#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_ORegAnno_bin	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
ADCK2	90956	genome.wustl.edu	37	7	140373767	140373767	+	Nonsense_Mutation	SNP	C	C	T			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr7:140373767C>T	ENST00000072869.4	+	1	815	c.637C>T	c.(637-639)Cag>Tag	p.Q213*	ADCK2_ENST00000476491.1_Nonsense_Mutation_p.Q213*	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	213	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					CTGCGTGGCCCAGGTGTACAA	0.602																																						dbGAP											0													67.0	72.0	70.0					7																	140373767		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.637C>T	7.37:g.140373767C>T	ENSP00000072869:p.Gln213*		Q96CN6|Q9Y6T5	Nonsense_Mutation	SNP	pfam_UbiB_dom,superfamily_Kinase-like_dom	p.Q213*	ENST00000072869.4	37	c.637	CCDS5861.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.796397|6.796397	0.97845|0.97845	.|.	.|.	ENSG00000133597|ENSG00000133597	ENST00000483369|ENST00000072869;ENST00000476491	.|.	.|.	.|.	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.73628|.	0.3611|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.76561|.	-0.2914|.	3|.	.|0.44086	.|T	.|0.13	-1.4195|-1.4195	17.5034|17.5034	0.87738|0.87738	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	50|213	.|.	.|ENSP00000072869:Q213X	P|Q	+|+	2|1	0|0	ADCK2|ADCK2	140020236|140020236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	7.433000|7.433000	0.80362|0.80362	2.136000|2.136000	0.66102|0.66102	0.561000|0.561000	0.74099|0.74099	CCA|CAG	ADCK2	-	NULL	ENSG00000133597		0.602	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADCK2	HGNC	protein_coding	OTTHUMT00000348734.1	56	0.00	0	C	NM_052853		140373767	140373767	+1	no_errors	ENST00000072869	ensembl	human	known	69_37n	nonsense	38	13.64	6	SNP	1.000	T
ANKRD22	118932	genome.wustl.edu	37	10	90583107	90583107	+	Missense_Mutation	SNP	C	C	T			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr10:90583107C>T	ENST00000371930.4	-	5	638	c.428G>A	c.(427-429)tGt>tAt	p.C143Y	ANKRD22_ENST00000476963.1_5'UTR	NM_144590.2	NP_653191.2	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	143										NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)		TTTCATTTCACAGGCATAATG	0.488																																						dbGAP											0													115.0	118.0	117.0					10																	90583107		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC021671	CCDS7390.1	10q23.31	2013-09-20			ENSG00000152766	ENSG00000152766		"""Ankyrin repeat domain containing"""	28321	protein-coding gene	gene with protein product						12477932	Standard	NM_144590		Approved	MGC22805	uc001kfj.4	Q5VYY1	OTTHUMG00000018699	ENST00000371930.4:c.428G>A	10.37:g.90583107C>T	ENSP00000360998:p.Cys143Tyr		B2R9Y7|Q8WU06	Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.C143Y	ENST00000371930.4	37	c.428	CCDS7390.1	10	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072021	0.76415	.	.	ENSG00000152766	ENST00000371930	T	0.65364	-0.15	5.74	5.74	0.90152	Ankyrin repeat-containing domain (4);	0.095475	0.85682	D	0.000000	T	0.80686	0.4670	M	0.77313	2.365	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.82265	-0.0543	10	0.87932	D	0	-13.974	18.4738	0.90783	0.0:1.0:0.0:0.0	.	143	Q5VYY1	ANR22_HUMAN	Y	143	ENSP00000360998:C143Y	ENSP00000360998:C143Y	C	-	2	0	ANKRD22	90573087	1.000000	0.71417	0.960000	0.40013	0.656000	0.38851	5.277000	0.65586	2.702000	0.92279	0.655000	0.94253	TGT	ANKRD22	-	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	ENSG00000152766		0.488	ANKRD22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD22	HGNC	protein_coding	OTTHUMT00000049262.1	47	0.00	0	C	NM_144590		90583107	90583107	-1	no_errors	ENST00000371930	ensembl	human	known	69_37n	missense	37	11.90	5	SNP	0.995	T
ARHGEF37	389337	genome.wustl.edu	37	5	149008411	149008411	+	Missense_Mutation	SNP	A	A	G			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr5:149008411A>G	ENST00000333677.6	+	12	1863	c.1700A>G	c.(1699-1701)tAc>tGc	p.Y567C		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	567	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						CTACAGCTGTACCATGTGGTC	0.602																																						dbGAP											0													38.0	42.0	41.0					5																	149008411		2024	4174	6198	-	-	-	SO:0001583	missense	0			BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1700A>G	5.37:g.149008411A>G	ENSP00000328083:p.Tyr567Cys		Q6ZW51	Missense_Mutation	SNP	pfam_DH-domain,pfam_BAR_dom,pfam_SH3_2,pfam_SH3_domain,superfamily_DH-domain,superfamily_SH3_domain,smart_DH-domain,smart_BAR_dom,smart_SH3_domain,pfscan_BAR_dom,pfscan_SH3_domain,pfscan_DH-domain	p.Y567C	ENST00000333677.6	37	c.1700	CCDS43385.1	5	.	.	.	.	.	.	.	.	.	.	A	17.81	3.480007	0.63849	.	.	ENSG00000183111	ENST00000333677	T	0.61274	0.12	5.47	5.47	0.80525	Src homology-3 domain (2);	0.000000	0.85682	D	0.000000	T	0.75561	0.3866	M	0.80746	2.51	0.46279	D	0.99896	D	0.89917	1.0	D	0.80764	0.994	T	0.79200	-0.1901	10	0.87932	D	0	-4.4355	11.934	0.52864	1.0:0.0:0.0:0.0	.	567	A1IGU5	ARH37_HUMAN	C	567	ENSP00000328083:Y567C	ENSP00000328083:Y567C	Y	+	2	0	ARHGEF37	148988604	0.990000	0.36364	0.357000	0.25798	0.788000	0.44548	4.841000	0.62824	2.082000	0.62665	0.402000	0.26972	TAC	ARHGEF37	-	superfamily_SH3_domain,smart_SH3_domain	ENSG00000183111		0.602	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF37	HGNC	protein_coding	OTTHUMT00000373763.1	57	0.00	0	A	NM_001001669		149008411	149008411	+1	no_errors	ENST00000333677	ensembl	human	known	69_37n	missense	36	18.18	8	SNP	0.554	G
CAPN13	92291	genome.wustl.edu	37	2	30968593	30968593	+	Missense_Mutation	SNP	G	G	A			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr2:30968593G>A	ENST00000295055.8	-	12	1420	c.1244C>T	c.(1243-1245)tCa>tTa	p.S415L	CAPN13_ENST00000534090.2_Intron	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	415					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					CCATACCTGTGAGCCAGCCTG	0.547																																						dbGAP											0													63.0	68.0	67.0					2																	30968593		2160	4258	6418	-	-	-	SO:0001583	missense	0				CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1244C>T	2.37:g.30968593G>A	ENSP00000295055:p.Ser415Leu		Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	pfam_Peptidase_C2_calpain_cat,pfam_Calpain_domain_III,superfamily_Calpain_domain_III,smart_Peptidase_C2_calpain_cat,pfscan_Peptidase_C2_calpain_cat,prints_Calpain_cysteine_protease	p.S415L	ENST00000295055.8	37	c.1244	CCDS46252.1	2	.	.	.	.	.	.	.	.	.	.	G	4.909	0.168863	0.09339	.	.	ENSG00000162949	ENST00000295055	D	0.88741	-2.42	4.11	1.02	0.19986	.	.	.	.	.	T	0.80560	0.4646	N	0.19112	0.55	0.09310	N	1	.	.	.	.	.	.	T	0.68697	-0.5340	7	0.40728	T	0.16	.	7.0195	0.24907	0.0:0.1609:0.4707:0.3684	.	.	.	.	L	415	ENSP00000295055:S415L	ENSP00000295055:S415L	S	-	2	0	CAPN13	30822097	0.054000	0.20591	0.000000	0.03702	0.180000	0.23129	0.888000	0.28268	0.071000	0.16664	0.561000	0.74099	TCA	CAPN13	-	pfam_Calpain_domain_III,superfamily_Calpain_domain_III	ENSG00000162949		0.547	CAPN13-001	KNOWN	basic|CCDS	protein_coding	CAPN13	HGNC	protein_coding	OTTHUMT00000325101.2	54	0.00	0	G	NM_144575		30968593	30968593	-1	no_errors	ENST00000295055	ensembl	human	known	69_37n	missense	54	11.48	7	SNP	0.000	A
CDH1	999	genome.wustl.edu	37	16	68849436	68849436	+	Nonsense_Mutation	SNP	A	A	T			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr16:68849436A>T	ENST00000261769.5	+	10	1530	c.1339A>T	c.(1339-1341)Aag>Tag	p.K447*	CDH1_ENST00000422392.2_Nonsense_Mutation_p.K386*|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	447	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.G441_E463del(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TTTTGAGGCCAAGCAGCAGTA	0.423			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	2	Unknown(1)|Deletion - In frame(1)	stomach(1)|breast(1)											120.0	101.0	108.0					16																	68849436		2198	4300	6498	-	-	-	SO:0001587	stop_gained	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1339A>T	16.37:g.68849436A>T	ENSP00000261769:p.Lys447*		A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Nonsense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.K447*	ENST00000261769.5	37	c.1339	CCDS10869.1	16	.	.	.	.	.	.	.	.	.	.	A	37	6.504620	0.97620	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	.	.	.	5.7	5.7	0.88788	.	0.000000	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4485	0.50138	0.8494:0.1506:0.0:0.0	.	.	.	.	X	447;465;447;386	.	ENSP00000261769:K447X	K	+	1	0	CDH1	67406937	0.004000	0.15560	1.000000	0.80357	0.989000	0.77384	2.022000	0.41030	2.176000	0.68965	0.454000	0.30748	AAG	CDH1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	ENSG00000039068		0.423	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	102	0.00	0	A	NM_004360		68849436	68849436	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	nonsense	62	20.51	16	SNP	0.992	T
CDH24	64403	genome.wustl.edu	37	14	23516833	23516833	+	3'UTR	SNP	G	G	T			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr14:23516833G>T	ENST00000397359.3	-	0	3075				CDH24_ENST00000485922.1_5'UTR|CDH24_ENST00000487137.2_3'UTR	NM_022478.3	NP_071923.2	Q86UP0	CAD24_HUMAN	cadherin 24, type 2						adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		GTATGGGCAAGGAAGACGCAG	0.532																																						dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000397359.3:c.*356C>A	14.37:g.23516833G>T			D3DS44|Q86UP1|Q9NT84	RNA	SNP	-	NULL	ENST00000397359.3	37	NULL	CCDS9585.1	14																																																																																			CDH24	-	-	ENSG00000139880		0.532	CDH24-201	KNOWN	basic|CCDS	protein_coding	CDH24	HGNC	protein_coding		25	0.00	0	G	NM_022478		23516833	23516833	-1	no_errors	ENST00000485922	ensembl	human	known	69_37n	rna	22	15.38	4	SNP	0.250	T
DSE	29940	genome.wustl.edu	37	6	116756765	116756765	+	Silent	SNP	G	G	A			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr6:116756765G>A	ENST00000331677.3	+	7	1578	c.1134G>A	c.(1132-1134)ttG>ttA	p.L378L	DSE_ENST00000359564.2_Silent_p.L378L|DSE_ENST00000452085.3_Silent_p.L378L|DSE_ENST00000537543.1_Silent_p.L397L			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	378					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		ATGGCAGCTTGAAATCGGTTC	0.403																																						dbGAP											0													81.0	82.0	82.0					6																	116756765		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.1134G>A	6.37:g.116756765G>A			Q5R3K6	Silent	SNP	superfamily_Chondroitin_lyas	p.L397	ENST00000331677.3	37	c.1191	CCDS5107.1	6																																																																																			DSE	-	NULL	ENSG00000111817		0.403	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	DSE	HGNC	protein_coding	OTTHUMT00000041940.2	37	0.00	0	G	NM_013352		116756765	116756765	+1	no_errors	ENST00000537543	ensembl	human	known	69_37n	silent	26	13.33	4	SNP	1.000	A
TNNI3	7137	genome.wustl.edu	37	19	55669006	55669006	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr19:55669006G>A	ENST00000344887.5	-	0	94				TNNI3_ENST00000588882.1_5'Flank|TNNI3_ENST00000590463.1_5'UTR|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.4_ENST00000587871.1_3'UTR|CTD-2587H24.5_ENST00000591665.1_RNA	NM_000363.4	NP_000354.4	P19429	TNNI3_HUMAN	troponin I type 3 (cardiac)						cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|heart contraction (GO:0060047)|heart development (GO:0007507)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|regulation of smooth muscle contraction (GO:0006940)|regulation of systemic arterial blood pressure by ischemic conditions (GO:0001980)|vasculogenesis (GO:0001570)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|troponin complex (GO:0005861)	actin binding (GO:0003779)|calcium channel inhibitor activity (GO:0019855)|calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|troponin C binding (GO:0030172)|troponin T binding (GO:0031014)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		GGACAGGGGCGTTTGGAGGGT	0.667																																						dbGAP											0													44.0	53.0	50.0					19																	55669006		1931	4132	6063	-	-	-			0			M64247	CCDS42628.1	19q13.4	2014-09-17	2005-09-12			ENSG00000129991			11947	protein-coding gene	gene with protein product		191044	"""troponin I, cardiac"", ""cardiomyopathy, dilated 2A (autosomal recessive)"""	CMD2A		9605869, 9241277, 10806205	Standard	NM_000363		Approved	TNNC1, CMH7	uc002qjg.4	P19429		ENST00000344887.5:c.-49C>T	19.37:g.55669006G>A				RNA	SNP	-	NULL	ENST00000344887.5	37	NULL	CCDS42628.1	19																																																																																			CTD-2587H24.4	-	-	ENSG00000267110		0.667	TNNI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000267110	Clone_based_vega_gene	protein_coding	OTTHUMT00000452098.1	54	0.00	0	G			55669006	55669006	-1	no_errors	ENST00000587871	ensembl	human	known	69_37n	rna	58	22.67	17	SNP	0.000	A
FAT4	79633	genome.wustl.edu	37	4	126372852	126372852	+	Missense_Mutation	SNP	A	A	G			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr4:126372852A>G	ENST00000394329.3	+	9	10694	c.10681A>G	c.(10681-10683)Agc>Ggc	p.S3561G	FAT4_ENST00000335110.5_Missense_Mutation_p.S1859G	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3561	Cadherin 34. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTTCAGTCTGAGCACTGCTGG	0.478																																						dbGAP											0													116.0	118.0	117.0					4																	126372852		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.10681A>G	4.37:g.126372852A>G	ENSP00000377862:p.Ser3561Gly		A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_dom,pfam_EGF-like_Ca-bd,superfamily_Cadherin-like,superfamily_ConA-like_lec_gl,smart_Cadherin,smart_EGF-like,smart_EGF-like_Ca-bd,smart_Laminin_G,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin,prints_Cadherin	p.S3561G	ENST00000394329.3	37	c.10681	CCDS3732.3	4	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720830	0.30503	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.37915	1.17;1.17	5.91	5.91	0.95273	Cadherin (4);Cadherin-like (1);	0.469281	0.14862	U	0.294014	T	0.41096	0.1144	L	0.49455	1.56	0.40779	D	0.983153	B;B;B	0.29037	0.231;0.112;0.144	B;B;B	0.34452	0.183;0.11;0.066	T	0.31530	-0.9940	10	0.59425	D	0.04	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	1859;3561;3561	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	G	3561;1859	ENSP00000377862:S3561G;ENSP00000335169:S1859G	ENSP00000335169:S1859G	S	+	1	0	FAT4	126592302	0.997000	0.39634	0.128000	0.21923	0.062000	0.15995	9.149000	0.94659	2.254000	0.74563	0.533000	0.62120	AGC	FAT4	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000196159		0.478	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAT4	HGNC	protein_coding	OTTHUMT00000256765.2	90	0.00	0	A	NM_024582		126372852	126372852	+1	no_errors	ENST00000394329	ensembl	human	known	69_37n	missense	64	15.79	12	SNP	0.728	G
HOXB5	3215	genome.wustl.edu	37	17	46669748	46669748	+	Missense_Mutation	SNP	C	C	A			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr17:46669748C>A	ENST00000239151.5	-	2	911	c.633G>T	c.(631-633)aaG>aaT	p.K211N	HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000498678.1_5'Flank|HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB3_ENST00000460160.1_5'Flank|HOXB-AS3_ENST00000465846.2_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	211					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						AGTGGAACTCCTTTTCCAGCT	0.617																																						dbGAP											0													91.0	91.0	91.0					17																	46669748		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"""Homeoboxes / ANTP class : HOXL subclass"""	5116	protein-coding gene	gene with protein product		142960	"""homeo box B5"""	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.633G>T	17.37:g.46669748C>A	ENSP00000239151:p.Lys211Asn		B2RC69|P09069|Q17RP4	Missense_Mutation	SNP	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain,prints_Homeobox_metazoa,prints_Homeobox_antennapedia	p.K211N	ENST00000239151.5	37	c.633	CCDS11530.1	17	.	.	.	.	.	.	.	.	.	.	C	15.97	2.989947	0.54041	.	.	ENSG00000120075	ENST00000239151	D	0.96491	-4.03	5.27	2.15	0.27550	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96178	0.8754	L	0.42632	1.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94108	0.7368	9	.	.	.	.	9.6807	0.40067	0.0:0.7156:0.0:0.2844	.	211	P09067	HXB5_HUMAN	N	211	ENSP00000239151:K211N	.	K	-	3	2	HOXB5	44024747	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.906000	0.28517	0.727000	0.32360	-0.379000	0.06801	AAG	HOXB5	-	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain	ENSG00000120075		0.617	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HOXB5	HGNC	protein_coding	OTTHUMT00000358148.2	152	0.00	0	C			46669748	46669748	-1	no_errors	ENST00000239151	ensembl	human	known	69_37n	missense	97	13.39	15	SNP	1.000	A
MUC20	200958	genome.wustl.edu	37	3	195453014	195453014	+	Missense_Mutation	SNP	G	G	A	rs3828410	byFrequency	TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr3:195453014G>A	ENST00000447234.2	+	2	1666	c.1540G>A	c.(1540-1542)Ggg>Agg	p.G514R	MUC20_ENST00000445522.2_Missense_Mutation_p.G479R|MUC20_ENST00000436408.1_Missense_Mutation_p.G514R|MUC20_ENST00000320736.6_Missense_Mutation_p.G343R	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	514	Involved in oligomerization.		G -> R (in dbSNP:rs3828410).|Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GACAGCACCCGGGGCCACGAC	0.582																																						dbGAP											0													56.0	52.0	53.0					3																	195453014		2138	4219	6357	-	-	-	SO:0001583	missense	0			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1540G>A	3.37:g.195453014G>A	ENSP00000414350:p.Gly514Arg		Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	NULL	p.G514R	ENST00000447234.2	37	c.1540		3	568	0.2600732600732601	178	0.3617886178861789	85	0.23480662983425415	231	0.40384615384615385	74	0.09762532981530343	A	2.041	-0.420045	0.04734	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.15139	2.88;2.91;3.04;2.45	3.41	-3.4	0.04853	.	1.360490	0.04987	N	0.466686	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45498	-0.9257	9	0.09084	T	0.74	0.7227	6.8673	0.24100	0.2228:0.346:0.4312:0.0	rs3828410;rs3828410	343	E9PH32	.	R	514;343;514;479	ENSP00000414350:G514R;ENSP00000325431:G343R;ENSP00000396774:G514R;ENSP00000405629:G479R	ENSP00000325431:G343R	G	+	1	0	MUC20	196938685	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.677000	0.05215	-1.154000	0.02825	-0.439000	0.05793	GGG	MUC20	-	NULL	ENSG00000176945		0.582	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	MUC20	HGNC	protein_coding	OTTHUMT00000341835.1	37	0.00	0	G	NM_152673		195453014	195453014	+1	no_errors	ENST00000447234	ensembl	human	known	69_37n	missense	19	25.93	7	SNP	0.000	A
OGFR	11054	genome.wustl.edu	37	20	61444665	61444665	+	Silent	SNP	G	G	A	rs6122314	byFrequency	TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr20:61444665G>A	ENST00000290291.6	+	7	1723	c.1698G>A	c.(1696-1698)ccG>ccA	p.P566P	OGFR_ENST00000370461.1_Silent_p.P514P	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	566	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					GCCCCCGCCCGGCAGGACCTG	0.736																																						dbGAP											0													2.0	5.0	4.0					20																	61444665		1163	2906	4069	-	-	-	SO:0001819	synonymous_variant	0			AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1698G>A	20.37:g.61444665G>A			O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	pfam_OGF_rcpt,pfam_OGF_rcpt_rpt	p.P566	ENST00000290291.6	37	c.1698	CCDS13504.1	20																																																																																			OGFR	-	pfam_OGF_rcpt_rpt	ENSG00000060491		0.736	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	OGFR	HGNC	protein_coding	OTTHUMT00000080067.1	19	0.00	0	G			61444665	61444665	+1	no_errors	ENST00000290291	ensembl	human	known	69_37n	silent	17	34.62	9	SNP	0.000	A
PDLIM2	64236	genome.wustl.edu	37	8	22451688	22451688	+	3'UTR	SNP	G	G	C	rs3064	byFrequency	TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr8:22451688G>C	ENST00000397760.4	+	0	1724				PDLIM2_ENST00000397761.2_3'UTR|PDLIM2_ENST00000308354.7_3'UTR|PDLIM2_ENST00000409417.1_3'UTR|PDLIM2_ENST00000409141.1_3'UTR|PDLIM2_ENST00000265810.4_Intron|PDLIM2_ENST00000339162.7_3'UTR|AC037459.4_ENST00000430850.2_Intron			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		CTTTGTGTGCGAGGGTCTAAG	0.532													C|||	1689	0.33726	0.3033	0.4049	5008	,	,		18667	0.2569		0.341	False		,,,				2504	0.4141					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.*265G>C	8.37:g.22451688G>C			D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	RNA	SNP	-	NULL	ENST00000397760.4	37	NULL		8																																																																																			PDLIM2	-	-	ENSG00000120913		0.532	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	PDLIM2	HGNC	protein_coding	OTTHUMT00000334167.1	9	0.00	0	G			22451688	22451688	+1	no_errors	ENST00000443561	ensembl	human	known	69_37n	rna	1	80.00	4	SNP	0.000	C
PIK3CA	5290	genome.wustl.edu	37	3	178921553	178921553	+	Missense_Mutation	SNP	T	T	A	rs121913284		TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr3:178921553T>A	ENST00000263967.3	+	5	1192	c.1035T>A	c.(1033-1035)aaT>aaA	p.N345K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	345	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.N345K(44)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CCTACGTGAATGTAAATATTC	0.308		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	44	Substitution - Missense(44)	breast(27)|endometrium(6)|large_intestine(6)|central_nervous_system(5)											67.0	66.0	66.0					3																	178921553		1807	4074	5881	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1035T>A	3.37:g.178921553T>A	ENSP00000263967:p.Asn345Lys		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.N345K	ENST00000263967.3	37	c.1035	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	T	16.01	3.002090	0.54254	.	.	ENSG00000121879	ENST00000263967	T	0.70164	-0.46	5.41	3.03	0.35002	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	T	0.77745	0.4176	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75465	-0.3308	10	0.49607	T	0.09	-21.0442	9.7159	0.40274	0.0:0.1415:0.0:0.8585	.	345	P42336	PK3CA_HUMAN	K	345	ENSP00000263967:N345K	ENSP00000263967:N345K	N	+	3	2	PIK3CA	180404247	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.030000	0.41108	0.441000	0.26529	0.402000	0.26972	AAT	PIK3CA	-	superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_C2_dom	ENSG00000121879		0.308	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	59	0.00	0	T			178921553	178921553	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	39	17.02	8	SNP	1.000	A
RB1CC1	9821	genome.wustl.edu	37	8	53568768	53568768	+	Silent	SNP	A	A	G			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr8:53568768A>G	ENST00000025008.5	-	15	4144	c.3621T>C	c.(3619-3621)gcT>gcC	p.A1207A	RB1CC1_ENST00000539297.1_Silent_p.A1207A|RB1CC1_ENST00000435644.2_Silent_p.A1207A|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1207					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TCTGGATAATAGCTTCGTATT	0.348																																					GBM(180;1701 2102 13475 42023 52570)	dbGAP											0													185.0	186.0	185.0					8																	53568768		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3621T>C	8.37:g.53568768A>G			Q86YR4|Q8WVU9|Q92601	Silent	SNP	pfam_Autophagy-rel_p11	p.A1207	ENST00000025008.5	37	c.3621	CCDS34892.1	8																																																																																			RB1CC1	-	NULL	ENSG00000023287		0.348	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RB1CC1	HGNC	protein_coding	OTTHUMT00000378011.1	106	0.00	0	A	NM_014781		53568768	53568768	-1	no_errors	ENST00000025008	ensembl	human	known	69_37n	silent	66	10.81	8	SNP	0.994	G
RPL23A	6147	genome.wustl.edu	37	17	27047044	27047044	+	Silent	SNP	G	G	A	rs539168874		TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr17:27047044G>A	ENST00000422514.2	+	1	634	c.21G>A	c.(19-21)aaG>aaA	p.K7K	RPL23A_ENST00000496182.1_5'Flank|SNORD4A_ENST00000459174.1_RNA|RAB34_ENST00000450529.1_5'Flank|RAB34_ENST00000395242.2_5'Flank|RAB34_ENST00000453384.3_5'Flank|RAB34_ENST00000415040.2_5'Flank|RAB34_ENST00000436730.3_5'Flank|RPL23A_ENST00000472628.1_5'Flank|SNORD42B_ENST00000458893.1_RNA|RAB34_ENST00000395245.3_5'Flank|RAB34_ENST00000301043.6_5'Flank|RAB34_ENST00000447716.1_5'Flank|AC010761.8_ENST00000582718.1_RNA|RPL23A_ENST00000394938.4_5'Flank|RAB34_ENST00000395243.3_5'Flank	NM_000984.5	NP_000975.2	P62750	RL23A_HUMAN	ribosomal protein L23a	7					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(3)|ovary(1)	5	Lung NSC(42;0.00431)					AAGCGAAGAAGGAAGGTGTGT	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17012	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													155.0	113.0	127.0					17																	27047044		2106	4068	6174	-	-	-	SO:0001819	synonymous_variant	0			U43701	CCDS11241.1	17q11.2	2011-04-06			ENSG00000198242	ENSG00000198242		"""L ribosomal proteins"""	10317	protein-coding gene	gene with protein product		602326				9417910	Standard	NM_000984		Approved	L23A	uc002hci.3	P62750	OTTHUMG00000132684	ENST00000422514.2:c.21G>A	17.37:g.27047044G>A			B2R5B2|P29316|P39024|Q92774	Silent	SNP	pfam_Ribosomal_L23/L25_N,pfam_Ribosomal_L25/23,superfamily_Ribosomal_L23/L15e_core_dom,tigrfam_Ribosomal_L23	p.K7	ENST00000422514.2	37	c.21	CCDS11241.1	17																																																																																			RPL23A	-	NULL	ENSG00000198242		0.572	RPL23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPL23A	HGNC	protein_coding	OTTHUMT00000255975.1	47	0.00	0	G	NM_000984		27047044	27047044	+1	no_errors	ENST00000422514	ensembl	human	known	69_37n	silent	39	22.00	11	SNP	1.000	A
SACS	26278	genome.wustl.edu	37	13	23914806	23914806	+	Missense_Mutation	SNP	C	C	T	rs201262590		TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr13:23914806C>T	ENST00000382292.3	-	9	3482	c.3209G>A	c.(3208-3210)gGa>gAa	p.G1070E	SACS_ENST00000402364.1_Missense_Mutation_p.G320E|SACS_ENST00000382298.3_Missense_Mutation_p.G1070E			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1070					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAAATAGGTTCCTTCTTCATT	0.373																																						dbGAP											0													121.0	125.0	124.0					13																	23914806		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.3209G>A	13.37:g.23914806C>T	ENSP00000371729:p.Gly1070Glu		O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	pfam_HEPN,pfam_Ubiquitin,superfamily_ATPase-like_ATP-bd,superfamily_DnaJ_N,smart_HEPN,pfscan_HEPN,pfscan_DnaJ_N,pfscan_Ubiquitin_supergroup	p.G1070E	ENST00000382292.3	37	c.3209	CCDS9300.2	13	.	.	.	.	.	.	.	.	.	.	C	0.196	-1.048815	0.01981	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86694	-2.01;-2.16;-2.01	6.05	2.28	0.28536	.	0.257739	0.45361	N	0.000378	T	0.61211	0.2329	N	0.01576	-0.805	0.25541	N	0.98718	B	0.02656	0.0	B	0.01281	0.0	T	0.53795	-0.8388	10	0.02654	T	1	.	8.4445	0.32834	0.0:0.0785:0.1253:0.7962	.	1070	Q9NZJ4	SACS_HUMAN	E	1070;320;1070	ENSP00000371729:G1070E;ENSP00000385844:G320E;ENSP00000371735:G1070E	ENSP00000371729:G1070E	G	-	2	0	SACS	22812806	1.000000	0.71417	0.898000	0.35279	0.867000	0.49689	3.899000	0.56288	0.158000	0.19367	-0.142000	0.14014	GGA	SACS	-	NULL	ENSG00000151835		0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SACS	HGNC	protein_coding	OTTHUMT00000044148.3	72	0.00	0	C	NM_014363		23914806	23914806	-1	no_errors	ENST00000382292	ensembl	human	known	69_37n	missense	33	21.43	9	SNP	0.977	T
SRC	6714	genome.wustl.edu	37	20	36033505	36033505	+	3'UTR	SNP	C	C	T			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr20:36033505C>T	ENST00000373578.2	+	0	3683				SRC_ENST00000360723.4_3'UTR|SRC_ENST00000358208.4_3'UTR|SRC_ENST00000445403.1_3'UTR|SRC_ENST00000373558.2_3'UTR|SRC_ENST00000373567.2_3'UTR|SRC_ENST00000477066.1_3'UTR	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase						axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	CTTTTCCTTTCATACGTCTTT	0.527																																						dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"""SH2 domain containing"""	11283	protein-coding gene	gene with protein product		190090	"""v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"""	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.*1723C>T	20.37:g.36033505C>T			E1P5V4|Q76P87|Q86VB9|Q9H5A8	RNA	SNP	-	NULL	ENST00000373578.2	37	NULL	CCDS13294.1	20																																																																																			SRC	-	-	ENSG00000197122		0.527	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	SRC	HGNC	protein_coding	OTTHUMT00000268142.1	53	0.00	0	C	NM_005417		36033505	36033505	+1	no_errors	ENST00000477066	ensembl	human	known	69_37n	rna	53	10.17	6	SNP	0.001	T
WSCD2	9671	genome.wustl.edu	37	12	108604028	108604028	+	Missense_Mutation	SNP	G	G	A			TCGA-MS-A51U-01A-31D-A25Q-09	TCGA-MS-A51U-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	875e4406-438d-4fbd-b9c1-38fb81d05ef9	f67e6bbe-66ee-43e3-ad4e-86416ce2cf15	g.chr12:108604028G>A	ENST00000332082.4	+	5	1446	c.628G>A	c.(628-630)Gcc>Acc	p.A210T	WSCD2_ENST00000547525.1_Missense_Mutation_p.A210T|WSCD2_ENST00000549903.1_Missense_Mutation_p.A210T|WSCD2_ENST00000261400.3_Missense_Mutation_p.A210T			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	210	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						GTGCGGCGGCGCCAACCGCCT	0.682																																						dbGAP											0													10.0	16.0	14.0					12																	108604028		2165	4253	6418	-	-	-	SO:0001583	missense	0				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.628G>A	12.37:g.108604028G>A	ENSP00000331933:p.Ala210Thr		B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	pfam_WSC_carb-bd,smart_WSC_carb-bd_subgr,pfscan_WSC_carb-bd	p.A210T	ENST00000332082.4	37	c.628	CCDS41828.1	12	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242963	0.58995	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000551638;ENST00000332082;ENST00000549903	T;T;T;T;T	0.30182	1.54;1.54;1.55;1.54;1.54	5.12	4.22	0.49857	Carbohydrate-binding WSC (1);Carbohydrate-binding WSC, subgroup (1);	0.366225	0.30620	N	0.009233	T	0.21962	0.0529	L	0.35854	1.095	0.30673	N	0.753139	B	0.28783	0.222	B	0.21151	0.033	T	0.12372	-1.0550	10	0.22109	T	0.4	-16.465	12.0	0.53224	0.0849:0.0:0.9151:0.0	.	210	Q2TBF2	WSCD2_HUMAN	T	210;210;57;210;210	ENSP00000448047:A210T;ENSP00000261400:A210T;ENSP00000446744:A57T;ENSP00000331933:A210T;ENSP00000447272:A210T	ENSP00000261400:A210T	A	+	1	0	WSCD2	107128158	0.982000	0.34865	0.938000	0.37757	0.987000	0.75469	2.174000	0.42482	1.148000	0.42385	0.555000	0.69702	GCC	WSCD2	-	smart_WSC_carb-bd_subgr,pfscan_WSC_carb-bd	ENSG00000075035		0.682	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	WSCD2	HGNC	protein_coding	OTTHUMT00000405554.1	29	0.00	0	G	NM_014653		108604028	108604028	+1	no_errors	ENST00000261400	ensembl	human	known	69_37n	missense	22	21.43	6	SNP	0.983	A
