGCAGCAGCAGCC	ENSP00000386894:p.Ala286_Ala292del	True	False		Somatic	1				RBM4_ENST00000578778.1_Intron|RBM4_ENST00000515838.2_3'UTR|RBM4_ENST00000396053.4_Intron|RBM4_ENST00000503028.2_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000514361.3_In_Frame_Del_p.AAAAAAA261del|RBM4_ENST00000408993.2_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000506523.2_Intron|RBM4_ENST00000310092.7_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000409406.1_In_Frame_Del_p.AAAAAAA286del|RBM14-RBM4_ENST00000500635.2_Intron	p.AAAAAAA261del	NM_001198845.1	NP_001185774.1	WXS	Illumina HiSeq	Phase_I					2	876_896	+			NA					B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	In_Frame_Del	DEL	ENST00000409406.1	37	c.781_801delGCTGCTGCTGCAGCAGCAGCC	CCDS41676.1																																																																																				0.615	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	0	NM_002896		11:66411364
MTMR2	8898	broad.mit.edu	37	11	95581065	95581066	+	Splice_Site	INS	-	-	TGTTGGCAACAGCATTAACACTTGGCCG			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:95581065_95581066insTGTTGGCAACAGCATTAACACTTGGCCG	ENST00000346299.5	-	10	1334		c.e10-2		MTMR2_ENST00000409459.1_Splice_Site|MTMR2_ENST00000352297.7_Splice_Site|MTMR2_ENST00000393223.3_Splice_Site|MTMR2_ENST00000484818.1_5'Flank	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2						cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACCCTTTGCCTGGAAAAAAGCA	0.342																																						ENST00000393223.3		NA																	0				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19						c.e12-2		myotubularin related protein 2																																				SO:0001630	splice_region_variant	8898					nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr11:95581065_95581066insTGTTGGCAACAGCATTAACACTTGGCCG	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.994-2->CGGCCAAGTGTTAATGCTGTTGCCAACA	11.37:g.95581065_95581066insTGTTGGCAACAGCATTAACACTTGGCCG		False	False		Somatic	0				MTMR2_ENST00000352297.7_Splice_Site|MTMR2_ENST00000409459.1_Splice_Site|MTMR2_ENST00000346299.5_Splice_Site		NM_001243571.1|NM_201278.2	NP_001230500.1|NP_958435.1	WXS	Illumina HiSeq	Phase_I	Q13614	MTMR2_HUMAN			12	1440	-		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)	NA					A6NN98|Q9UPS9	Splice_Site	INS	ENST00000346299.5	37		CCDS8305.1																																																																																				0.342	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	0	NM_016156	Intron	11:95581065
FAM118B	79607	broad.mit.edu	37	11	126131333	126131335	+	In_Frame_Del	DEL	AGA	AGA	-	rs138767340		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AGA	AGA	-	-	AGA	AGA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:126131333_126131335delAGA	ENST00000533050.1	+	8	1489_1491	c.996_998delAGA	c.(994-999)agagaa>aga	p.E333del	FAM118B_ENST00000360194.4_In_Frame_Del_p.E332del|FAM118B_ENST00000529731.1_In_Frame_Del_p.E257del	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	333										breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		GGATGGTGAGAGAAGGTCAGCTA	0.379																																						ENST00000533050.1		NA																	0				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13						c.(994-999)agagaa>aga		family with sequence similarity 118, member B				1,4263		0,1,2131						4.1	1.0			166	2,8252		0,2,4125	no	coding	FAM118B	NM_024556.3		0,3,6256	A1A1,A1R,RR		0.0242,0.0235,0.024				3,12515				SO:0001651	inframe_deletion	79607							g.chr11:126131333_126131335delAGA	BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.996_998delAGA	11.37:g.126131333_126131335delAGA	ENSP00000433343:p.Glu333del	True	False		Somatic	1				FAM118B_ENST00000360194.4_In_Frame_Del_p.E332del	p.E333del	NM_024556.3	NP_078832.1	WXS	Illumina HiSeq	Phase_I	Q9BPY3	F118B_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)	8	1489_1491	+	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	333					Q9H7B0	In_Frame_Del	DEL	ENST00000533050.1	37	c.996_998delAGA	CCDS8470.1																																																																																				0.379	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	0	NM_024556		11:126131333
TDRD3	81550	broad.mit.edu	37	13	61102576	61102578	+	In_Frame_Del	DEL	ATA	ATA	-	rs148917045|rs75684327	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	ATA	ATA	-	-	ATA	ATA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:61102576_61102578delATA	ENST00000196169.3	+	11	1726_1728	c.938_940delATA	c.(937-942)gataat>gat	p.N315del	TDRD3_ENST00000377881.2_In_Frame_Del_p.N315del|TDRD3_ENST00000377894.2_In_Frame_Del_p.N315del|TDRD3_ENST00000535286.1_In_Frame_Del_p.N408del	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	315					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GGAGTAAAAGATAATAATCATCT	0.384														604	0.120607	0.0325	0.1153	5008	,	,		16312	0.0129		0.1889	False		,,,				2504	0.2843				Colon(36;164 906 35820 50723)	ENST00000196169.3		NA																	0				breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40						c.(937-942)gataat>gat		tudor domain containing 3			,,	224,4040		12,200,1920					,,	6.1	1.0		dbSNP_134	101	1585,6669		152,1281,2694	no	coding,coding,coding	TDRD3	NM_030794.2,NM_001146071.1,NM_001146070.1	,,	164,1481,4614	A1A1,A1R,RR		19.2028,5.2533,14.4512	,,	,,		1809,10709				SO:0001651	inframe_deletion	81550				chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity	g.chr13:61102576_61102578delATA	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"""Tudor domain containing"""	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.938_940delATA	13.37:g.61102579_61102581delATA	ENSP00000196169:p.Asn315del	False	False		Somatic	2				TDRD3_ENST00000377894.2_In_Frame_Del_p.N315del|TDRD3_ENST00000535286.1_In_Frame_Del_p.N408del|TDRD3_ENST00000377881.2_In_Frame_Del_p.N315del	p.N315del	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	WXS	Illumina HiSeq	Phase_I	Q9H7E2	TDRD3_HUMAN		GBM - Glioblastoma multiforme(99;0.000291)	11	1726_1728	+		Prostate(109;0.173)|Breast(118;0.174)	315					B2MWP9|Q53XA6|Q6P992	In_Frame_Del	DEL	ENST00000196169.3	37	c.938_940delATA	CCDS9441.1																																																																																				0.384	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	0	NM_030794		13:61102576
GPHB5	122876	broad.mit.edu	37	14	63784404	63784405	+	RNA	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:63784404_63784405insG	ENST00000539258.1	-	0	215_216							Q86YW7	GPHB5_HUMAN	glycoprotein hormone beta 5						regulation of thyroid hormone mediated signaling pathway (GO:0002155)	extracellular region (GO:0005576)		p.R53W(1)		breast(1)|endometrium(1)|lung(4)|urinary_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(108;0.00372)|all cancers(60;0.0226)|BRCA - Breast invasive adenocarcinoma(234;0.0978)		CGTGGTGATCCGAAGCCCCTGC	0.599																																						ENST00000539258.1		NA																	1	Substitution - Missense(1)	p.R53W(1)	breast(1)	breast(1)|endometrium(1)|lung(4)|urinary_tract(1)	7								glycoprotein hormone beta 5																																						122876					extracellular region	hormone activity	g.chr14:63784404_63784405insG	AF467770	CCDS73643.1	14q23.3	2006-09-25				ENSG00000179600			18055	protein-coding gene	gene with protein product		609652					Standard	NM_145171		Approved	ZLUT1, GPB5	uc021rud.1	Q86YW7			14.37:g.63784405_63784405dupG		False	False		Somatic	1								WXS	Illumina HiSeq	Phase_I	Q86YW7	GPHB5_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.00372)|all cancers(60;0.0226)|BRCA - Breast invasive adenocarcinoma(234;0.0978)	0	215_216	-			NA					Q6NTD0|Q8NFW2	RNA	INS	ENST00000539258.1	37																																																																																						0.599	GPHB5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000400582.1	0	NM_145171		14:63784404
SYNE3	161176	broad.mit.edu	37	14	95903308	95903310	+	In_Frame_Del	DEL	AGA	AGA	-	rs76499929|rs201240192	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AGA	AGA	-	-	AGA	AGA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:95903308_95903310delAGA	ENST00000334258.5	-	14	2399_2401	c.2385_2387delTCT	c.(2383-2388)cttcta>cta	p.795_796LL>L	SYNE3_ENST00000557275.1_Intron|SYNE3_ENST00000554873.1_In_Frame_Del_p.552_553LL>L	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	795			Missing (in dbSNP:rs76499929). {ECO:0000269|PubMed:15489334}.		cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.L796delL(1)		breast(1)|endometrium(2)|lung(25)	28						TTCTTCCTGTAGAAGATTTGCCT	0.542																																						ENST00000334258.5		NA																	1	Deletion - In frame(1)	p.L796delL(1)	breast(1)	breast(1)|endometrium(2)|lung(25)	28						c.(2383-2388)cttcta>cta		spectrin repeat containing, nuclear envelope family member 3				458,3806		19,420,1693						-1.8	0.0		dbSNP_131	71	906,7348		46,814,3267	no	coding	C14orf49	NM_152592.3		65,1234,4960	A1A1,A1R,RR		10.9765,10.7411,10.8963				1364,11154				SO:0001651	inframe_deletion	161176							g.chr14:95903308_95903310delAGA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2385_2387delTCT	14.37:g.95903311_95903313delAGA	ENSP00000334308:p.Leu796del	False	False		Somatic	2				SYNE3_ENST00000557275.1_Intron|SYNE3_ENST00000554873.1_In_Frame_Del_p.552_553LL>L	p.795_796LL>L	NM_152592.3	NP_689805.3	WXS	Illumina HiSeq	Phase_I					14	2399_2401	-			NA					A6H8H3|Q86SX5|Q8N7G8	In_Frame_Del	DEL	ENST00000334258.5	37	c.2385_2387delTCT	CCDS9935.1																																																																																				0.542	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	0	NM_152592		14:95903308
DNAJA4	55466	broad.mit.edu	37	15	78558585	78558586	+	Intron	DEL	AT	AT	-	rs142025971	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AT	AT	-	-	AT	AT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:78558585_78558586delAT	ENST00000394852.3	+	1	322				RP11-762H8.3_ENST00000558971.1_RNA|DNAJA4_ENST00000446172.2_Start_Codon_Del|RP11-762H8.3_ENST00000559954.1_RNA|DNAJA4_ENST00000343789.3_Intron|DNAJA4_ENST00000394855.3_Intron	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4						negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						GGCTAAAGACATGTGGGAAAGC	0.45														92	0.0183706	0.0015	0.0274	5008	,	,		20491	0.0		0.0646	False		,,,				2504	0.0061					ENST00000446172.2		NA																	0				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8								DnaJ (Hsp40) homolog, subfamily A, member 4			,,	31,3321		1,29,1646					,,	1.7	0.0		dbSNP_134	79	337,6755		9,319,3218	no	intron,frameshift,intron	DNAJA4	NM_018602.3,NM_001130183.1,NM_001130182.1	,,	10,348,4864	A1A1,A1R,RR		4.7518,0.9248,3.5236	,,	,,		368,10076				SO:0001627	intron_variant	55466				protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding	g.chr15:78558585_78558586delAT	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"""Heat shock proteins / DNAJ (HSP40)"""	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.132+1348AT>-	15.37:g.78558585_78558586delAT		False	False		Somatic	1				DNAJA4_ENST00000394855.3_Intron|DNAJA4_ENST00000394852.3_Intron|DNAJA4_ENST00000343789.3_Intron		NM_001130183.1	NP_001123655.1	WXS	Illumina HiSeq	Phase_I	Q8WW22	DNJA4_HUMAN			0	63_64	+			NA					E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Translation_Start_Site	DEL	ENST00000394852.3	37		CCDS45316.1																																																																																				0.450	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	0	NM_018602		15:78558585
DNM1P47	100216544	broad.mit.edu	37	15	102292783	102292786	+	RNA	DEL	CTCA	CTCA	-	rs61084368|rs143389223	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CTCA	CTCA	-	-	CTCA	CTCA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:102292783_102292786delCTCA	ENST00000561463.1	+	0	829_832									DNM1 pseudogene 47									p.Q125E(1)									GATGCTGCTTCTCAGAGCTGCTGT	0.603														1404	0.280351	0.2383	0.2939	5008	,	,		40661	0.3135		0.2406	False		,,,				2504	0.3344					ENST00000561463.1		NA																	1	Substitution - Missense(1)	p.Q125E(1)	kidney(1)		NA																																														0							g.chr15:102292783_102292786delCTCA	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102292783_102292786delCTCA		False	False		Somatic	1								WXS	Illumina HiSeq	Phase_I					0	829_832	+			NA						RNA	DEL	ENST00000561463.1	37																																																																																						0.603	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	0	NG_009149		15:102292783
OGFOD1	55239	broad.mit.edu	37	16	56509440	56509441	+	Frame_Shift_Ins	INS	-	-	GTTTTTTT	rs147207036		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:56509440_56509441insGTTTTTTT	ENST00000566157.1	+	12	1553_1554	c.1430_1431insGTTTTTTT	c.(1429-1434)ggttttfs	p.-478fs	OGFOD1_ENST00000568397.1_Frame_Shift_Ins_p.-435fs	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1						cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	GAATATGGCGGTTTTACTTCTT	0.366																																						ENST00000566157.1		NA																	0				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						c.(1429-1434)ggttttfs		2-oxoglutarate and iron-dependent oxygenase domain containing 1	Vitamin C(DB00126)																																			SO:0001589	frameshift_variant	55239						iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	g.chr16:56509440_56509441insGTTTTTTT	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	Exception_encountered	16.37:g.56509440_56509441insGTTTTTTT	ENSP00000457258:p.Phe478fs	True	False		Somatic	0				OGFOD1_ENST00000568397.1_Frame_Shift_Ins_p.-435fs	p.-478fs	NM_018233.3	NP_060703.3	WXS	Illumina HiSeq	Phase_I	Q8N543	OGFD1_HUMAN			12	1553_1554	+			NA					H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Frame_Shift_Ins	INS	ENST00000566157.1	37	c.1430_1431insGTTTTTTT	CCDS10761.2																																																																																				0.366	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	0	NM_018233		16:56509440
MT1A	4489	broad.mit.edu	37	16	56670304	56670306	+	5'Flank	DEL	CTT	CTT	-	rs527712973	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CTT	CTT	-	-	CTT	CTT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:56670304_56670306delCTT	ENST00000290705.8	+	0	0				MT1JP_ENST00000564564.1_RNA	NM_005946.2	NP_005937.2	P04731	MT1A_HUMAN	metallothionein 1A						cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)	3					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACTGCTGTACCTTCTTCATCTCA	0.581														9	0.00179712	0.0	0.0	5008	,	,		21738	0.0		0.003	False		,,,				2504	0.0061					ENST00000564564.1		NA																	0					NA																																												SO:0001631	upstream_gene_variant	0							g.chr16:56670304_56670306delCTT	BC029475	CCDS32454.1	16q13	2012-10-02	2007-03-02			ENSG00000205362		"""Metallothioneins"""	7393	protein-coding gene	gene with protein product		156350	"""metallothionein 1S"""	MT1, MT1S		6089206, 6327055	Standard	NM_005946		Approved		uc002ejq.3	P04731			16.37:g.56670307_56670309delCTT	Exception_encountered	False	False		Somatic	2								WXS	Illumina HiSeq	Phase_I					0	630_632	+			NA					Q86YX5	RNA	DEL	ENST00000290705.8	37		CCDS32454.1																																																																																				0.581	MT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434324.1	0	NM_005946		16:56670304
KRT24	192666	broad.mit.edu	37	17	38858135	38858135	+	Frame_Shift_Del	DEL	A	A	-	rs11309872	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:38858135delA	ENST00000264651.2	-	2	722	c.666delT	c.(664-666)aatfs	p.N222fs		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	222	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CCAATCTGGCATTGTCAATGT	0.333													A|A|-|deletion	2328	0.464856	0.1921	0.6282	5008	,	,		13424	0.5952		0.4563	False		,,,				2504	0.592				GBM(61;380 1051 14702 23642 31441)	ENST00000264651.2		NA																	0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(664-666)aatfs		keratin 24				1041,3223		135,771,1226	70.0	54.0	60.0			5.1	1.0	17	dbSNP_120	79	3574,4680		756,2062,1309	no	frameshift	KRT24	NM_019016.2		891,2833,2535	A1A1,A1R,RR		43.3002,24.4137,36.8669			38858135	4615,7903	2078	3619	5697	SO:0001589	frameshift_variant	192666					cytoplasm|intermediate filament	structural molecule activity	g.chr17:38858135delA		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.666delT	17.37:g.38858135delA	ENSP00000264651:p.Asn222fs	False	False		Somatic	1					p.N222fs	NM_019016.2	NP_061889.2	WXS	Illumina HiSeq	Phase_I	Q2M2I5	K1C24_HUMAN			2	722	-		Breast(137;0.00526)	222			Coil 1B.|Rod.		Q9NXG7	Frame_Shift_Del	DEL	ENST00000264651.2	37	c.666delT	CCDS11372.1																																																																																				0.333	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	0	NM_019016		17:38858135
LAMA1	284217	broad.mit.edu	37	18	7007226	7007227	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CT	CT	-	-	CT	CT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr18:7007226_7007227delCT	ENST00000389658.3	-	29	4264_4265	c.4171_4172delAG	c.(4171-4173)aggfs	p.R1391fs		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1391	Laminin EGF-like 14; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GCGTGGTCCCCTGTCACTCCCT	0.559																																						ENST00000389658.3		NA																	0				NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205						c.(4171-4173)aggfs		laminin, alpha 1	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)																																			SO:0001589	frameshift_variant	284217				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding	g.chr18:7007226_7007227delCT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4171_4172delAG	18.37:g.7007226_7007227delCT	ENSP00000374309:p.Arg1391fs	True	False		Somatic	1					p.R1391fs	NM_005559.3	NP_005550.2	WXS	Illumina HiSeq	Phase_I	P25391	LAMA1_HUMAN			29	4264_4265	-		Colorectal(10;0.172)	1391			Laminin EGF-like 14; second part.			Frame_Shift_Del	DEL	ENST00000389658.3	37	c.4171_4172delAG	CCDS32787.1																																																																																				0.559	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	0	NM_005559		18:7007226
ZNF101	94039	broad.mit.edu	37	19	19790877	19790878	+	Frame_Shift_Del	DEL	AT	AT	-	rs34704748|rs71172514	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AT	AT	-	-	AT	AT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:19790877_19790878delAT	ENST00000592502.1	+	4	1189_1190	c.1079_1080delAT	c.(1078-1080)catfs	p.H360fs	ZNF101_ENST00000415784.2_Frame_Shift_Del_p.H240fs			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	360					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H360L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						AAAAAAACTCATAGTGGAGAAA	0.401														46	0.0091853	0.0008	0.0086	5008	,	,		20259	0.0		0.0368	False		,,,				2504	0.002					ENST00000592502.1		NA																	1	Substitution - Missense(1)	p.H360L(1)	lung(1)	breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						c.(1078-1080)catfs		zinc finger protein 101				48,4216		6,36,2090						0.2	0.7		dbSNP_126	69	292,7960		18,256,3852	no	frameshift	ZNF101	NM_033204.2		24,292,5942	A1A1,A1R,RR		3.5385,1.1257,2.7165				340,12176				SO:0001589	frameshift_variant	94039				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:19790877_19790878delAT	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"""Zinc fingers, C2H2-type"", ""-"""	12881	protein-coding gene	gene with protein product		603983	"""zinc finger protein 101 (Y2)"""			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.1079_1080delAT	19.37:g.19790877_19790878delAT	ENSP00000468049:p.His360fs	False	False		Somatic	1				ZNF101_ENST00000415784.2_Frame_Shift_Del_p.H240fs	p.H360fs			WXS	Illumina HiSeq	Phase_I	Q8IZC7	ZN101_HUMAN			4	1189_1190	+			360					C9JU83|Q0VDG9	Frame_Shift_Del	DEL	ENST00000592502.1	37	c.1079_1080delAT	CCDS32971.1																																																																																				0.401	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	0	NM_033204		19:19790877
ZNF134	7693	broad.mit.edu	37	19	58132432	58132432	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:58132432delT	ENST00000396161.5	+	3	1255	c.945delT	c.(943-945)cctfs	p.P315fs		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		GAGAAAATCCTTATGATTGCA	0.413																																						ENST00000396161.5		NA																	0				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11						c.(943-945)cctfs		zinc finger protein 134							133.0	136.0	135.0					19																	58132432		2201	4300	6501	SO:0001589	frameshift_variant	7693					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:58132432delT	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.945delT	19.37:g.58132432delT	ENSP00000379464:p.Pro315fs	False	False		Somatic	2					p.P315fs	NM_003435.3	NP_003426.3	WXS	Illumina HiSeq	Phase_I	P52741	ZN134_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)	3	1255	+		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)	315					Q9Y4B2	Frame_Shift_Del	DEL	ENST00000396161.5	37	c.945delT	CCDS42638.1																																																																																				0.413	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	0	NM_003435		19:58132432
IFNAR2	3455	broad.mit.edu	37	21	34619148	34619149	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AC	AC	-	-	AC	AC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr21:34619148_34619149delAC	ENST00000342136.4	+	5	673_674	c.347_348delAC	c.(346-348)aacfs	p.N116fs	IFNAR2_ENST00000382241.3_Frame_Shift_Del_p.N116fs|IFNAR2_ENST00000342101.3_Frame_Shift_Del_p.N116fs|AP000295.9_ENST00000433395.2_Frame_Shift_Del_p.T24fs|IFNAR2_ENST00000413881.1_Frame_Shift_Del_p.N44fs|IFNAR2_ENST00000404220.3_Frame_Shift_Del_p.N116fs|IFNAR2_ENST00000420068.1_3'UTR|IFNAR2_ENST00000382264.3_Frame_Shift_Del_p.N116fs			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	116					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	TTCAGCGGGAACACAACGTTGT	0.446																																						ENST00000404220.3		NA																	0				cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11						c.(346-348)aacfs		interferon (alpha, beta and omega) receptor 2	Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)																																			SO:0001589	frameshift_variant	3455				JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to interferon-alpha|response to virus|type I interferon-mediated signaling pathway	extracellular region|extracellular space|integral to plasma membrane	protein kinase binding|type I interferon binding|type I interferon receptor activity	g.chr21:34619148_34619149delAC		CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"""Interferons"""	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.347_348delAC	21.37:g.34619150_34619151delAC	ENSP00000343957:p.Asn116fs	False	False		Somatic	2				IFNAR2_ENST00000382264.3_Frame_Shift_Del_p.N116fs|AP000295.9_ENST00000433395.2_Frame_Shift_Del_p.T24fs|IFNAR2_ENST00000342101.3_Frame_Shift_Del_p.N116fs|IFNAR2_ENST00000342136.4_Frame_Shift_Del_p.N116fs|IFNAR2_ENST00000382241.3_Frame_Shift_Del_p.N116fs|IFNAR2_ENST00000413881.1_Frame_Shift_Del_p.N44fs|IFNAR2_ENST00000420068.1_3'UTR	p.N116fs			WXS	Illumina HiSeq	Phase_I	P48551	INAR2_HUMAN			5	676_677	+			116					A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Frame_Shift_Del	DEL	ENST00000342136.4	37	c.347_348delAC	CCDS13621.1																																																																																				0.446	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1	0			21:34619148
TRIOBP	11078	broad.mit.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs201160789|rs71322688|rs55745992|rs67890459|rs77530465|rs199535040	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CAA	CAA	-	-	CAA	CAA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:38119755_38119757delCAA	ENST00000406386.3	+	7	1447_1449	c.1192_1194delCAA	c.(1192-1194)caadel	p.Q398del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.Q398R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGAACCACTCAACGAGAGAATT	0.552														1684	0.336262	0.1536	0.2853	5008	,	,		18750	0.5863		0.3877	False		,,,				2504	0.3088					ENST00000406386.3		NA																	1	Substitution - Missense(1)	p.Q398R(1)	lung(1)	central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(1192-1194)caadel		TRIO and F-actin binding protein				658,3014		76,506,1254						-4.9	0.1		dbSNP_132	129	3439,4489		755,1929,1280	no	coding	TRIOBP	NM_001039141.2		831,2435,2534	A1A1,A1R,RR		43.3779,17.9194,35.319				4097,7503				SO:0001651	inframe_deletion	11078				actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	g.chr22:38119755_38119757delCAA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1192_1194delCAA	22.37:g.38119755_38119757delCAA	ENSP00000384312:p.Gln398del	False	False		Somatic	1				RP1-37E16.12_ENST00000455236.1_RNA	p.Q398del	NM_001039141.2	NP_001034230.1	WXS	Illumina HiSeq	Phase_I	Q9H2D6	TARA_HUMAN			7	1447_1449	+	Melanoma(58;0.0574)		398					B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	In_Frame_Del	DEL	ENST00000406386.3	37	c.1192_1194delCAA	CCDS43015.1																																																																																				0.552	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2	0			22:38119755
ANKRD36	375248	broad.mit.edu	37	2	97779488	97779488	+	Frame_Shift_Del	DEL	C	C	-	rs141447363	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:97779488delC	ENST00000461153.2	+	1	256	c.12delC	c.(10-12)ggcfs	p.G4fs	ANKRD36_ENST00000420699.2_Frame_Shift_Del_p.G4fs			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	4										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						TGGAAGACGGCAAGCGGGAGA	0.562													?|C|-|unsure	121	0.0241613	0.0023	0.0389	5008	,	,		10528	0.0		0.0845	False		,,,				2504	0.0061					ENST00000461153.2		NA																	0				endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						c.(10-12)ggcfs		ankyrin repeat domain 36				57,3647		4,49,1799	69.0	65.0	66.0			-0.9	0.0	2	dbSNP_134	69	690,7198		41,608,3295	no	frameshift	ANKRD36	NM_001164315.1		45,657,5094	A1A1,A1R,RR		8.7475,1.5389,6.4441			97779488	747,10845	1923	4101	6024	SO:0001589	frameshift_variant	375248							g.chr2:97779488delC	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.12delC	2.37:g.97779488delC	ENSP00000419530:p.Gly4fs	False	False		Somatic	1				ANKRD36_ENST00000420699.2_Frame_Shift_Del_p.G4fs	p.G4fs			WXS	Illumina HiSeq	Phase_I	A6QL64	AN36A_HUMAN			1	256	+			4					B4E3I8|Q6UX02|Q86X62|Q9HCD1	Frame_Shift_Del	DEL	ENST00000461153.2	37	c.12delC	CCDS54379.1																																																																																				0.562	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5	0			2:97779488
KDF1	126695	broad.mit.edu	37	1	27277240	27277241	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	TG	TG	-	-	TG	TG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:27277240_27277241delTG	ENST00000320567.5	-	3	1134_1135	c.1046_1047delCA	c.(1045-1047)acafs	p.T349fs		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		349					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		AGATCTGCACTGTCAGCTCTAG	0.569																																						ENST00000320567.5		NA																	0				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17						c.(1045-1047)acafs		chromosome 1 open reading frame 172																																				SO:0001589	frameshift_variant	126695							g.chr1:27277240_27277241delTG																												ENST00000320567.5:c.1046_1047delCA	1.37:g.27277240_27277241delTG	ENSP00000319179:p.Thr349fs	False	False		Somatic	1					p.T349fs	NM_152365.2	NP_689578.2	WXS	Illumina HiSeq	Phase_I	Q8NAX2	CA172_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)	3	1134_1135	-		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)	349					Q5QP32|Q8N0S7	Frame_Shift_Del	DEL	ENST00000320567.5	37	c.1046_1047delCA	CCDS293.1																																																																																				0.569	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1	0			1:27277240
CCR5	1234	broad.mit.edu	37	3	46414944	46414975	+	Frame_Shift_Del	DEL	ACAGTCAGTATCAATTCTGGAAGAATTTCCAG	ACAGTCAGTATCAATTCTGGAAGAATTTCCAG	-	rs372782701|rs333|rs62625034|rs112590754|rs201797884|rs562091107|rs56345960|rs111718604|rs199827265|rs113869679	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	ACAGTCAGTATCAATTCTGGAAGAATTTCCAG	ACAGTCAGTATCAATTCTGGAAGAATTTCCAG	-	-	ACAGTCAGTATCAATTCTGGAAGAATTTCCAG	ACAGTCAGTATCAATTCTGGAAGAATTTCCAG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:46414944_46414975delACAGTCAGTATCAATTCTGGAAGAATTTCCAG	ENST00000292303.4	+	2	697_728	c.551_582delACAGTCAGTATCAATTCTGGAAGAATTTCCAG	c.(550-582)tacagtcagtatcaattctggaagaatttccagfs	p.YSQYQFWKNFQ184fs	CCR5_ENST00000445772.1_Frame_Shift_Del_p.YSQYQFWKNFQ184fs|CCR5_ENST00000343801.4_Frame_Shift_Del_p.YSQYQFWKNFQ184fs|RP11-24F11.2_ENST00000451485.1_RNA	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	184					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.Y187*(1)|p.K191N(1)		central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	CATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGA	0.453														146	0.0291534	0.003	0.0317	5008	,	,		26634	0.0		0.1103	False		,,,				2504	0.0092					ENST00000292303.4		NA																	2	Substitution - Nonsense(1)|Substitution - Missense(1)	p.Y187*(1)|p.K191N(1)	lung(2)	central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20						c.(550-582)tacagtcagtatcaattctggaagaatttccagfs		chemokine (C-C motif) receptor 5 (gene/pseudogene)	Maraviroc(DB04835)		,	58,4208		0,58,2075					,	-10.8	0.0		dbSNP_36	152	697,7531		36,625,3453	no	frameshift,frameshift	CCR5	NM_001100168.1,NM_000579.3	,	36,683,5528	A1A1,A1R,RR		8.4711,1.3596,6.0429	,	,		755,11739				SO:0001589	frameshift_variant	1234				cell-cell signaling|cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|immune response|inflammatory response|initiation of viral infection	endosome|external side of plasma membrane|integral to plasma membrane	actin binding|C-C chemokine receptor activity|coreceptor activity|phosphatidylinositol phospholipase C activity	g.chr3:46414944_46414975delACAGTCAGTATCAATTCTGGAAGAATTTCCAG		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1606	protein-coding gene	gene with protein product		601373	"""chemokine (C-C motif) receptor 5"""	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.551_582delACAGTCAGTATCAATTCTGGAAGAATTTCCAG	3.37:g.46414944_46414975delACAGTCAGTATCAATTCTGGAAGAATTTCCAG	ENSP00000292303:p.Tyr184fs	False	False		Somatic	1				CCR5_ENST00000445772.1_Frame_Shift_Del_p.YSQYQFWKNFQ184fs|CCR5_ENST00000343801.4_Frame_Shift_Del_p.YSQYQFWKNFQ184fs|RP11-24F11.2_ENST00000451485.1_RNA	p.YSQYQFWKNFQ184fs	NM_001100168.1	NP_001093638.1	WXS	Illumina HiSeq	Phase_I	P51681	CCR5_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	2	697_728	+			184					O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Frame_Shift_Del	DEL	ENST00000292303.4	37	c.551_582delACAGTCAGTATCAATTCTGGAAGAATTTCCAG	CCDS2739.1																																																																																				0.453	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	0	NM_000579		3:46414944
SIDT1	54847	broad.mit.edu	37	3	113286403	113286403	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:113286403delA	ENST00000264852.4	+	3	1087	c.361delA	c.(361-363)aacfs	p.N121fs	SIDT1_ENST00000393830.3_Frame_Shift_Del_p.N121fs	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	121					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GAGGAGCTACAACTATCAAGA	0.468																																						ENST00000264852.4		NA																	0				breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						c.(361-363)aacfs		SID1 transmembrane family, member 1							85.0	79.0	81.0					3																	113286403		2203	4300	6503	SO:0001589	frameshift_variant	54847					integral to membrane		g.chr3:113286403delA	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.361delA	3.37:g.113286403delA	ENSP00000264852:p.Asn121fs	False	False		Somatic	2				SIDT1_ENST00000393830.3_Frame_Shift_Del_p.N121fs	p.N121fs	NM_017699.2	NP_060169.2	WXS	Illumina HiSeq	Phase_I	Q9NXL6	SIDT1_HUMAN			3	1087	+			121					Q17RR4	Frame_Shift_Del	DEL	ENST00000264852.4	37	c.361delA	CCDS2974.1																																																																																				0.468	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	0	NM_017699		3:113286403
DBR1	51163	broad.mit.edu	37	3	137880741	137880743	+	In_Frame_Del	DEL	TCG	TCG	-	rs376362448|rs2622736	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	TCG	TCG	-	-	TCG	TCG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:137880741_137880743delTCG	ENST00000260803.4	-	8	1776_1778	c.1623_1625delCGA	c.(1621-1626)gacgat>gat	p.541_542DD>D	DBR1_ENST00000505015.2_In_Frame_Del_p.307_308DD>D	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	541					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						TTAAGCTGCATCGTCATCATCAT	0.394																																						ENST00000260803.4		NA																	0				NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						c.(1621-1626)gacgat>gat		debranching RNA lariats 1																																				SO:0001651	inframe_deletion	51163					nucleus	metal ion binding|RNA lariat debranching enzyme activity	g.chr3:137880741_137880743delTCG	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"""debranching enzyme (S. Cerevisiae) homolog 1"", ""debranching enzyme homolog 1 (S. cerevisiae)"""			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.1623_1625delCGA	3.37:g.137880741_137880743delTCG	ENSP00000260803:p.Asp542del	False	False		Somatic	1				DBR1_ENST00000505015.2_In_Frame_Del_p.307_308DD>D	p.541_542DD>D	NM_016216.3	NP_057300.2	WXS	Illumina HiSeq	Phase_I	Q9UK59	DBR1_HUMAN			8	1776_1778	-			541					Q96GH0|Q9NXQ6	In_Frame_Del	DEL	ENST00000260803.4	37	c.1623_1625delCGA	CCDS33863.1																																																																																				0.394	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1	0			3:137880741
ATR	545	broad.mit.edu	37	3	142241646	142241648	+	In_Frame_Del	DEL	AAT	AAT	-	rs562594343		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AAT	AAT	-	-	AAT	AAT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:142241646_142241648delAAT	ENST00000350721.4	-	23	4309_4311	c.4188_4190delATT	c.(4186-4191)ttattg>ttg	p.1396_1397LL>L	ATR_ENST00000383101.3_In_Frame_Del_p.1332_1333LL>L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1396					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TAGCTCCATCAATAATCCATAGG	0.379								Other conserved DNA damage response genes																														ENST00000350721.4		NA																	0				NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						c.(4186-4191)ttattg>ttg	Other conserved DNA damage response genes	ataxia telangiectasia and Rad3 related																																				SO:0001651	inframe_deletion	545				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity	g.chr3:142241646_142241648delAAT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4188_4190delATT	3.37:g.142241649_142241651delAAT	ENSP00000343741:p.Leu1397del	False	False		Somatic	2				ATR_ENST00000383101.3_In_Frame_Del_p.1332_1333LL>L	p.1396_1397LL>L	NM_001184.3	NP_001175.2	WXS	Illumina HiSeq	Phase_I	Q13535	ATR_HUMAN			23	4309_4311	-			1396					Q59HB2|Q7KYL3|Q93051|Q9BXK4	In_Frame_Del	DEL	ENST00000350721.4	37	c.4188_4190delATT	CCDS3124.1																																																																																				0.379	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	0	NM_001184		3:142241646
OTOP1	133060	broad.mit.edu	37	4	4198949	4198954	+	In_Frame_Del	DEL	CGTTGC	CGTTGC	-	rs200964011|rs374875261|rs547040796|rs141181262|rs200550998|rs112623841	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CGTTGC	CGTTGC	-	-	CGTTGC	CGTTGC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr4:4198949_4198954delCGTTGC	ENST00000296358.4	-	5	1631_1636	c.1607_1612delGCAACG	c.(1606-1614)ggcaacgcc>gcc	p.GN536del		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	536					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTTCTCTTGGCGTTGCCCTGTAAGAA	0.476														384	0.0766773	0.1074	0.1585	5008	,	,		20491	0.0		0.0457	False		,,,				2504	0.0879					ENST00000296358.4		NA																	0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						c.(1606-1614)ggcaacgcc>gcc		otopetrin 1				431,3833		23,385,1724						0.8	0.0		dbSNP_132	60	431,7823		11,409,3707	no	coding	OTOP1	NM_177998.1		34,794,5431	A1A1,A1R,RR		5.2217,10.1079,6.8861				862,11656				SO:0001651	inframe_deletion	133060				biomineral tissue development	extracellular space|integral to membrane		g.chr4:4198949_4198954delCGTTGC	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1607_1612delGCAACG	4.37:g.4198949_4198954delCGTTGC	ENSP00000296358:p.Gly536_Asn537del	False	False		Somatic	1					p.GN536del	NM_177998.1	NP_819056.1	WXS	Illumina HiSeq	Phase_I	Q7RTM1	OTOP1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	5	1631_1636	-			536					A1L476	In_Frame_Del	DEL	ENST00000296358.4	37	c.1607_1612delGCAACG	CCDS3372.1																																																																																				0.476	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	0	NM_177998		4:4198949
AMBN	258	broad.mit.edu	37	4	71468346	71468348	+	In_Frame_Del	DEL	AGG	AGG	-	rs368655454|rs141384720|rs199556863	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AGG	AGG	-	-	AGG	AGG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr4:71468346_71468348delAGG	ENST00000322937.6	+	7	640_642	c.537_539delAGG	c.(535-540)ccagga>cca	p.G180del	AMBN_ENST00000449493.2_In_Frame_Del_p.G165del	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	180				G -> R (in Ref. 3; AAG35772 and 4; AAG27036). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			TATAGCTCCCAGGAGTAGATTTT	0.261														603	0.120407	0.1483	0.0749	5008	,	,		15284	0.1577		0.0646	False		,,,				2504	0.1339					ENST00000322937.6		NA																	0				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29						c.(535-540)ccagga>cca		ameloblastin (enamel matrix protein)				554,3682		46,462,1610						3.3	0.0		dbSNP_134	48	593,7635		24,545,3545	no	coding	AMBN	NM_016519.5		70,1007,5155	A1A1,A1R,RR		7.2071,13.0784,9.2025				1147,11317				SO:0001651	inframe_deletion	258				bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel	g.chr4:71468346_71468348delAGG	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.537_539delAGG	4.37:g.71468346_71468348delAGG	ENSP00000313809:p.Gly180del	False	False		Somatic	1				AMBN_ENST00000449493.2_In_Frame_Del_p.G165del	p.G180del	NM_016519.5	NP_057603.1	WXS	Illumina HiSeq	Phase_I	Q9NP70	AMBN_HUMAN	Lung(101;0.235)		7	640_642	+			180	G -> R (in Ref. 3; AAG35772 and 4; AAG27036).				Q3B862|Q9H2X1|Q9H4L1	In_Frame_Del	DEL	ENST00000322937.6	37	c.537_539delAGG	CCDS3543.1																																																																																				0.261	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	0	NM_016519		4:71468346
C1QTNF3	114899	broad.mit.edu	37	5	34042955	34042955	+	Intron	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:34042955delT	ENST00000231338.7	-	1	172				RP11-1084J3.4_ENST00000382079.3_Intron|C1QTNF3_ENST00000382065.3_Frame_Shift_Del_p.L92fs	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3						cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					TGATCTGGGCTAGGTCATCTA	0.453																																						ENST00000382065.3		NA																	0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17						c.(274-276)ctafs		C1q and tumor necrosis factor related protein 3			,	0,4266		0,0,2133	103.0	107.0	106.0		,	5.6	1.0	5		104	2,8252		0,2,4125	no	frameshift,intron	C1QTNF3	NM_181435.5,NM_030945.3	,	0,2,6258	A1A1,A1R,RR		0.0242,0.0,0.016	,	,	34042955	2,12518	2203	4300	6503	SO:0001627	intron_variant	114899					collagen		g.chr5:34042955delT	AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"""cartonectin"""	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.84+191A>-	5.37:g.34042955delT		False	False		Somatic	1				C1QTNF3_ENST00000231338.7_Intron	p.L92fs	NM_181435.5	NP_852100.3	WXS	Illumina HiSeq	Phase_I	Q9BXJ4	C1QT3_HUMAN			1	982	-	all_lung(31;0.0207)		0			Collagen-like.		Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Frame_Shift_Del	DEL	ENST00000231338.7	37	c.276delA	CCDS3904.1																																																																																				0.453	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207469.1	0	NM_030945		5:34042955
MAST4	375449	broad.mit.edu	37	5	66461050	66461052	+	In_Frame_Del	DEL	CTC	CTC	-	rs568806328		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	CTC	CTC	-	-	CTC	CTC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:66461050_66461052delCTC	ENST00000403625.2	+	29	6338_6340	c.6043_6045delCTC	c.(6043-6045)ctcdel	p.L2016del	MAST4_ENST00000403666.1_In_Frame_Del_p.L1827del|MAST4_ENST00000405643.1_In_Frame_Del_p.L1837del|MAST4_ENST00000404260.3_In_Frame_Del_p.L2019del|MAST4_ENST00000261569.7_In_Frame_Del_p.L1822del	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2019						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CTCCAAAAATCTCCTCTCTGTGG	0.552																																						ENST00000403625.2		NA																	0				breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13						c.(6043-6045)ctcdel		microtubule associated serine/threonine kinase family member 4			,	0,3628		0,0,1814					,	-6.8	0.0			23	21,7867		2,17,3925	no	coding,coding	MAST4	NM_015183.2,NM_001164664.1	,	2,17,5739	A1A1,A1R,RR		0.2662,0.0,0.1824	,	,		21,11495				SO:0001651	inframe_deletion	375449					cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	g.chr5:66461050_66461052delCTC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6043_6045delCTC	5.37:g.66461053_66461055delCTC	ENSP00000385727:p.Leu2016del	False	False		Somatic	2				MAST4_ENST00000404260.3_In_Frame_Del_p.L2019del|MAST4_ENST00000403666.1_In_Frame_Del_p.L1827del|MAST4_ENST00000261569.7_In_Frame_Del_p.L1822del|MAST4_ENST00000405643.1_In_Frame_Del_p.L1837del	p.L2016del	NM_001164664.1	NP_001158136.1	WXS	Illumina HiSeq	Phase_I	O15021	MAST4_HUMAN		Lung(70;0.011)	29	6338_6340	+		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)	2019					A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	In_Frame_Del	DEL	ENST00000403625.2	37	c.6043_6045delCTC	CCDS54861.1																																																																																				0.552	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2	0			5:66461050
STK10	6793	broad.mit.edu	37	5	171583751	171583760	+	Frame_Shift_Del	DEL	GACTTTGGCC	GACTTTGGCC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	GACTTTGGCC	GACTTTGGCC	-	-	GACTTTGGCC	GACTTTGGCC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:171583751_171583760delGACTTTGGCC	ENST00000176763.5	-	2	532_541	c.189_198delGGCCAAAGTC	c.(187-198)gcggccaaagtcfs	p.AAKV63fs		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	63	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGGTTTCAATGACTTTGGCCGCAGCCAAAG	0.552																																						ENST00000176763.5		NA																	0				breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47						c.(187-198)gcggccaaagtcfs		serine/threonine kinase 10																																				SO:0001589	frameshift_variant	6793						ATP binding|protein serine/threonine kinase activity	g.chr5:171583751_171583760delGACTTTGGCC	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.189_198delGGCCAAAGTC	5.37:g.171583751_171583760delGACTTTGGCC	ENSP00000176763:p.Ala63fs	True	False		Somatic	1					p.AAKV63fs	NM_005990.3	NP_005981.3	WXS	Illumina HiSeq	Phase_I	O94804	STK10_HUMAN	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		2	532_541	-	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	63			Protein kinase.		A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Frame_Shift_Del	DEL	ENST00000176763.5	37	c.189_198delGGCCAAAGTC	CCDS34290.1																																																																																				0.552	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	0	NM_005990		5:171583751
DNAH8	1769	broad.mit.edu	37	6	38783392	38783398	+	Frame_Shift_Del	DEL	TGACCCA	TGACCCA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	TGACCCA	TGACCCA	-	-	TGACCCA	TGACCCA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:38783392_38783398delTGACCCA	ENST00000359357.3	+	24	3085_3091	c.2831_2837delTGACCCA	c.(2830-2838)gtgacccatfs	p.VTH944fs	DNAH8_ENST00000449981.2_Frame_Shift_Del_p.VTH1161fs|DNAH8_ENST00000441566.1_Frame_Shift_Del_p.VTH944fs			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	944					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACTACTGACGTGACCCATCAAAACACA	0.44																																						ENST00000359357.3		NA																	0				NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						c.(2830-2838)gtgacccatfs		dynein, axonemal, heavy chain 8				0,4264		0,0,2132						-9.4	0.0			71	2,8252		0,2,4125	no	frameshift	DNAH8	NM_001206927.1		0,2,6257	A1A1,A1R,RR		0.0242,0.0,0.016				2,12516				SO:0001589	frameshift_variant	1769							g.chr6:38783392_38783398delTGACCCA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2831_2837delTGACCCA	6.37:g.38783392_38783398delTGACCCA	ENSP00000352312:p.Val944fs	True	False		Somatic	1				DNAH8_ENST00000441566.1_Frame_Shift_Del_p.VTH944fs|DNAH8_ENST00000449981.2_Frame_Shift_Del_p.VTH1161fs	p.VTH944fs			WXS	Illumina HiSeq	Phase_I					24	3085_3091	+			NA					O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Frame_Shift_Del	DEL	ENST00000359357.3	37	c.2831_2837delTGACCCA																																																																																					0.440	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	0	NM_001206927		6:38783392
SRSF12	135295	broad.mit.edu	37	6	89814896	89814898	+	In_Frame_Del	DEL	TTC	TTC	-	rs569581969	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	TTC	TTC	-	-	TTC	TTC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:89814896_89814898delTTC	ENST00000452027.2	-	4	549_551	c.356_358delGAA	c.(355-360)agaact>act	p.R119del		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	119	Arg/Ser-rich (RS domain).				cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						CTACTTCGAGTTCTTCTTTGGCT	0.414														3	0.000599042	0.0	0.0	5008	,	,		18403	0.0		0.001	False		,,,				2504	0.002					ENST00000452027.2		NA																	0				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						c.(355-360)agaact>act		serine/arginine-rich splicing factor 12				0,3548		0,0,1774						5.2	1.0			77	21,7793		0,21,3886	no	coding	SRSF12	NM_080743.4		0,21,5660	A1A1,A1R,RR		0.2687,0.0,0.1848				21,11341				SO:0001651	inframe_deletion	135295				assembly of spliceosomal tri-snRNP|cytoplasmic transport|negative regulation of nuclear mRNA splicing, via spliceosome|nuclear mRNA 5'-splice site recognition|regulation of alternative nuclear mRNA splicing, via spliceosome	nucleoplasm	nucleotide binding|RNA binding|RS domain binding|unfolded protein binding	g.chr6:89814896_89814898delTTC	AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	21220	protein-coding gene	gene with protein product	"""splicing factor, arginine/serine-rich 19"", ""SR splicing factor 12"""		"""splicing factor, arginine/serine-rich 13B"""	SFRS13B		11684676, 20516191	Standard	NM_080743		Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.356_358delGAA	6.37:g.89814899_89814901delTTC	ENSP00000414302:p.Arg119del	False	False		Somatic	2					p.R119del	NM_080743.4	NP_542781.3	WXS	Illumina HiSeq	Phase_I	Q8WXF0	SRS12_HUMAN			4	549_551	-			119			Arg/Ser-rich (RS domain).		B2RA22|Q5T7K0|Q8WW25	In_Frame_Del	DEL	ENST00000452027.2	37	c.356_358delGAA	CCDS47459.1																																																																																				0.414	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041474.2	0	NM_080743		6:89814896
SLC22A1	6580	broad.mit.edu	37	6	160560881	160560883	+	In_Frame_Del	DEL	ATG	ATG	-	rs202220802|rs72552763|rs35191146|rs142448543|rs34305973|rs35167514	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	ATG	ATG	-	-	ATG	ATG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:160560881_160560883delATG	ENST00000366963.4	+	7	1405_1407	c.1258_1260delATG	c.(1258-1260)atgdel	p.M420del	SLC22A1_ENST00000324965.4_In_Frame_Del_p.M420del|SLC22A1_ENST00000457470.2_In_Frame_Del_p.M420del	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	420			Missing (no changes in the MPP uptake. No changes in the MPP uptake; when associated with V-408). {ECO:0000269|PubMed:12439218, ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14702039}.		dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	CTGCCTCGTCATGATTTTTATCT	0.517														592	0.118211	0.0454	0.2882	5008	,	,		14486	0.005		0.1839	False		,,,				2504	0.1452					ENST00000324965.4		NA																SLC22A1/CUTA(2)	0				breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21	GRCh37	CD072492	SLC22A1	D	rs35191146	c.(1258-1260)atgdel		solute carrier family 22 (organic cation transporter), member 1																																				SO:0001651	inframe_deletion	6580					basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding	g.chr6:160560881_160560883delATG	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.1258_1260delATG	6.37:g.160560881_160560883delATG	ENSP00000355930:p.Met420del	False	False		Somatic	1				SLC22A1_ENST00000457470.2_In_Frame_Del_p.M420del|SLC22A1_ENST00000366963.4_In_Frame_Del_p.M420del	p.M420del			WXS	Illumina HiSeq	Phase_I	O15245	S22A1_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	7	1258_1260	+		Breast(66;0.000776)|Ovarian(120;0.00556)	420		Missing (no changes in the MPP uptake. No changes in the MPP uptake; when associated with V-408).			A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	In_Frame_Del	DEL	ENST00000366963.4	37	c.1258_1260delATG	CCDS5274.1																																																																																				0.517	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2	0			6:160560881
AEBP1	165	broad.mit.edu	37	7	44153778	44153780	+	In_Frame_Del	DEL	AGA	AGA	-	rs13928	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	AGA	AGA	-	-	AGA	AGA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:44153778_44153780delAGA	ENST00000223357.3	+	21	3700_3702	c.3395_3397delAGA	c.(3394-3399)gagaaa>gaa	p.K1133del	AEBP1_ENST00000450684.2_In_Frame_Del_p.K708del	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	1133	Glu-rich.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for transcriptional repression. {ECO:0000250}.		K -> E (in dbSNP:rs13928). {ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						gaggaggaggagaaagaggagga	0.552																																						ENST00000223357.3		NA																	0				NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						c.(3394-3399)gagaaa>gaa		AE binding protein 1																																				SO:0001651	inframe_deletion	165				cell adhesion|muscle organ development|proteolysis|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr7:44153778_44153780delAGA	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.3395_3397delAGA	7.37:g.44153778_44153780delAGA	ENSP00000223357:p.Lys1133del	True	False		Somatic	1				AEBP1_ENST00000450684.2_In_Frame_Del_p.K708del	p.K1133del	NM_001129.3	NP_001120.3	WXS	Illumina HiSeq	Phase_I	Q8IUX7	AEBP1_HUMAN			21	3700_3702	+			1133		K -> E (in dbSNP:rs13928).	Glu-rich.|Interaction with MAPK1 and MAPK3 (By similarity).|Required for transcriptional repression (By similarity).		Q14113|Q59ER7|Q6ZSC7|Q7KZ79	In_Frame_Del	DEL	ENST00000223357.3	37	c.3395_3397delAGA	CCDS5476.1																																																																																				0.552	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	0	NM_001129		7:44153778
ZMIZ2	83637	broad.mit.edu	37	7	44797065	44797109	+	In_Frame_Del	DEL	GTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	GTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	-	rs557719047|rs142075074|rs371185257	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	GTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	GTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	-	-	GTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	GTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:44797065_44797109delGTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	ENST00000309315.4	+	5	580_624	c.457_501delGTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	c.(457-501)gtggctgctgcggcagccactgccaccgccacagccacagccaccdel	p.VAAAAATATATATAT153del	ZMIZ2_ENST00000413916.1_In_Frame_Del_p.VAAAAATATATATAT121del|ZMIZ2_ENST00000441627.1_In_Frame_Del_p.VAAAAATATATATAT153del|ZMIZ2_ENST00000433667.1_In_Frame_Del_p.VAAAAATATATATAT121del|ZMIZ2_ENST00000265346.7_In_Frame_Del_p.VAAAAATATATATAT153del	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	153	Ala-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)	p.A164G(1)|p.A147_A155del(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						tgctgcagctgtggctgctgcggcagccactgccaccgccacagccacagccaccgtggctgctC	0.678																																					NSCLC(20;604 852 1948 16908 50522)	ENST00000309315.4		NA																	2	Substitution - Missense(1)|Deletion - In frame(1)	p.A164G(1)|p.A147_A155del(1)	large_intestine(1)|breast(1)	breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(457-501)gtggctgctgcggcagccactgccaccgccacagccacagccaccdel		zinc finger, MIZ-type containing 2																																				SO:0001651	inframe_deletion	83637				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding	g.chr7:44797065_44797109delGTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.457_501delGTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	7.37:g.44797065_44797109delGTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	ENSP00000311778:p.Val153_Thr167del	False	False		Somatic	1				ZMIZ2_ENST00000441627.1_In_Frame_Del_p.VAAAAATATATATAT153del|ZMIZ2_ENST00000433667.1_In_Frame_Del_p.VAAAAATATATATAT121del|ZMIZ2_ENST00000265346.7_In_Frame_Del_p.VAAAAATATATATAT153del|ZMIZ2_ENST00000413916.1_In_Frame_Del_p.VAAAAATATATATAT121del	p.VAAAAATATATATAT153del	NM_031449.3	NP_113637.3	WXS	Illumina HiSeq	Phase_I	Q8NF64	ZMIZ2_HUMAN			5	580_624	+			153			Ala-rich.		A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	In_Frame_Del	DEL	ENST00000309315.4	37	c.457_501delGTGGCTGCTGCGGCAGCCACTGCCACCGCCACAGCCACAGCCACC	CCDS43576.1																																																																																				0.678	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	0	NM_031449		7:44797065
COBL	23242	broad.mit.edu	37	7	51098568	51098570	+	In_Frame_Del	DEL	TCT	TCT	-	rs201819395|rs398095077|rs58682836|rs142060269|rs75207469	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	TCT	TCT	-	-	TCT	TCT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:51098568_51098570delTCT	ENST00000265136.7	-	9	1608_1610	c.1443_1445delAGA	c.(1441-1446)gaagac>gac	p.E481del	COBL_ENST00000395542.2_In_Frame_Del_p.E563del	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	481				Missing (in Ref. 5; AAH29275). {ECO:0000305}.	actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					AATTAATAGGTCTTCTTCATCAT	0.409																																					NSCLC(189;2119 2138 12223 30818 34679)	ENST00000265136.7		NA																	0				NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65						c.(1441-1446)gaagac>gac		cordon-bleu WH2 repeat protein				1826,2438		396,1034,702						-2.4	0.0		dbSNP_131	158	2452,5802		364,1724,2039	no	coding	COBL	NM_015198.3		760,2758,2741	A1A1,A1R,RR		29.7068,42.8236,34.1748				4278,8240				SO:0001651	inframe_deletion	23242							g.chr7:51098568_51098570delTCT	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1443_1445delAGA	7.37:g.51098571_51098573delTCT	ENSP00000265136:p.Glu481del	False	False		Somatic	2				COBL_ENST00000395542.2_In_Frame_Del_p.E563del	p.E481del	NM_015198.3	NP_056013.2	WXS	Illumina HiSeq	Phase_I	O75128	COBL_HUMAN			9	1608_1610	-	Glioma(55;0.08)		481	Missing (in Ref. 5; AAH29275).				A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	In_Frame_Del	DEL	ENST00000265136.7	37	c.1443_1445delAGA	CCDS34637.1																																																																																				0.409	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	0	NM_015198		7:51098568
DTX2P1-UPK3BP1-PMS2P11	441263	broad.mit.edu	37	7	76653035	76653036	+	RNA	INS	-	-	AGAT			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:76653035_76653036insAGAT	ENST00000584900.1	+	0	1593_1594					NR_023383.1				DTX2P1-UPK3BP1-PMS2P11 readthrough transcribed pseudogene																		TCTCCTCCTTCCTGATGTCTGC	0.48																																						ENST00000584900.1		NA																	0					NA																																														0							g.chr7:76653035_76653036insAGAT	U38980		7q11.23	2014-09-10	2012-12-07		ENSG00000265479	ENSG00000265479			42360	other	readthrough			"""DTX2P1-UPK3BP1-PMS2P11 readthrough (non-protein coding)"""				Standard	NR_023383		Approved		uc003ufw.4		OTTHUMG00000179528		7.37:g.76653035_76653036insAGAT		True	False		Somatic	0						NR_023383.1		WXS	Illumina HiSeq	Phase_I					0	1593_1594	+			NA						RNA	INS	ENST00000584900.1	37																																																																																						0.480	DTX2P1-UPK3BP1-PMS2P11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000446923.2	0	NR_023383		7:76653035
TBC1D4	9882	broad.mit.edu	37	13	75884223	75884223	+	Silent	SNP	C	C	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:75884223C>T	ENST00000377636.3	-	14	2794	c.2448G>A	c.(2446-2448)ccG>ccA	p.P816P	TBC1D4_ENST00000431480.2_Silent_p.P808P|TBC1D4_ENST00000425511.1_Silent_p.P33P|TBC1D4_ENST00000377625.2_Silent_p.P753P	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	816					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)			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)		ATACAACCAGCGGTTCCTCCT	0.493																																						ENST00000377636.3		NA																	0				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						c.(2446-2448)ccG>ccA		TBC1 domain family, member 4							77.0	70.0	72.0					13																	75884223		1869	4097	5966	SO:0001819	synonymous_variant	9882					cytoplasm	Rab GTPase activator activity	g.chr13:75884223C>T	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.2448G>A	13.37:g.75884223C>T		False	False		Somatic	0				TBC1D4_ENST00000425511.1_Silent_p.P33P|TBC1D4_ENST00000377625.2_Silent_p.P753P|TBC1D4_ENST00000431480.2_Silent_p.P808P	p.P816P	NM_014832.2	NP_055647.2	WXS	Illumina HiSeq	Phase_I	O60343	TBCD4_HUMAN		GBM - Glioblastoma multiforme(99;0.0116)	14	2794	-		Prostate(6;0.014)|Breast(118;0.0982)	816					A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	c.2448G>A	CCDS41901.1																																																																																				0.493	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	0	NM_014832		13:75884223
ARHGEF10L	55160	broad.mit.edu	37	1	18023723	18023723	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:18023723G>A	ENST00000361221.3	+	29	3847	c.3688G>A	c.(3688-3690)Gcc>Acc	p.A1230T	ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A1003T|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A933T|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A1191T	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	1230						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CGCCCGCGACGCCCACCGCAA	0.677																																						ENST00000361221.3		NA																	0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43						c.(3688-3690)Gcc>Acc		Rho guanine nucleotide exchange factor (GEF) 10-like							24.0	25.0	25.0					1																	18023723		2189	4258	6447	SO:0001583	missense	55160				regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity	g.chr1:18023723G>A	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.3688G>A	1.37:g.18023723G>A	ENSP00000355060:p.Ala1230Thr	True	False		Somatic	0				ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A933T|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A1003T	p.A1230T	NM_018125.3	NP_060595	WXS	Illumina HiSeq	Phase_I	Q9HCE6	ARGAL_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)	29	3847	+		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)	1230					B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	c.3688G>A	CCDS182.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293646	0.80914	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000375415;ENST00000375408;ENST00000167825	T;T;T;T;T	0.61510	0.35;0.39;0.39;0.1;2.37	5.0	3.13	0.36017	.	0.166885	0.39544	N	0.001340	T	0.64929	0.2643	L	0.52364	1.645	0.39278	D	0.964508	P;D;P;D;D;D	0.89917	0.669;0.979;0.669;0.999;1.0;1.0	B;B;B;P;D;D	0.71870	0.115;0.389;0.115;0.847;0.975;0.961	T	0.61898	-0.6968	10	0.33141	T	0.24	-14.259	8.6006	0.33742	0.1809:0.0:0.8191:0.0	.	1003;933;991;1186;1191;1230	Q5VXI4;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;ARGAL_HUMAN	T	1230;1191;1191;1003;933	ENSP00000355060:A1230T;ENSP00000399401:A1191T;ENSP00000364564:A1191T;ENSP00000364557:A1003T;ENSP00000167825:A933T	ENSP00000167825:A933T	A	+	1	0	ARHGEF10L	17896310	0.538000	0.26394	0.984000	0.44739	0.967000	0.64934	1.279000	0.33191	0.507000	0.28148	-0.136000	0.14681	GCC		0.677	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	0	NM_018125		1:18023723
PCYT2	5833	broad.mit.edu	37	17	79866486	79866486	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:79866486C>T	ENST00000538936.2	-	4	473	c.365G>A	c.(364-366)gGc>gAc	p.G122D	PCYT2_ENST00000571105.1_Missense_Mutation_p.G122D|PCYT2_ENST00000570391.1_Missense_Mutation_p.G90D|PCYT2_ENST00000538721.2_Missense_Mutation_p.G122D|PCYT2_ENST00000331285.3_Missense_Mutation_p.G44D|PCYT2_ENST00000570388.1_Missense_Mutation_p.G44D	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	122					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	GGTGTCCCGGCCATCTACAGT	0.597																																						ENST00000538936.2		NA																	0				breast(2)|endometrium(1)|lung(4)|ovary(1)	8						c.(364-366)gGc>gAc		phosphate cytidylyltransferase 2, ethanolamine							117.0	98.0	105.0					17																	79866486		2202	4300	6502	SO:0001583	missense	5833				phospholipid biosynthetic process		ethanolamine-phosphate cytidylyltransferase activity	g.chr17:79866486C>T	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.365G>A	17.37:g.79866486C>T	ENSP00000439245:p.Gly122Asp	False	False		Somatic	0				PCYT2_ENST00000571105.1_Missense_Mutation_p.G122D|PCYT2_ENST00000570388.1_Missense_Mutation_p.G44D|PCYT2_ENST00000570391.1_Missense_Mutation_p.G90D|PCYT2_ENST00000331285.3_Missense_Mutation_p.G44D|PCYT2_ENST00000538721.2_Missense_Mutation_p.G122D	p.G122D	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	WXS	Illumina HiSeq	Phase_I	Q99447	PCY2_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		4	473	-	all_neural(118;0.0878)|Ovarian(332;0.12)		122			Catalytic 1 (Potential).		B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Missense_Mutation	SNP	ENST00000538936.2	37	c.365G>A	CCDS11791.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.925191	0.92319	.	.	ENSG00000185813	ENST00000538721;ENST00000538936;ENST00000331285	D;D	0.96396	-4.0;-4.0	4.61	4.61	0.57282	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.98604	0.9533	M	0.93594	3.435	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0	D	0.99780	1.1027	10	0.87932	D	0	-34.8642	17.6458	0.88148	0.0:1.0:0.0:0.0	.	90;90;122;44;122	B7Z4W6;B7ZAS0;F5H8B1;B7Z7A5;Q99447	.;.;.;.;PCY2_HUMAN	D	122;122;44	ENSP00000442050:G122D;ENSP00000439245:G122D	ENSP00000331719:G44D	G	-	2	0	PCYT2	77459778	1.000000	0.71417	0.997000	0.53966	0.841000	0.47740	5.058000	0.64300	2.380000	0.81148	0.650000	0.86243	GGC		0.597	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	0	NM_002861		17:79866486
SPAG4	6676	broad.mit.edu	37	20	34204182	34204182	+	Missense_Mutation	SNP	A	A	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:34204182A>G	ENST00000374273.3	+	1	369	c.257A>G	c.(256-258)aAc>aGc	p.N86S		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	86					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CGGAGCCACAACTGGCAGACA	0.736																																						ENST00000374273.3		NA																	0				NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21						c.(256-258)aAc>aGc		sperm associated antigen 4							4.0	7.0	6.0					20																	34204182		1811	3791	5602	SO:0001583	missense	6676				spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity	g.chr20:34204182A>G	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.257A>G	20.37:g.34204182A>G	ENSP00000363391:p.Asn86Ser	False	False		Somatic	0					p.N86S	NM_003116.1	NP_003107.1	WXS	Illumina HiSeq	Phase_I	Q9NPE6	SPAG4_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.0127)		1	369	+	Lung NSC(9;0.0053)|all_lung(11;0.00785)		86					O43648	Missense_Mutation	SNP	ENST00000374273.3	37	c.257A>G	CCDS13259.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.867046	0.32977	.	.	ENSG00000061656	ENST00000374273	T	0.13778	2.56	4.62	-0.622	0.11560	.	0.444886	0.20171	N	0.097736	T	0.07548	0.0190	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.23048	-1.0199	10	0.49607	T	0.09	-15.5229	4.3605	0.11199	0.4206:0.3763:0.2031:0.0	.	86	Q9NPE6	SPAG4_HUMAN	S	86	ENSP00000363391:N86S	ENSP00000363391:N86S	N	+	2	0	SPAG4	33667596	0.094000	0.21725	0.452000	0.26994	0.806000	0.45545	0.219000	0.17641	0.001000	0.14605	0.459000	0.35465	AAC		0.736	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	0	NM_003116		20:34204182
GRIN2A	2903	broad.mit.edu	37	16	10274206	10274206	+	Silent	SNP	C	C	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:10274206C>T	ENST00000396573.2	-	3	372	c.63G>A	c.(61-63)ccG>ccA	p.P21P	GRIN2A_ENST00000396575.2_Silent_p.P21P|GRIN2A_ENST00000330684.3_Silent_p.P21P|GRIN2A_ENST00000562109.1_Silent_p.P21P|GRIN2A_ENST00000404927.2_Silent_p.P21P	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	21					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGCTCGGCGCCGGACCGCGCC	0.647																																						ENST00000396573.2		NA																	0				NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198						c.(61-63)ccG>ccA		glutamate receptor, ionotropic, N-methyl D-aspartate 2A	Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)						16.0	20.0	19.0					16																	10274206		2189	4283	6472	SO:0001819	synonymous_variant	0				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding	g.chr16:10274206C>T		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.63G>A	16.37:g.10274206C>T		False	False		Somatic	0				GRIN2A_ENST00000562109.1_Silent_p.P21P|GRIN2A_ENST00000330684.3_Silent_p.P21P|GRIN2A_ENST00000396575.2_Silent_p.P21P|GRIN2A_ENST00000404927.2_Silent_p.P21P	p.P21P	NM_000833.3	NP_000824.1	WXS	Illumina HiSeq	Phase_I	Q12879	NMDE1_HUMAN			3	372	-			21					O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	c.63G>A	CCDS10539.1																																																																																				0.647	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3	0			16:10274206
GLB1L3	112937	broad.mit.edu	37	11	134182352	134182352	+	Missense_Mutation	SNP	G	G	A	rs376238782		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:134182352G>A	ENST00000431683.2	+	14	1397	c.1397G>A	c.(1396-1398)cGc>cAc	p.R466H		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	466					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			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)		TCCGGAGGCCGCCTCCGTGCC	0.607																																						ENST00000431683.2		NA																	0				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13						c.(1396-1398)cGc>cAc		galactosidase, beta 1-like 3		G	HIS/ARG	0,4206		0,0,2103	38.0	41.0	40.0		1397	-9.4	0.0	11		40	1,8443		0,1,4221	no	missense	GLB1L3	NM_001080407.2	29	0,1,6324	AA,AG,GG		0.0118,0.0,0.0079	benign	466/654	134182352	1,12649	2103	4222	6325	SO:0001583	missense	112937				carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds	g.chr11:134182352G>A		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.1397G>A	11.37:g.134182352G>A	ENSP00000396615:p.Arg466His	False	False		Somatic	0					p.R466H	NM_001080407.2	NP_001073876.2	WXS	Illumina HiSeq	Phase_I	Q8NCI6	GLBL3_HUMAN		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)	14	1397	+	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)	466					A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	37	c.1397G>A	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	6.749	0.507092	0.12883	0.0	1.18E-4	ENSG00000166105	ENST00000431683	D	0.92752	-3.1	4.69	-9.38	0.00623	.	5.286760	0.00166	N	0.000000	D	0.83760	0.5324	L	0.28400	0.85	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.71444	-0.4591	10	0.44086	T	0.13	.	4.4312	0.11529	0.0864:0.1553:0.3909:0.3674	.	466	Q8NCI6	GLBL3_HUMAN	H	466	ENSP00000396615:R466H	ENSP00000396615:R466H	R	+	2	0	GLB1L3	133687562	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.437000	0.02419	-3.768000	0.00109	-1.608000	0.00805	CGC		0.607	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	0	NM_138416		11:134182352
ATXN3L	92552	broad.mit.edu	37	X	13337260	13337260	+	Missense_Mutation	SNP	T	T	C			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:13337260T>C	ENST00000380622.2	-	1	1258	c.794A>G	c.(793-795)gAt>gGt	p.D265G	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	265					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTTTGGAAGATCTTGCGATGT	0.428																																						ENST00000380622.2		NA																	0				endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						c.(793-795)gAt>gGt		ataxin 3-like							345.0	294.0	310.0					X																	13337260		1568	3582	5150	SO:0001583	missense	92552				protein deubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ubiquitin-specific protease activity	g.chrX:13337260T>C		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.794A>G	X.37:g.13337260T>C	ENSP00000369996:p.Asp265Gly	False	False		Somatic	0				GS1-600G8.3_ENST00000431486.1_RNA	p.D265G	NM_001135995.1	NP_001129467.1	WXS	Illumina HiSeq	Phase_I	Q9H3M9	ATX3L_HUMAN			1	1258	-			265					B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	c.794A>G	CCDS48080.1	.	.	.	.	.	.	.	.	.	.	t	7.958	0.746349	0.15710	.	.	ENSG00000123594	ENST00000380622	T	0.70869	-0.52	0.793	0.793	0.18632	.	0.520162	0.22506	N	0.059168	T	0.52484	0.1737	L	0.29908	0.895	0.22017	N	0.99941	P	0.41313	0.745	B	0.38880	0.284	T	0.49390	-0.8945	10	0.72032	D	0.01	.	5.5756	0.17220	0.0:0.0:0.0:1.0	.	265	Q9H3M9	ATX3L_HUMAN	G	265	ENSP00000369996:D265G	ENSP00000369996:D265G	D	-	2	0	ATXN3L	13247181	0.112000	0.22096	0.277000	0.24703	0.064000	0.16182	0.777000	0.26718	0.549000	0.28973	0.341000	0.21757	GAT		0.428	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	0	NM_001135995		X:13337260
ADAMTS4	9507	broad.mit.edu	37	1	161166457	161166457	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:161166457G>A	ENST00000367996.5	-	2	1275	c.847C>T	c.(847-849)Ccc>Tcc	p.P283S	ADAMTS4_ENST00000367995.3_Missense_Mutation_p.P283S|NDUFS2_ENST00000367993.3_5'Flank|ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	283	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GCAGCACTGGGCCCCACTTGG	0.632																																						ENST00000367996.5		NA																	0				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43						c.(847-849)Ccc>Tcc		ADAM metallopeptidase with thrombospondin type 1 motif, 4							65.0	72.0	70.0					1																	161166457		2203	4300	6503	SO:0001583	missense	9507				proteolysis|skeletal system development	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|protease binding|zinc ion binding	g.chr1:161166457G>A	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.847C>T	1.37:g.161166457G>A	ENSP00000356975:p.Pro283Ser	True	False		Somatic	0				ADAMTS4_ENST00000367995.3_Missense_Mutation_p.P283S	p.P283S	NM_005099.4	NP_005090.3	WXS	Illumina HiSeq	Phase_I	O75173	ATS4_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00275)		2	1275	-	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		NA			Peptidase M12B.		Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	c.847C>T	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	G	1.536	-0.543024	0.04053	.	.	ENSG00000158859	ENST00000367996;ENST00000367995	D;D	0.85556	-2.0;-2.0	5.02	4.1	0.47936	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.197780	0.34932	N	0.003569	T	0.53674	0.1811	N	0.11789	0.175	0.39026	D	0.959836	B;B	0.17667	0.014;0.023	B;B	0.16722	0.005;0.016	T	0.50988	-0.8762	10	0.17369	T	0.5	.	9.3761	0.38283	0.1728:0.0:0.8272:0.0	.	283;283	Q5VTW1;O75173	.;ATS4_HUMAN	S	283	ENSP00000356975:P283S;ENSP00000356974:P283S	ENSP00000356974:P283S	P	-	1	0	ADAMTS4	159433081	0.000000	0.05858	0.959000	0.39883	0.998000	0.95712	-0.310000	0.08135	1.350000	0.45770	0.555000	0.69702	CCC		0.632	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	0	NM_005099		1:161166457
CHD6	84181	broad.mit.edu	37	20	40127944	40127944	+	Silent	SNP	A	A	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:40127944A>G	ENST00000373233.3	-	6	1083	c.906T>C	c.(904-906)acT>acC	p.T302T	CHD6_ENST00000373222.3_Silent_p.T337T|CHD6_ENST00000309279.7_Silent_p.T302T	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	302	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCTCCTGGACAGTCTTAGATG	0.398																																						ENST00000373233.3		NA																	0				breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129						c.(904-906)acT>acC		chromodomain helicase DNA binding protein 6							79.0	66.0	71.0					20																	40127944		2203	4300	6503	SO:0001819	synonymous_variant	0				chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding	g.chr20:40127944A>G	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.906T>C	20.37:g.40127944A>G		False	False		Somatic	0				CHD6_ENST00000309279.7_Silent_p.T302T|CHD6_ENST00000373222.3_Silent_p.T337T	p.T302T	NM_032221.3	NP_115597.3	WXS	Illumina HiSeq	Phase_I	Q8TD26	CHD6_HUMAN			6	1083	-		Myeloproliferative disorder(115;0.00425)	302			Chromo 1.		Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	c.906T>C	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.275613	0.23307	.	.	ENSG00000124177	ENST00000440697	.	.	.	4.44	-6.54	0.01860	.	.	.	.	.	T	0.46386	0.1390	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47711	-0.9096	4	.	.	.	-6.3713	6.0898	0.19989	0.1718:0.214:0.5181:0.0962	.	.	.	.	P	5	.	.	L	-	2	0	CHD6	39561358	0.465000	0.25815	0.861000	0.33841	0.991000	0.79684	-0.339000	0.07832	-1.366000	0.02155	0.459000	0.35465	CTG		0.398	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1	0			20:40127944
TRIOBP	11078	broad.mit.edu	37	22	38120431	38120431	+	Missense_Mutation	SNP	A	A	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:38120431A>T	ENST00000406386.3	+	7	2123	c.1868A>T	c.(1867-1869)aAc>aTc	p.N623I		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	623					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					ACACGAGATAACCCCAGAACA	0.587																																						ENST00000406386.3		NA																	0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(1867-1869)aAc>aTc		TRIO and F-actin binding protein							124.0	139.0	134.0					22																	38120431		1943	4152	6095	SO:0001583	missense	11078				actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	g.chr22:38120431A>T	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1868A>T	22.37:g.38120431A>T	ENSP00000384312:p.Asn623Ile	True	False		Somatic	0					p.N623I	NM_001039141.2	NP_001034230.1	WXS	Illumina HiSeq	Phase_I	Q9H2D6	TARA_HUMAN			7	2123	+	Melanoma(58;0.0574)		623					B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	c.1868A>T	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	9.134	1.012121	0.19277	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	2.17	-0.564	0.11774	.	.	.	.	.	T	0.11922	0.0290	L	0.46157	1.445	0.09310	N	1	P	0.38565	0.637	B	0.23574	0.047	T	0.21211	-1.0252	9	0.56958	D	0.05	.	2.4349	0.04480	0.5132:0.2956:0.1911:0.0	.	623	Q9H2D6	TARA_HUMAN	I	623	ENSP00000384312:N623I	ENSP00000384312:N623I	N	+	2	0	TRIOBP	36450377	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	-2.334000	0.01107	0.103000	0.17682	0.254000	0.18369	AAC		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2	0			22:38120431
