#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ABL2	27	genome.wustl.edu	37	1	179078567	179078567	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr1:179078567C>T	ENST00000502732.1	-	12	2038	c.1835G>A	c.(1834-1836)aGa>aAa	p.R612K	ABL2_ENST00000504405.1_Missense_Mutation_p.R576K|ABL2_ENST00000344730.3_Missense_Mutation_p.R597K|ABL2_ENST00000408940.3_Missense_Mutation_p.R576K|ABL2_ENST00000367623.4_Missense_Mutation_p.R591K|ABL2_ENST00000511413.1_Missense_Mutation_p.R612K|ABL2_ENST00000507173.1_Missense_Mutation_p.R591K|ABL2_ENST00000512653.1_Missense_Mutation_p.R597K	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	612					actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	CTGTGCACCTCTGATGAACCC	0.473			T	ETV6	AML																																	dbGAP		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	0													62.0	67.0	66.0					1																	179078567		2203	4300	6503	-	-	-	SO:0001583	missense	0			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"""SH2 domain containing"""	77	protein-coding gene	gene with protein product	"""Abelson-related gene"""	164690	"""v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)"", ""v-abl Abelson murine leukemia viral oncogene homolog 2"", ""c-abl oncogene 2, non-receptor tyrosine kinase"""	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1835G>A	1.37:g.179078567C>T	ENSP00000427562:p.Arg612Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_F-actin_binding,pfam_Prot_kinase_cat_dom,pfam_SH2,pfam_SH3_domain,pfam_SH3_2,pfam_SH3-like_bac,superfamily_Kinase-like_dom,superfamily_SH3_domain,smart_SH3_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_F-actin_binding,pfscan_SH2,pfscan_SH3_domain,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2	p.R612K	ENST00000502732.1	37	c.1835	CCDS30947.1	1	.	.	.	.	.	.	.	.	.	.	C	0.104	-1.148177	0.01714	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413	T;T;T;T;T;T;T;T	0.08896	3.04;3.04;3.04;3.04;3.04;3.04;3.04;3.04	5.63	5.63	0.86233	.	0.000000	0.53938	D	0.000048	T	0.08447	0.0210	L	0.38175	1.15	0.38162	D	0.939051	B;B;P;B;B;P;B;P	0.46220	0.372;0.414;0.776;0.064;0.123;0.545;0.123;0.874	B;B;P;B;B;B;B;B	0.46076	0.163;0.293;0.503;0.07;0.076;0.15;0.076;0.262	T	0.09840	-1.0656	10	0.05833	T	0.94	.	12.0541	0.53524	0.0:0.9224:0.0:0.0776	.	591;591;612;576;612;597;576;597	P42684-6;P42684-7;P42684-5;P42684-4;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;ABL2_HUMAN;.;.;.	K	612;576;597;597;576;591;591;612	ENSP00000427562:R612K;ENSP00000386152:R576K;ENSP00000339209:R597K;ENSP00000423578:R597K;ENSP00000426831:R576K;ENSP00000356595:R591K;ENSP00000423413:R591K;ENSP00000424697:R612K	ENSP00000339209:R597K	R	-	2	0	ABL2	177345190	1.000000	0.71417	1.000000	0.80357	0.064000	0.16182	3.141000	0.50593	2.652000	0.90054	0.655000	0.94253	AGA	ABL2	-	NULL	ENSG00000143322		0.473	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ABL2	HGNC	protein_coding	OTTHUMT00000085174.3	52	0.00	0	C	NM_005158		179078567	179078567	-1	no_errors	ENST00000502732	ensembl	human	known	69_37n	missense	16	42.86	12	SNP	1.000	T
AFG3L2	10939	genome.wustl.edu	37	18	12329635	12329635	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr18:12329635C>T	ENST00000269143.3	-	17	2554	c.2323G>A	c.(2323-2325)Ggc>Agc	p.G775S	TUBB6_ENST00000590967.1_Intron|TUBB6_ENST00000591909.1_3'UTR	NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	775					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	TCCTTAAGGCCTTCTGGAAGT	0.527																																						dbGAP											0													99.0	103.0	102.0					18																	12329635		2203	4300	6503	-	-	-	SO:0001583	missense	0			Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"""ATPases / AAA-type"""	315	protein-coding gene	gene with protein product		604581	"""AFG3 (ATPase family gene 3, yeast)-like 2"", ""spinocerebellar ataxia 28"", ""AFG3 ATPase family gene 3-like 2 (yeast)"", ""AFG3 ATPase family gene 3-like 2 (S. cerevisiae)"", ""AFG3 ATPase family member 3-like 2 (S. cerevisiae)"""	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.2323G>A	18.37:g.12329635C>T	ENSP00000269143:p.Gly775Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P1L0	Missense_Mutation	SNP	pfam_Peptidase_M41,pfam_ATPase_AAA_core,pfam_Pept_M41_FtsH_extracell,smart_AAA+_ATPase,tigrfam_FtsH	p.G775S	ENST00000269143.3	37	c.2323	CCDS11859.1	18	.	.	.	.	.	.	.	.	.	.	C	35	5.562723	0.96527	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	D	0.93547	-3.24	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.96318	0.8799	M	0.79805	2.47	0.80722	D	1	D	0.54047	0.964	P	0.58873	0.847	D	0.95195	0.8311	10	0.40728	T	0.16	-1.0015	20.0627	0.97684	0.0:1.0:0.0:0.0	.	775	Q9Y4W6	AFG32_HUMAN	S	775;790	ENSP00000269143:G775S	ENSP00000269143:G775S	G	-	1	0	AFG3L2	12319635	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.431000	0.80335	2.816000	0.96949	0.563000	0.77884	GGC	AFG3L2	-	NULL	ENSG00000141385		0.527	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AFG3L2	HGNC	protein_coding	OTTHUMT00000254603.2	171	0.00	0	C	NM_006796		12329635	12329635	-1	no_errors	ENST00000269143	ensembl	human	known	69_37n	missense	49	37.97	30	SNP	1.000	T
ARHGEF18	23370	genome.wustl.edu	37	19	7504982	7504982	+	Silent	SNP	C	C	T	rs10422503	byFrequency	TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr19:7504982C>T	ENST00000359920.6	+	1	409	c.156C>T	c.(154-156)ggC>ggT	p.G52G	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	52					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GAGCCCCGGGCGCGAACATGG	0.652													C|||	1727	0.344848	0.211	0.4078	5008	,	,		11852	0.4196		0.326	False		,,,				2504	0.4233					dbGAP											0													17.0	19.0	18.0					19																	7504982		692	1591	2283	-	-	-	SO:0001819	synonymous_variant	0			AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.156C>T	19.37:g.7504982C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	pfam_DH-domain,pfam_Pleckstrin_homology,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_DH-domain	p.G52	ENST00000359920.6	37	c.156	CCDS45946.1	19																																																																																			ARHGEF18	-	NULL	ENSG00000104880		0.652	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ARHGEF18	HGNC	protein_coding	OTTHUMT00000436340.1	9	0.00	0	C	NM_015318		7504982	7504982	+1	no_errors	ENST00000359920	ensembl	human	known	69_37n	silent	15	51.61	16	SNP	0.000	T
CABS1	85438	genome.wustl.edu	37	4	71200897	71200897	+	Silent	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr4:71200897C>T	ENST00000273936.5	+	1	215	c.141C>T	c.(139-141)caC>caT	p.H47H		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	47					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AAGGAGACCACGTCACTTCAG	0.368																																						dbGAP											0													100.0	105.0	103.0					4																	71200897		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"""casein-like phosphoprotein"""		"""chromosome 4 open reading frame 35"""	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.141C>T	4.37:g.71200897C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RCB5|Q86UE0|Q96M17	Silent	SNP	NULL	p.H47	ENST00000273936.5	37	c.141	CCDS3539.1	4																																																																																			CABS1	-	NULL	ENSG00000145309		0.368	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	CABS1	HGNC	protein_coding	OTTHUMT00000251561.3	86	0.00	0	C	NM_033122		71200897	71200897	+1	no_errors	ENST00000273936	ensembl	human	known	69_37n	silent	65	51.85	70	SNP	0.095	T
CIRH1A	84916	genome.wustl.edu	37	16	69184739	69184739	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr16:69184739C>T	ENST00000314423.7	+	8	1111	c.934C>T	c.(934-936)Cgt>Tgt	p.R312C	CIRH1A_ENST00000352319.4_Missense_Mutation_p.R312C|CIRH1A_ENST00000563094.1_Missense_Mutation_p.R312C			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	312					maturation of SSU-rRNA (GO:0030490)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(108;0.125)		CTTAGTCTTTCGTCCTCTCAT	0.512											OREG0023906	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Melanoma(69;1156 1278 4951 8715 52012)	dbGAP											0													187.0	156.0	166.0					16																	69184739		2198	4300	6498	-	-	-	SO:0001583	missense	0			AB075868	CCDS10872.1	16q22	2014-04-07			ENSG00000141076	ENSG00000141076		"""WD repeat domain containing"""	1983	protein-coding gene	gene with protein product	"""UTP4, small subunit (SSU) processome component, homolog (yeast)"""	607456				10820129, 20385600	Standard	NM_032830		Approved	NAIC, FLJ14728, KIAA1988, TEX292, CIRHIN, UTP4	uc002ews.4	Q969X6	OTTHUMG00000137570	ENST00000314423.7:c.934C>T	16.37:g.69184739C>T	ENSP00000327179:p.Arg312Cys	Somatic	1112	WXS	Illumina GAIIx	Phase_IV	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,superfamily_Quinonprotein_ADH-like,smart_WD40_repeat,pfscan_WD40_repeat_dom	p.R312C	ENST00000314423.7	37	c.934	CCDS10872.1	16	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520690	0.85495	.	.	ENSG00000141076	ENST00000314423;ENST00000352319	T;T	0.29655	1.56;2.28	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.53206	0.1782	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.80764	0.994;0.899;0.978	T	0.49925	-0.8887	10	0.54805	T	0.06	.	19.1545	0.93504	0.0:1.0:0.0:0.0	.	312;312;312	Q969X6-2;Q969X6;Q969X6-3	.;CIR1A_HUMAN;.	C	312	ENSP00000327179:R312C;ENSP00000339164:R312C	ENSP00000327179:R312C	R	+	1	0	CIRH1A	67742240	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	3.970000	0.56824	2.618000	0.88619	0.514000	0.50259	CGT	CIRH1A	-	superfamily_Quinonprotein_ADH-like,smart_WD40_repeat,pfscan_WD40_repeat_dom	ENSG00000141076		0.512	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CIRH1A	HGNC	protein_coding	OTTHUMT00000268950.2	115	0.00	0	C	NM_032830		69184739	69184739	+1	no_errors	ENST00000314423	ensembl	human	known	69_37n	missense	51	33.77	26	SNP	1.000	T
COL5A1	1289	genome.wustl.edu	37	9	137591855	137591855	+	Silent	SNP	G	G	A	rs145178917	byFrequency	TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr9:137591855G>A	ENST00000371817.3	+	3	792	c.378G>A	c.(376-378)caG>caA	p.Q126Q	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	126	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGGGTATCCAGCAGATTGGGC	0.597																																						dbGAP											0													85.0	87.0	86.0					9																	137591855		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.378G>A	9.37:g.137591855G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q15094|Q5SUX4	Silent	SNP	pfam_Collagen,pfam_Fib_collagen_C,pfam_Laminin_G,superfamily_ConA-like_lec_gl,superfamily_Fibrinogen_a/b/g_C,smart_Laminin_G,smart_Fib_collagen_C	p.Q126	ENST00000371817.3	37	c.378	CCDS6982.1	9																																																																																			COL5A1	-	pfam_Laminin_G,superfamily_ConA-like_lec_gl,smart_Laminin_G	ENSG00000130635		0.597	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL5A1	HGNC	protein_coding	OTTHUMT00000054954.2	16	0.00	0	G	NM_000093		137591855	137591855	+1	no_errors	ENST00000371817	ensembl	human	known	69_37n	silent	6	40.00	4	SNP	1.000	A
DMTF1	9988	genome.wustl.edu	37	7	86811354	86811354	+	Intron	DEL	T	T	-			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr7:86811354delT	ENST00000394703.5	+	12	1273				DMTF1_ENST00000394702.3_Frame_Shift_Del_p.C244fs|DMTF1_ENST00000432937.2_Intron|DMTF1_ENST00000411766.2_Frame_Shift_Del_p.C203fs|DMTF1_ENST00000414194.2_Intron|DMTF1_ENST00000413276.2_Intron|DMTF1_ENST00000331242.7_Intron	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1						cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					TTGCTGCCTGTTTTTTTTTCA	0.418																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.711-190T>-	7.37:g.86811354delT		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	NULL	p.F247fs	ENST00000394703.5	37	c.732	CCDS5601.1	7																																																																																			DMTF1	-	NULL	ENSG00000135164		0.418	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	DMTF1	HGNC	protein_coding	OTTHUMT00000334025.5	8	0.00	0	T	NM_021145		86811354	86811354	+1	no_errors	ENST00000394702	ensembl	human	known	69_37n	frame_shift_del	5	37.50	3	DEL	1.000	-
DNASE1L3	1776	genome.wustl.edu	37	3	58190568	58190568	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr3:58190568C>T	ENST00000394549.2	-	4	677	c.361G>A	c.(361-363)Gac>Aac	p.D121N	DNASE1L3_ENST00000483681.1_Missense_Mutation_p.D121N|DNASE1L3_ENST00000318316.3_Missense_Mutation_p.D121N|DNASE1L3_ENST00000486455.1_Missense_Mutation_p.D91N	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	121					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		TCCTGATAGTCATGGTAGTGA	0.488																																					Esophageal Squamous(96;1069 1424 4841 43466 52325)	dbGAP											0													128.0	115.0	119.0					3																	58190568		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.361G>A	3.37:g.58190568C>T	ENSP00000378053:p.Asp121Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R8B1|B7Z707|O75803	Missense_Mutation	SNP	pfam_Endo/exonuclease/phosphatase,superfamily_Endo/exonuclease/phosphatase,smart_DNase_I_euk,pirsf_DNase_I_euk,prints_DNase_I_euk	p.D121N	ENST00000394549.2	37	c.361	CCDS2886.1	3	.	.	.	.	.	.	.	.	.	.	C	17.21	3.332469	0.60853	.	.	ENSG00000163687	ENST00000486455;ENST00000450710;ENST00000318316;ENST00000483681;ENST00000394549;ENST00000461914	T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61	5.81	5.81	0.92471	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.79299	0.4422	H	0.94620	3.56	0.53005	D	0.999965	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.84379	0.0548	10	0.87932	D	0	.	20.0628	0.97684	0.0:1.0:0.0:0.0	.	91;121;121	B7Z707;E9PES0;Q13609	.;.;DNSL3_HUMAN	N	91;121;121;121;121;121	ENSP00000419052:D91N;ENSP00000316193:D121N;ENSP00000417047:D121N;ENSP00000378053:D121N;ENSP00000418113:D121N	ENSP00000316193:D121N	D	-	1	0	DNASE1L3	58165608	1.000000	0.71417	0.999000	0.59377	0.041000	0.13682	7.349000	0.79376	2.745000	0.94114	0.655000	0.94253	GAC	DNASE1L3	-	pfam_Endo/exonuclease/phosphatase,superfamily_Endo/exonuclease/phosphatase,smart_DNase_I_euk,pirsf_DNase_I_euk,prints_DNase_I_euk	ENSG00000163687		0.488	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNASE1L3	HGNC	protein_coding	OTTHUMT00000353533.1	126	0.00	0	C	NM_004944		58190568	58190568	-1	no_errors	ENST00000318316	ensembl	human	known	69_37n	missense	83	29.06	34	SNP	0.983	T
FAM47C	442444	genome.wustl.edu	37	X	37027222	37027222	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chrX:37027222C>T	ENST00000358047.3	+	1	791	c.739C>T	c.(739-741)Cgc>Tgc	p.R247C		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	247										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GTCCCATCTCCGCCCAGAGCC	0.627																																						dbGAP											0													53.0	50.0	51.0					X																	37027222		2202	4300	6502	-	-	-	SO:0001583	missense	0			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.739C>T	X.37:g.37027222C>T	ENSP00000367913:p.Arg247Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ZU46	Missense_Mutation	SNP	NULL	p.R247C	ENST00000358047.3	37	c.739	CCDS35227.1	X	.	.	.	.	.	.	.	.	.	.	c	1.813	-0.474182	0.04414	.	.	ENSG00000198173	ENST00000358047	T	0.21543	2.0	0.959	-1.92	0.07618	.	.	.	.	.	T	0.11750	0.0286	L	0.31065	0.9	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29549	-1.0008	9	0.52906	T	0.07	.	1.5054	0.02485	0.3313:0.3568:0.0:0.3118	.	247	Q5HY64	FA47C_HUMAN	C	247	ENSP00000367913:R247C	ENSP00000367913:R247C	R	+	1	0	FAM47C	36937143	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-1.500000	0.02283	-0.865000	0.04073	-0.872000	0.02987	CGC	FAM47C	-	NULL	ENSG00000198173		0.627	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM47C	HGNC	protein_coding	OTTHUMT00000060508.1	162	0.61	1	C	NM_001013736		37027222	37027222	+1	no_errors	ENST00000358047	ensembl	human	known	69_37n	missense	24	35.14	13	SNP	0.090	T
GALNT12	79695	genome.wustl.edu	37	9	101589095	101589095	+	Silent	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr9:101589095C>T	ENST00000375011.3	+	3	603	c.603C>T	c.(601-603)cgC>cgT	p.R201R		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	201	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				GCCTGATCCGCGCCAACAAGA	0.632																																						dbGAP											0													37.0	35.0	36.0					9																	101589095		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19877	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 12"""	610290	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"""			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.603C>T	9.37:g.101589095C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Silent	SNP	pfam_Glyco_trans_2,pfam_Ricin_B_lectin,superfamily_Ricin_B_lectin,smart_Ricin_B_lectin,pfscan_Ricin_B_lectin	p.R201	ENST00000375011.3	37	c.603	CCDS6737.1	9																																																																																			GALNT12	-	pfam_Glyco_trans_2	ENSG00000119514		0.632	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GALNT12	HGNC	protein_coding	OTTHUMT00000053382.1	93	0.00	0	C	NM_024642		101589095	101589095	+1	no_errors	ENST00000375011	ensembl	human	known	69_37n	silent	136	40.87	94	SNP	0.133	T
GYS1	2997	genome.wustl.edu	37	19	49472669	49472669	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr19:49472669G>A	ENST00000323798.3	-	16	2286	c.2090C>T	c.(2089-2091)gCg>gTg	p.A697V	GYS1_ENST00000263276.6_Missense_Mutation_p.A633V|GYS1_ENST00000541188.1_Missense_Mutation_p.A617V|GYS1_ENST00000544287.1_Missense_Mutation_p.A330V	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	697					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		GGTGCAGGACGCTCGGCGCGG	0.701																																						dbGAP											0													32.0	23.0	26.0					19																	49472669		2176	4253	6429	-	-	-	SO:0001583	missense	0				CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.2090C>T	19.37:g.49472669G>A	ENSP00000317904:p.Ala697Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9BTT9	Missense_Mutation	SNP	pfam_Glycogen_synth,pfam_Glyco_trans_1,pfam_Starch_synth_cat_dom	p.A697V	ENST00000323798.3	37	c.2090	CCDS12747.1	19	.	.	.	.	.	.	.	.	.	.	G	12.27	1.886249	0.33348	.	.	ENSG00000104812	ENST00000323798;ENST00000263276;ENST00000541188;ENST00000544287	T;T;T;T	0.74209	-0.14;-0.43;-0.01;-0.82	5.57	3.35	0.38373	.	0.382139	0.29335	N	0.012442	T	0.53916	0.1826	N	0.14661	0.345	0.80722	D	1	B;B;B	0.31519	0.327;0.327;0.118	B;B;B	0.12156	0.007;0.007;0.007	T	0.48854	-0.8998	10	0.27785	T	0.31	-16.198	14.2684	0.66135	0.0:0.2697:0.7303:0.0	.	617;633;697	B7Z806;Q9BTT9;P13807	.;.;GYS1_HUMAN	V	697;633;617;330	ENSP00000317904:A697V;ENSP00000263276:A633V;ENSP00000437922:A617V;ENSP00000444004:A330V	ENSP00000263276:A633V	A	-	2	0	GYS1	54164481	0.994000	0.37717	0.933000	0.37362	0.091000	0.18340	3.594000	0.54008	0.765000	0.33221	0.557000	0.71058	GCG	GYS1	-	NULL	ENSG00000104812		0.701	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GYS1	HGNC	protein_coding	OTTHUMT00000319791.1	18	0.00	0	G	NM_002103		49472669	49472669	-1	no_errors	ENST00000323798	ensembl	human	known	69_37n	missense	10	44.44	8	SNP	0.993	A
IFI35	3430	genome.wustl.edu	37	17	41164295	41164295	+	Splice_Site	SNP	G	G	A			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr17:41164295G>A	ENST00000415816.2	+	2	343		c.e2+1		IFI35_ENST00000438323.2_Splice_Site|IFI35_ENST00000536969.1_Splice_Site	NM_005533.4	NP_005524.2	P80217	IN35_HUMAN	interferon-induced protein 35						cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)		CAAAGACAAGGTAAGGTGGGA	0.607																																						dbGAP											0													37.0	40.0	39.0					17																	41164295		2179	4279	6458	-	-	-	SO:0001630	splice_region_variant	0			BC001356	CCDS11450.1	17q21	2006-04-05			ENSG00000068079	ENSG00000068079			5399	protein-coding gene	gene with protein product		600735					Standard	NM_005533		Approved	IFP35	uc021txx.1	P80217	OTTHUMG00000167720	ENST00000415816.2:c.120+1G>A	17.37:g.41164295G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	C9JGX1|Q92984|Q99537|Q9BV98	Splice_Site	SNP	-	e2+1	ENST00000415816.2	37	c.120+1		17	.	.	.	.	.	.	.	.	.	.	G	14.48	2.546845	0.45383	.	.	ENSG00000068079	ENST00000415816;ENST00000438323	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7658	0.62995	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IFI35	38417821	1.000000	0.71417	0.976000	0.42696	0.044000	0.14063	4.060000	0.57477	2.711000	0.92665	0.655000	0.94253	.	IFI35	-	-	ENSG00000068079		0.607	IFI35-002	KNOWN	basic|appris_candidate	protein_coding	IFI35	HGNC	protein_coding	OTTHUMT00000395851.1	93	0.00	0	G	NM_005533	Intron	41164295	41164295	+1	no_errors	ENST00000438323	ensembl	human	known	69_37n	splice_site	56	32.53	27	SNP	0.992	A
IGHV3-30	28439	genome.wustl.edu	37	14	106791268	106791268	+	RNA	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr14:106791268C>T	ENST00000390613.2	-	0	167									immunoglobulin heavy variable 3-30																		GGCTGGACCACGCCTCCCCCA	0.572																																						dbGAP											0													56.0	84.0	75.0					14																	106791268		1821	4114	5935	-	-	-			0			M83134		14q32.33	2012-02-08			ENSG00000211953	ENSG00000270550		"""Immunoglobulins / IGH locus"""	5591	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152069		14.37:g.106791268C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Ig_V-set,smart_Ig_V-set_subgr,pfscan_Ig-like	p.V30M	ENST00000390613.2	37	c.88		14																																																																																			IGHV3-30	-	pfam_Ig_V-set	ENSG00000211953		0.572	IGHV3-30-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IGHV3-30	HGNC	IG_V_gene	OTTHUMT00000325163.1	290	0.00	0	C	NG_001019		106791268	106791268	-1	no_stop_codon	ENST00000390613	ensembl	human	known	69_37n	missense	54	27.03	20	SNP	0.145	T
IKBKB	3551	genome.wustl.edu	37	8	42178341	42178342	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr8:42178341_42178342insG	ENST00000520810.1	+	16	1853_1854	c.1667_1668insG	c.(1666-1671)caggggfs	p.QG556fs	IKBKB_ENST00000379708.3_Frame_Shift_Ins_p.QG333fs|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Frame_Shift_Ins_p.QG554fs|IKBKB_ENST00000416505.2_Frame_Shift_Ins_p.QG497fs	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	556					B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	GGCCGGAAGCAGGGGGGAACGC	0.594																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1673dupG	8.37:g.42178347_42178347dupG	ENSP00000430684:p.Gln556fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DZ30|B4E0U4|O75327	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_IKKbetaNEMObind,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,pfscan_Ubiquitin_supergroup,prints_Ser-Thr/Tyr_kinase_cat_dom	p.T559fs	ENST00000520810.1	37	c.1667_1668	CCDS6128.1	8																																																																																			IKBKB	-	NULL	ENSG00000104365		0.594	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	IKBKB	HGNC	protein_coding	OTTHUMT00000377214.1	55	0.00	0	-			42178341	42178342	+1	no_errors	ENST00000520810	ensembl	human	known	69_37n	frame_shift_ins	24	14.29	4	INS	1.000:1.000	G
ITSN2	50618	genome.wustl.edu	37	2	24531572	24531572	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr2:24531572G>A	ENST00000355123.4	-	8	1150	c.707C>T	c.(706-708)tCa>tTa	p.S236L	ITSN2_ENST00000407704.1_5'Flank|ITSN2_ENST00000361999.3_Missense_Mutation_p.S236L|ITSN2_ENST00000406921.3_Missense_Mutation_p.S236L	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	236					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCCCACTCTGAGGTCCCAGT	0.353																																						dbGAP											0													90.0	92.0	91.0					2																	24531572		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.707C>T	2.37:g.24531572G>A	ENSP00000347244:p.Ser236Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	pfam_SH3_domain,pfam_SH3_2,pfam_DH-domain,pfam_C2_Ca-dep,superfamily_DH-domain,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_SH3_domain,smart_EPS15_homology,smart_EF_hand_Ca-bd,smart_SH3_domain,smart_DH-domain,smart_Pleckstrin_homology,smart_C2_Ca-dep,pfscan_EF_HAND_2,pfscan_EPS15_homology,pfscan_C2_membr_targeting,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_DH-domain,prints_SH3_domain,prints_p67phox	p.S236L	ENST00000355123.4	37	c.707	CCDS1710.2	2	.	.	.	.	.	.	.	.	.	.	G	13.87	2.366431	0.41902	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	4.69	3.81	0.43845	.	0.269718	0.19248	U	0.118984	T	0.27663	0.0680	N	0.21097	0.63	0.36856	D	0.888148	P;P;P;B	0.43885	0.811;0.663;0.82;0.125	B;B;P;B	0.46685	0.425;0.343;0.524;0.141	T	0.21621	-1.0240	10	0.39692	T	0.17	.	13.3956	0.60851	0.0765:0.0:0.9235:0.0	.	236;236;236;236	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	L	236;236;236;260;236;261	ENSP00000354561:S236L;ENSP00000347244:S236L;ENSP00000370250:S236L;ENSP00000384499:S236L;ENSP00000391224:S261L	ENSP00000347244:S236L	S	-	2	0	ITSN2	24385076	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.953000	0.40352	1.340000	0.45581	0.462000	0.41574	TCA	ITSN2	-	NULL	ENSG00000198399		0.353	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ITSN2	HGNC	protein_coding	OTTHUMT00000207620.2	114	0.00	0	G	NM_006277		24531572	24531572	-1	no_errors	ENST00000355123	ensembl	human	known	69_37n	missense	93	41.25	66	SNP	1.000	A
IQCA1	79781	genome.wustl.edu	37	2	237308121	237308121	+	Missense_Mutation	SNP	T	T	G			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr2:237308121T>G	ENST00000409907.3	-	9	1419	c.1145A>C	c.(1144-1146)gAa>gCa	p.E382A	IQCA1_ENST00000309507.5_Missense_Mutation_p.E378A|IQCA1_ENST00000431676.2_Missense_Mutation_p.E341A|IQCA1_ENST00000465621.1_5'UTR	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	382	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TTTCCATTTTTCGTCTTCTTC	0.453																																						dbGAP											0													138.0	135.0	136.0					2																	237308121		1951	4147	6098	-	-	-	SO:0001583	missense	0			AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1145A>C	2.37:g.237308121T>G	ENSP00000387347:p.Glu382Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	pfam_ATPase_AAA_core,pfscan_IQ_motif_EF-hand-BS	p.E382A	ENST00000409907.3	37	c.1145	CCDS46549.1	2	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990729	0.35131	.	.	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	D;D;D	0.94457	-3.35;-3.35;-3.43	4.0	4.0	0.46444	.	0.000000	0.53938	D	0.000052	D	0.90511	0.7027	L	0.54323	1.7	0.20563	N	0.999886	B;B;B	0.27679	0.048;0.185;0.052	B;B;B	0.24974	0.015;0.057;0.028	T	0.77175	-0.2684	10	0.09590	T	0.72	.	12.1636	0.54117	0.0:0.0:0.0:1.0	.	341;389;382	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	A	382;389;378;341;378	ENSP00000387347:E382A;ENSP00000311951:E378A;ENSP00000407213:E341A	ENSP00000254653:E382A	E	-	2	0	IQCA1	236972860	0.900000	0.30661	0.054000	0.19295	0.737000	0.42083	2.953000	0.49105	2.030000	0.59900	0.533000	0.62120	GAA	IQCA1	-	NULL	ENSG00000132321		0.453	IQCA1-001	KNOWN	basic|CCDS	protein_coding	IQCA1	HGNC	protein_coding	OTTHUMT00000329266.1	244	0.00	0	T	NM_024726		237308121	237308121	-1	no_errors	ENST00000409907	ensembl	human	known	69_37n	missense	91	44.85	74	SNP	0.289	G
KIAA0226	9711	genome.wustl.edu	37	3	197427914	197427915	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr3:197427914_197427915insG	ENST00000296343.5	-	7	829_830	c.830_831insC	c.(829-831)ccafs	p.P277fs	KIAA0226_ENST00000273582.5_Frame_Shift_Ins_p.P217fs|KIAA0226_ENST00000389665.5_Frame_Shift_Ins_p.P277fs|KIAA0226_ENST00000449205.1_Frame_Shift_Ins_p.P277fs|KIAA0226_ENST00000467303.1_5'Flank	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	277	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		AGACTGAAACTGGGGGGGCTTG	0.554																																					Esophageal Squamous(3;167 355 3763 15924)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.831dupC	3.37:g.197427921_197427921dupG	ENSP00000296343:p.Pro277fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96CK5	Frame_Shift_Ins	INS	pfam_Run,smart_Run,pfscan_Run	p.V278fs	ENST00000296343.5	37	c.831_830	CCDS43195.1	3																																																																																			KIAA0226	-	NULL	ENSG00000145016		0.554	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIAA0226	HGNC	protein_coding	OTTHUMT00000340184.1	31	0.00	0	-	XM_032901		197427914	197427915	-1	no_errors	ENST00000296343	ensembl	human	known	69_37n	frame_shift_ins	10	23.08	3	INS	0.000:0.000	G
MUC5B	727897	genome.wustl.edu	37	11	1269750	1269750	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr11:1269750delC	ENST00000529681.1	+	31	11698	c.11640delC	c.(11638-11640)agcfs	p.S3880fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Del_p.S3883fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3880	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				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)		CCTCCTCCAGCCCAGGGACGG	0.662																																						dbGAP											0													131.0	156.0	147.0					11																	1269750		2108	4214	6322	-	-	-	SO:0001589	frameshift_variant	0			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.11640delC	11.37:g.1269750delC	ENSP00000436812:p.Ser3880fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,pfam_VWF_C,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_VWF_C,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_VWF_C	p.P3884fs	ENST00000529681.1	37	c.11649	CCDS44515.2	11																																																																																			MUC5B	-	NULL	ENSG00000117983		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	MUC5B	HGNC	protein_coding	OTTHUMT00000390041.2	60	0.00	0	C	XM_001126093		1269750	1269750	+1	no_errors	ENST00000447027	ensembl	human	known	69_37n	frame_shift_del	17	10.53	2	DEL	0.000	-
NEDD4L	23327	genome.wustl.edu	37	18	55990551	55990551	+	Silent	SNP	G	G	A			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr18:55990551G>A	ENST00000400345.3	+	8	781	c.498G>A	c.(496-498)caG>caA	p.Q166Q	NEDD4L_ENST00000382850.4_Silent_p.Q166Q|NEDD4L_ENST00000256830.9_Silent_p.Q166Q|NEDD4L_ENST00000435432.2_Silent_p.Q45Q|NEDD4L_ENST00000357895.5_Silent_p.Q158Q|NEDD4L_ENST00000356462.6_Silent_p.Q166Q|NEDD4L_ENST00000586263.1_Silent_p.Q158Q|NEDD4L_ENST00000256832.7_Silent_p.Q45Q|NEDD4L_ENST00000456173.2_Silent_p.Q45Q|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000431212.2_Silent_p.Q45Q|NEDD4L_ENST00000456986.1_Silent_p.Q45Q	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	166					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						ACAGTGACCAGAGGGATGACA	0.403																																						dbGAP											0													73.0	73.0	73.0					18																	55990551		1935	4136	6071	-	-	-	SO:0001819	synonymous_variant	0			AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.498G>A	18.37:g.55990551G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	pfam_HECT,pfam_WW_Rsp5_WWP,pfam_C2_Ca-dep,superfamily_HECT,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_WW_Rsp5_WWP,smart_C2_Ca-dep,smart_WW_Rsp5_WWP,smart_HECT,pfscan_HECT,pfscan_C2_membr_targeting,pfscan_WW_Rsp5_WWP,prints_C2_dom	p.Q166	ENST00000400345.3	37	c.498	CCDS45872.1	18																																																																																			NEDD4L	-	NULL	ENSG00000049759		0.403	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NEDD4L	HGNC	protein_coding	OTTHUMT00000448749.1	165	0.60	1	G			55990551	55990551	+1	no_errors	ENST00000400345	ensembl	human	known	69_37n	silent	89	38.62	56	SNP	0.998	A
PHF3	23469	genome.wustl.edu	37	6	64395792	64395793	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr6:64395792_64395793insA	ENST00000262043.3	+	4	2509_2510	c.2169_2170insA	c.(2170-2172)aaafs	p.K724fs	PHF3_ENST00000393387.1_Frame_Shift_Ins_p.K724fs|PHF3_ENST00000509330.1_Frame_Shift_Ins_p.K724fs			Q92576	PHF3_HUMAN	PHD finger protein 3	724					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GTGGGTTTTGCAAAAAACCACA	0.396																																					GBM(135;136 1820 29512 34071 46235)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2175dupA	6.37:g.64395798_64395798dupA	ENSP00000262043:p.Lys724fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Ins	INS	pfam_TFIIS_cen_dom,pfam_SPOC_C,pfam_Znf_PHD-finger,superfamily_TFIIS_cen_dom,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,smart_TFS2M,pfscan_Znf_PHD-finger	p.P725fs	ENST00000262043.3	37	c.2169_2170	CCDS4966.1	6																																																																																			PHF3	-	pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,pfscan_Znf_PHD-finger	ENSG00000118482		0.396	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHF3	HGNC	protein_coding	OTTHUMT00000041086.2	12	0.00	0	-			64395792	64395793	+1	no_errors	ENST00000262043	ensembl	human	known	69_37n	frame_shift_ins	10	16.67	2	INS	1.000:1.000	A
PIM2	11040	genome.wustl.edu	37	X	48772372	48772372	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chrX:48772372G>A	ENST00000376509.4	-	4	709	c.520C>T	c.(520-522)Cgc>Tgc	p.R174C	PIM2_ENST00000485431.1_5'Flank	NM_006875.3	NP_006866.2	Q9P1W9	PIM2_HUMAN	Pim-2 proto-oncogene, serine/threonine kinase	174	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic mitochondrial changes (GO:0008637)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|response to virus (GO:0009615)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			lung(3)|stomach(1)	4						CAGCCACGGCGTAGGTCTATC	0.512																																						dbGAP											0													84.0	64.0	71.0					X																	48772372		2203	4300	6503	-	-	-	SO:0001583	missense	0			U77735	CCDS14312.1	Xp11.23	2014-06-25	2014-06-25		ENSG00000102096	ENSG00000102096			8987	protein-coding gene	gene with protein product		300295	"""pim-2 oncogene"""			9804974	Standard	NM_006875		Approved		uc004dls.3	Q9P1W9	OTTHUMG00000024132	ENST00000376509.4:c.520C>T	X.37:g.48772372G>A	ENSP00000365692:p.Arg174Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4G6|Q99739	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.R174C	ENST00000376509.4	37	c.520	CCDS14312.1	X	.	.	.	.	.	.	.	.	.	.	G	9.929	1.214253	0.22289	.	.	ENSG00000102096	ENST00000376509;ENST00000442430	T;T	0.66815	-0.23;-0.23	5.59	3.16	0.36331	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.139018	0.41396	N	0.000900	T	0.57504	0.2058	L	0.55990	1.75	0.20489	N	0.999893	B	0.16166	0.016	B	0.15484	0.013	T	0.52741	-0.8535	10	0.51188	T	0.08	.	7.586	0.27993	0.13:0.0:0.684:0.186	.	174	Q9P1W9	PIM2_HUMAN	C	174;62	ENSP00000365692:R174C;ENSP00000410960:R62C	ENSP00000365692:R174C	R	-	1	0	PIM2	48657316	0.000000	0.05858	0.990000	0.47175	0.844000	0.47949	-0.325000	0.07976	0.858000	0.35431	0.529000	0.55759	CGC	PIM2	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000102096		0.512	PIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIM2	HGNC	protein_coding	OTTHUMT00000060805.1	56	0.00	0	G			48772372	48772372	-1	no_errors	ENST00000376509	ensembl	human	known	69_37n	missense	94	38.96	60	SNP	0.121	A
PIP5K1C	23396	genome.wustl.edu	37	19	3633459	3633460	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr19:3633459_3633460insG	ENST00000335312.3	-	17	2067_2068	c.1979_1980insC	c.(1978-1980)ccgfs	p.P660fs	PIP5K1C_ENST00000539785.1_Intron	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	660	Mediates interaction with TLN2.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)	p.P660fs*>9(1)		large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		CGTCGGAGGCCGGGGGGGCCTG	0.698																																					Esophageal Squamous(135;99 1744 12852 27186 39851)	dbGAP											1	Deletion - Frameshift(1)	ovary(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1980dupC	19.37:g.3633466_3633466dupG	ENSP00000335333:p.Pro660fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Frame_Shift_Ins	INS	pfam_PInositol-4-P-5-kinase_core,smart_PInositol-4P-5-kinase_core_sub	p.A661fs	ENST00000335312.3	37	c.1980_1979	CCDS32872.1	19																																																																																			PIP5K1C	-	NULL	ENSG00000186111		0.698	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PIP5K1C	HGNC	protein_coding	OTTHUMT00000453432.2	8	0.00	0	-	NM_012398		3633459	3633460	-1	no_errors	ENST00000335312	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	0.922:0.997	G
PRAM1	84106	genome.wustl.edu	37	19	8564392	8564393	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr19:8564392_8564393insC	ENST00000423345.4	-	2	819_820	c.299_300insG	c.(298-300)gtcfs	p.V100fs	PRAM1_ENST00000255612.3_Frame_Shift_Ins_p.V100fs			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	148	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						GGAGGTCAGTGACCTCAGGCGG	0.649																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.299_300insG	19.37:g.8564392_8564393insC	ENSP00000408342:p.Val100fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N6W7	Frame_Shift_Ins	INS	superfamily_SH3_domain	p.T101fs	ENST00000423345.4	37	c.300_299	CCDS45954.2	19																																																																																			PRAM1	-	NULL	ENSG00000133246		0.649	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRAM1	HGNC	protein_coding	OTTHUMT00000397040.3	18	0.00	0	-	NM_032152		8564392	8564393	-1	no_errors	ENST00000423345	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	0.001:0.000	C
PRAM1	84106	genome.wustl.edu	37	19	8564394	8564395	+	Frame_Shift_Ins	INS	-	-	CAAA	rs189361135		TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr19:8564394_8564395insCAAA	ENST00000423345.4	-	2	817_818	c.297_298insTTTG	c.(295-300)gaggtcfs	p.V100fs	PRAM1_ENST00000255612.3_Frame_Shift_Ins_p.V100fs			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	148	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						AGGTCAGTGACCTCAGGCGGCG	0.644																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.297_298insTTTG	19.37:g.8564394_8564395insCAAA	ENSP00000408342:p.Val100fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N6W7	Frame_Shift_Ins	INS	superfamily_SH3_domain	p.V99fs	ENST00000423345.4	37	c.298_297	CCDS45954.2	19																																																																																			PRAM1	-	NULL	ENSG00000133246		0.644	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRAM1	HGNC	protein_coding	OTTHUMT00000397040.3	18	0.00	0	-	NM_032152		8564394	8564395	-1	no_errors	ENST00000423345	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	0.000:0.000	CAAA
PRRG3	79057	genome.wustl.edu	37	X	150869296	150869297	+	Frame_Shift_Ins	INS	-	-	G	rs139807152	byFrequency	TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chrX:150869296_150869297insG	ENST00000370353.3	+	4	877_878	c.487_488insG	c.(487-489)cggfs	p.R163fs	PRRG3_ENST00000538575.1_Frame_Shift_Ins_p.R163fs			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	163						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.R163P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGCCCAGTCGGGGGGGCAGG	0.673																																						dbGAP											1	Substitution - Missense(1)	lung(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.494dupG	X.37:g.150869303_150869303dupG	ENSP00000359378:p.Arg163fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A1A523|A1A575|Q8N2N6	Frame_Shift_Ins	INS	pfam_GLA_domain,superfamily_GLA_domain,smart_GLA_domain,prints_GLA_domain,pfscan_GLA_domain	p.R166fs	ENST00000370353.3	37	c.487_488	CCDS14699.1	X																																																																																			PRRG3	-	NULL	ENSG00000130032		0.673	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRRG3	HGNC	protein_coding	OTTHUMT00000060880.1	48	0.00	0	-	NM_024082		150869296	150869297	+1	no_errors	ENST00000370353	ensembl	human	known	69_37n	frame_shift_ins	31	13.89	5	INS	0.000:0.000	G
RAB3GAP2	25782	genome.wustl.edu	37	1	220325077	220325077	+	Silent	SNP	G	G	C			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr1:220325077G>C	ENST00000358951.2	-	34	4013	c.3897C>G	c.(3895-3897)gtC>gtG	p.V1299V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	1299					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		GAGAGGCAAGGACCTCTTTGT	0.488																																						dbGAP											0													95.0	95.0	95.0					1																	220325077		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.3897C>G	1.37:g.220325077G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	superfamily_WD40_repeat_dom	p.V1299	ENST00000358951.2	37	c.3897	CCDS31028.1	1																																																																																			RAB3GAP2	-	NULL	ENSG00000118873		0.488	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB3GAP2	HGNC	protein_coding	OTTHUMT00000090205.2	99	0.00	0	G	NM_012414		220325077	220325077	-1	no_errors	ENST00000358951	ensembl	human	known	69_37n	silent	65	43.48	50	SNP	0.956	C
RAI1	10743	genome.wustl.edu	37	17	17697697	17697697	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr17:17697697C>T	ENST00000353383.1	+	3	1904	c.1435C>T	c.(1435-1437)Cag>Tag	p.Q479*	RAI1_ENST00000261641.6_Nonsense_Mutation_p.Q479*	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	479					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GCATAAAAGCCAGCACTGCAG	0.647																																						dbGAP											0													41.0	45.0	44.0					17																	17697697		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.1435C>T	17.37:g.17697697C>T	ENSP00000323074:p.Gln479*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Nonsense_Mutation	SNP	smart_Znf_PHD	p.Q479*	ENST00000353383.1	37	c.1435	CCDS11188.1	17	.	.	.	.	.	.	.	.	.	.	C	41	8.853192	0.98978	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	.	.	.	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	19.1717	0.93580	0.0:1.0:0.0:0.0	.	.	.	.	X	479;479;479;479;479;431	.	ENSP00000261641:Q479X	Q	+	1	0	RAI1	17638422	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.241000	0.43097	2.541000	0.85698	0.561000	0.74099	CAG	RAI1	-	NULL	ENSG00000108557		0.647	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAI1	HGNC	protein_coding	OTTHUMT00000131775.1	9	0.00	0	C	NM_030665		17697697	17697697	+1	no_errors	ENST00000353383	ensembl	human	known	69_37n	nonsense	9	43.75	7	SNP	1.000	T
RICTOR	253260	genome.wustl.edu	37	5	38952359	38952359	+	Silent	SNP	T	T	C	rs111395471	byFrequency	TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr5:38952359T>C	ENST00000357387.3	-	30	3096	c.3066A>G	c.(3064-3066)ctA>ctG	p.L1022L	RICTOR_ENST00000503698.1_5'Flank|RICTOR_ENST00000296782.5_Silent_p.L1022L	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AGTTCAAACTTAGAGTGCTTG	0.438																																						dbGAP											0													115.0	110.0	112.0					5																	38952359		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3066A>G	5.37:g.38952359T>C		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	superfamily_ARM-type_fold	p.L1022	ENST00000357387.3	37	c.3066	CCDS34148.1	5																																																																																			RICTOR	-	NULL	ENSG00000164327		0.438	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RICTOR	HGNC	protein_coding	OTTHUMT00000366985.1	117	0.00	0	T	NM_152756		38952359	38952359	-1	no_errors	ENST00000296782	ensembl	human	known	69_37n	silent	65	41.44	46	SNP	0.123	C
RPS6KA1	6195	genome.wustl.edu	37	1	26885310	26885311	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr1:26885310_26885311insC	ENST00000374168.2	+	14	1251_1252	c.1097_1098insC	c.(1096-1101)atccccfs	p.IP366fs	RPS6KA1_ENST00000374166.4_Frame_Shift_Ins_p.IP355fs|RPS6KA1_ENST00000531382.1_Frame_Shift_Ins_p.IP375fs|RPS6KA1_ENST00000374162.2_Frame_Shift_Ins_p.IP274fs|RPS6KA1_ENST00000526792.1_Frame_Shift_Ins_p.IP274fs|RPS6KA1_ENST00000530003.1_Frame_Shift_Ins_p.IP350fs	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	366	AGC-kinase C-terminal.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		TCCCCAGGCATCCCCCCCAGCG	0.673																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.1104dupC	1.37:g.26885317_26885317dupC	ENSP00000363283:p.Ile366fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,pfam_Pkinase_C,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Ribosomal_S6_kinase_II,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.S378fs	ENST00000374168.2	37	c.1124_1125	CCDS284.1	1																																																																																			RPS6KA1	-	pfam_Pkinase_C,smart_AGC-kinase_C,pirsf_Ribosomal_S6_kinase_II	ENSG00000117676		0.673	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS6KA1	HGNC	protein_coding	OTTHUMT00000011431.1	26	0.00	0	-	NM_002953		26885310	26885311	+1	no_errors	ENST00000531382	ensembl	human	known	69_37n	frame_shift_ins	12	20.00	3	INS	1.000:0.993	C
RREB1	6239	genome.wustl.edu	37	6	7247180	7247181	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr6:7247180_7247181insC	ENST00000349384.6	+	11	4646_4647	c.4332_4333insC	c.(4333-4335)cccfs	p.P1445fs	RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379938.2_Frame_Shift_Ins_p.P1500fs|RREB1_ENST00000379933.3_Frame_Shift_Ins_p.P1445fs	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1445					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AGGAGGAGAAGCCCCCCGAGAC	0.743																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4338dupC	6.37:g.7247186_7247186dupC	ENSP00000305560:p.Pro1445fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Frame_Shift_Ins	INS	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.E1501fs	ENST00000349384.6	37	c.4497_4498	CCDS34336.1	6																																																																																			RREB1	-	NULL	ENSG00000124782		0.743	RREB1-002	KNOWN	basic|CCDS	protein_coding	RREB1	HGNC	protein_coding	OTTHUMT00000352985.1	12	0.00	0	-			7247180	7247181	+1	no_errors	ENST00000379938	ensembl	human	known	69_37n	frame_shift_ins	13	13.33	2	INS	0.080:0.159	C
RTF1	23168	genome.wustl.edu	37	15	41770786	41770788	+	In_Frame_Del	DEL	TTA	TTA	-			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	TTA	TTA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr15:41770786_41770788delTTA	ENST00000389629.4	+	15	1793_1795	c.1781_1783delTTA	c.(1780-1785)tttact>tct	p.594_595FT>S		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	594					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		ATGGATCCCTTTACTCGGCGGCA	0.453																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1781_1783delTTA	15.37:g.41770786_41770788delTTA	ENSP00000374280:p.Phe594_Thr595delinsSer	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96BX6	In_Frame_Del	DEL	pfam_Plus-3,smart_Plus3-dom_subgr	p.FT594in_frame_delS	ENST00000389629.4	37	c.1781_1783	CCDS32200.2	15																																																																																			RTF1	-	NULL	ENSG00000137815		0.453	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RTF1	HGNC	protein_coding	OTTHUMT00000258111.1	123	0.00	0	TTA	NM_015138		41770786	41770788	+1	no_errors	ENST00000389629	ensembl	human	known	69_37n	in_frame_del	148	61.89	354	DEL	1.000:0.972:1.000	-
RTF1	23168	genome.wustl.edu	37	15	41770809	41770809	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr15:41770809delA	ENST00000389629.4	+	15	1816	c.1804delA	c.(1804-1806)accfs	p.T602fs		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	602					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		GTGCAAGCCTACCATCGTTTC	0.418																																						dbGAP											0													166.0	168.0	167.0					15																	41770809		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1804delA	15.37:g.41770809delA	ENSP00000374280:p.Thr602fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96BX6	Frame_Shift_Del	DEL	pfam_Plus-3,smart_Plus3-dom_subgr	p.T602fs	ENST00000389629.4	37	c.1804	CCDS32200.2	15																																																																																			RTF1	-	NULL	ENSG00000137815		0.418	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RTF1	HGNC	protein_coding	OTTHUMT00000258111.1	123	0.00	0	A	NM_015138		41770809	41770809	+1	no_errors	ENST00000389629	ensembl	human	known	69_37n	frame_shift_del	142	64.16	256	DEL	1.000	-
SPACA1	81833	genome.wustl.edu	37	6	88769255	88769255	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr6:88769255G>T	ENST00000237201.1	+	5	676	c.559G>T	c.(559-561)Gat>Tat	p.D187Y	SPACA1_ENST00000462690.1_3'UTR	NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	187					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		TGACACACTGGATAATAATGA	0.358																																						dbGAP											0													100.0	97.0	98.0					6																	88769255		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.559G>T	6.37:g.88769255G>T	ENSP00000237201:p.Asp187Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.D187Y	ENST00000237201.1	37	c.559	CCDS5014.1	6	.	.	.	.	.	.	.	.	.	.	G	14.84	2.655995	0.47467	.	.	ENSG00000118434	ENST00000237201	T	0.31769	1.48	5.5	5.5	0.81552	.	0.264885	0.32608	N	0.005866	T	0.45054	0.1323	M	0.63428	1.95	0.39373	D	0.96612	D	0.76494	0.999	D	0.65874	0.939	T	0.44467	-0.9326	10	0.87932	D	0	-9.2632	17.1731	0.86834	0.0:0.0:1.0:0.0	.	187	Q9HBV2	SACA1_HUMAN	Y	187	ENSP00000237201:D187Y	ENSP00000237201:D187Y	D	+	1	0	SPACA1	88825974	0.996000	0.38824	0.342000	0.25602	0.270000	0.26580	3.341000	0.52151	2.571000	0.86741	0.650000	0.86243	GAT	SPACA1	-	NULL	ENSG00000118434		0.358	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SPACA1	HGNC	protein_coding	OTTHUMT00000041459.1	105	0.00	0	G			88769255	88769255	+1	no_errors	ENST00000237201	ensembl	human	known	69_37n	missense	60	38.78	38	SNP	0.764	T
SOBP	55084	genome.wustl.edu	37	6	107955025	107955025	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr6:107955025C>T	ENST00000317357.5	+	6	1636	c.977C>T	c.(976-978)cCg>cTg	p.P326L		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		GGCCCTGGCCCGTCGGCGTCC	0.617																																						dbGAP											0													56.0	65.0	62.0					6																	107955025		1988	4138	6126	-	-	-	SO:0001583	missense	0			AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.977C>T	6.37:g.107955025C>T	ENSP00000318900:p.Pro326Leu	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.P326L	ENST00000317357.5	37	c.977	CCDS43488.1	6	.	.	.	.	.	.	.	.	.	.	C	12.15	1.850608	0.32699	.	.	ENSG00000112320	ENST00000317357	T	0.36520	1.25	5.7	4.82	0.62117	.	0.153716	0.44285	D	0.000465	T	0.09730	0.0239	N	0.08118	0	0.80722	D	1	B	0.21452	0.056	B	0.14578	0.011	T	0.06041	-1.0849	10	0.59425	D	0.04	-1.1691	11.9973	0.53209	0.0:0.8592:0.0:0.1408	.	326	A7XYQ1	SOBP_HUMAN	L	326	ENSP00000318900:P326L	ENSP00000318900:P326L	P	+	2	0	SOBP	108061718	1.000000	0.71417	0.912000	0.35992	0.985000	0.73830	3.523000	0.53488	1.377000	0.46286	0.655000	0.94253	CCG	SOBP	-	NULL	ENSG00000112320		0.617	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SOBP	HGNC	protein_coding	OTTHUMT00000041693.2	51	0.00	0	C	NM_018013		107955025	107955025	+1	no_errors	ENST00000317357	ensembl	human	known	69_37n	missense	22	56.86	29	SNP	1.000	T
TMIGD2	126259	genome.wustl.edu	37	19	4292606	4292606	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr19:4292606delC	ENST00000301272.2	-	5	884	c.839delG	c.(838-840)ggafs	p.G280fs	TMIGD2_ENST00000595645.1_Frame_Shift_Del_p.G276fs|TMIGD2_ENST00000600114.1_Frame_Shift_Del_p.G160fs|TMIGD2_ENST00000600349.1_Frame_Shift_Del_p.G108fs	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	280					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACTCCTCTCCCACTTTGGG	0.622																																						dbGAP											0													95.0	107.0	103.0					19																	4292606		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.839delG	19.37:g.4292606delC	ENSP00000301272:p.Gly280fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6UW59	Frame_Shift_Del	DEL	smart_Ig_sub,pfscan_Ig-like	p.G280fs	ENST00000301272.2	37	c.839	CCDS12126.1	19																																																																																			TMIGD2	-	NULL	ENSG00000167664		0.622	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TMIGD2	HGNC	protein_coding	OTTHUMT00000458088.1	31	0.00	0	C	NM_144615		4292606	4292606	-1	no_errors	ENST00000301272	ensembl	human	known	69_37n	frame_shift_del	10	16.67	2	DEL	0.002	-
TTN	7273	genome.wustl.edu	37	2	179499272	179499272	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr2:179499272C>T	ENST00000591111.1	-	180	37537	c.37313G>A	c.(37312-37314)cGa>cAa	p.R12438Q	TTN_ENST00000359218.5_Missense_Mutation_p.R5139Q|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R5014Q|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R14079Q|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R11511Q|TTN_ENST00000342175.6_Missense_Mutation_p.R5206Q			Q8WZ42	TITIN_HUMAN	titin	12438					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTGCCTCTCGGGTGAGGAC	0.398																																						dbGAP											0													88.0	90.0	89.0					2																	179499272		1892	4122	6014	-	-	-	SO:0001583	missense	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.37313G>A	2.37:g.179499272C>T	ENSP00000465570:p.Arg12438Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.R11511Q	ENST00000591111.1	37	c.34532		2	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436487	0.62955	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55210	0.1906	L	0.31371	0.925	0.39323	D	0.965278	P;P;P;P	0.40398	0.716;0.716;0.716;0.716	B;B;B;B	0.28385	0.089;0.089;0.089;0.089	T	0.63139	-0.6704	9	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	5014;5139;5206;12438	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	11511;5014;5206;5139;5014	ENSP00000343764:R11511Q;ENSP00000434586:R5014Q;ENSP00000340554:R5206Q;ENSP00000352154:R5139Q	ENSP00000340554:R5206Q	R	-	2	0	TTN	179207517	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.908000	0.63307	2.941000	0.99782	0.655000	0.94253	CGA	TTN	-	pfam_Ig_I-set,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2	ENSG00000155657		0.398	TTN-019	PUTATIVE	basic	protein_coding	TTN	HGNC	protein_coding	OTTHUMT00000460310.1	29	0.00	0	C	NM_133378		179499272	179499272	-1	no_errors	ENST00000342992	ensembl	human	known	69_37n	missense	18	56.10	23	SNP	1.000	T
WBSCR22	114049	genome.wustl.edu	37	7	73107983	73107983	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chr7:73107983C>T	ENST00000265758.2	+	9	684	c.626C>T	c.(625-627)tCg>tTg	p.S209L	WBSCR22_ENST00000423497.1_Missense_Mutation_p.S209L|WBSCR22_ENST00000423166.2_3'UTR	NM_017528.4	NP_059998.2	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22	209					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|large_intestine(2)|lung(9)|prostate(1)	13		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCTGGGCCTTCGACCTTTATA	0.562																																						dbGAP											0													214.0	196.0	202.0					7																	73107983		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF420248	CCDS5557.1, CCDS56490.1	7q11.23	2012-06-12			ENSG00000071462	ENSG00000071462			16405	protein-coding gene	gene with protein product	"""metastasis-related methyltransferase 1"""	615733				12073013, 11978965, 21148752	Standard	NM_001202560		Approved	MGC19709, MGC2022, MGC5140, PP3381, WBMT, MERM1	uc003tyt.3	O43709	OTTHUMG00000023306	ENST00000265758.2:c.626C>T	7.37:g.73107983C>T	ENSP00000265758:p.Ser209Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K501|C9K060|Q96P12|Q9BQ58|Q9HBP9	Missense_Mutation	SNP	pfam_Unchr_MeTrfase_Williams-Beuren,pfam_Methyltransf_11	p.S209L	ENST00000265758.2	37	c.626	CCDS5557.1	7	.	.	.	.	.	.	.	.	.	.	C	12.52	1.963323	0.34659	.	.	ENSG00000071462	ENST00000265758;ENST00000423497	T;T	0.65732	-0.17;-0.17	4.61	3.68	0.42216	.	0.393294	0.26571	N	0.023637	T	0.52853	0.1760	M	0.65498	2.005	0.80722	D	1	B;P;B	0.42039	0.35;0.769;0.35	B;B;B	0.33254	0.16;0.16;0.16	T	0.54470	-0.8289	10	0.38643	T	0.18	-11.6505	9.4346	0.38630	0.0:0.8861:0.0:0.1139	.	209;209;209	A8K501;C9K060;O43709	.;.;WBS22_HUMAN	L	209	ENSP00000265758:S209L;ENSP00000401191:S209L	ENSP00000265758:S209L	S	+	2	0	WBSCR22	72745919	0.980000	0.34600	0.442000	0.26870	0.848000	0.48234	3.370000	0.52372	1.226000	0.43582	0.411000	0.27672	TCG	WBSCR22	-	pfam_Unchr_MeTrfase_Williams-Beuren	ENSG00000071462		0.562	WBSCR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WBSCR22	HGNC	protein_coding	OTTHUMT00000252303.1	622	0.16	1	C			73107983	73107983	+1	no_errors	ENST00000265758	ensembl	human	known	69_37n	missense	242	34.77	129	SNP	0.768	T
ZCCHC5	203430	genome.wustl.edu	37	X	77913883	77913883	+	Missense_Mutation	SNP	A	A	C			TCGA-BH-A0HL-01A-11W-A050-09	TCGA-BH-A0HL-10A-11W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1fd1db26-79e0-4018-8548-8fd20a96c479	f3a79920-cdfb-4dc7-b10b-9c143fd3d274	g.chrX:77913883A>C	ENST00000321110.1	-	2	330	c.35T>G	c.(34-36)cTg>cGg	p.L12R		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	12							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						CTCCAATTTCAGAACAATATA	0.468																																						dbGAP											0													46.0	39.0	41.0					X																	77913883		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"""Zinc fingers, CCHC domain containing"""	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.35T>G	X.37:g.77913883A>C	ENSP00000316794:p.Leu12Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	pfam_Znf_CCHC,superfamily_Znf_CCHC,smart_Znf_CCHC,pfscan_Znf_CCHC	p.L12R	ENST00000321110.1	37	c.35	CCDS14440.1	X	.	.	.	.	.	.	.	.	.	.	A	13.48	2.250482	0.39797	.	.	ENSG00000179300	ENST00000321110	T	0.40756	1.02	3.24	3.24	0.37175	.	.	.	.	.	T	0.42131	0.1189	N	0.24115	0.695	0.29292	N	0.869252	D	0.61080	0.989	P	0.59221	0.854	T	0.27938	-1.0059	9	0.87932	D	0	.	7.2241	0.26005	1.0:0.0:0.0:0.0	.	12	Q8N8U3	ZCHC5_HUMAN	R	12	ENSP00000316794:L12R	ENSP00000316794:L12R	L	-	2	0	ZCCHC5	77800539	1.000000	0.71417	0.999000	0.59377	0.585000	0.36419	2.025000	0.41059	1.513000	0.48852	0.417000	0.27973	CTG	ZCCHC5	-	NULL	ENSG00000179300		0.468	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZCCHC5	HGNC	protein_coding	OTTHUMT00000057319.1	66	0.00	0	A	NM_152694		77913883	77913883	-1	no_errors	ENST00000321110	ensembl	human	known	69_37n	missense	41	48.10	38	SNP	0.999	C
