#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
ASF1A	25842	genome.wustl.edu	37	6	119228580	119228580	+	Frame_Shift_Del	DEL	T	T	-			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr6:119228580delT	ENST00000229595.5	+	4	610	c.416delT	c.(415-417)attfs	p.I139fs	MCM9_ENST00000316316.6_Intron	NM_014034.2	NP_054753.1	Q9Y294	ASF1A_HUMAN	anti-silencing function 1A histone chaperone	139	Interaction with histone H3, CHAF1B, and HIRA.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|muscle cell differentiation (GO:0042692)|negative regulation of chromatin silencing (GO:0031936)|nucleosome assembly (GO:0006334)|osteoblast differentiation (GO:0001649)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)			endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0633)|OV - Ovarian serous cystadenocarcinoma(136;0.188)		CAAAGGAATATTTTGGCATCT	0.343																																						dbGAP											0													57.0	51.0	53.0					6																	119228580		1843	4081	5924	-	-	-	SO:0001589	frameshift_variant	0			AF279306	CCDS47469.1	6q22.31	2013-05-01	2013-05-01		ENSG00000111875	ENSG00000111875			20995	protein-coding gene	gene with protein product		609189	"""ASF1 anti-silencing function 1 homolog A (S. cerevisiae)"""			10810093, 11042152	Standard	NM_014034		Approved	DKFZP547E2110, CIA	uc011ebn.2	Q9Y294	OTTHUMG00000015470	ENST00000229595.5:c.416delT	6.37:g.119228580delT	ENSP00000229595:p.Ile139fs		Q6IA08|Q9P014	Frame_Shift_Del	DEL	pfam_Histone_chaperone_ASF1-like,superfamily_Histone_chaperone_ASF1-like	p.L140fs	ENST00000229595.5	37	c.416	CCDS47469.1	6																																																																																			ASF1A	-	pfam_Histone_chaperone_ASF1-like,superfamily_Histone_chaperone_ASF1-like	ENSG00000111875		0.343	ASF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ASF1A	HGNC	protein_coding	OTTHUMT00000361910.1	76	0.00	0	T	NM_014034		119228580	119228580	+1	no_errors	ENST00000229595	ensembl	human	known	69_37n	frame_shift_del	36	26.53	13	DEL	1.000	-
ASXL3	80816	genome.wustl.edu	37	18	31325521	31325521	+	Silent	SNP	G	G	A	rs367848609		TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr18:31325521G>A	ENST00000269197.5	+	12	5709	c.5709G>A	c.(5707-5709)tcG>tcA	p.S1903S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1903					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						TGCTCCCCTCGTGTAGCTTCC	0.498																																						dbGAP											0													126.0	130.0	129.0					18																	31325521		2006	4166	6172	-	-	-	SO:0001819	synonymous_variant	0			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.5709G>A	18.37:g.31325521G>A			Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	superfamily_Znf_FYVE_PHD	p.S1903	ENST00000269197.5	37	c.5709	CCDS45847.1	18																																																																																			ASXL3	-	NULL	ENSG00000141431		0.498	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ASXL3	HGNC	protein_coding	OTTHUMT00000441865.2	52	0.00	0	G			31325521	31325521	+1	no_errors	ENST00000269197	ensembl	human	known	69_37n	silent	31	16.22	6	SNP	0.003	A
C1QTNF3	114899	genome.wustl.edu	37	5	34024111	34024111	+	Missense_Mutation	SNP	C	C	A	rs368266969		TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr5:34024111C>A	ENST00000231338.7	-	5	571	c.484G>T	c.(484-486)Gtg>Ttg	p.V162L	RP11-1084J3.4_ENST00000382079.3_Missense_Mutation_p.V146L|C1QTNF3_ENST00000513065.1_5'UTR|C1QTNF3_ENST00000382065.3_Missense_Mutation_p.V235L	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3	162	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					AAGAAATACACACCTGAAAAA	0.408																																						dbGAP											0													190.0	142.0	158.0					5																	34024111		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"""cartonectin"""	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.484G>T	5.37:g.34024111C>A	ENSP00000231338:p.Val162Leu		Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Missense_Mutation	SNP	pfam_C1q,pfam_Collagen,superfamily_Tumour_necrosis_fac-like,smart_C1q,pfscan_C1q,prints_C1q	p.V235L	ENST00000231338.7	37	c.703	CCDS3904.1	5	.	.	.	.	.	.	.	.	.	.	C	14.79	2.640688	0.47153	.	.	ENSG00000082196	ENST00000382056;ENST00000382065;ENST00000231338	T;T	0.73469	-0.75;-0.75	5.48	5.48	0.80851	Tumour necrosis factor-like (2);Complement C1q protein (4);	.	.	.	.	T	0.57272	0.2042	N	0.20685	0.6	0.44006	D	0.99671	B;B	0.29766	0.256;0.051	B;B	0.28305	0.088;0.088	T	0.54543	-0.8278	9	0.11794	T	0.64	.	12.6665	0.56846	0.0:0.9245:0.0:0.0755	.	235;162	Q0VAN4;Q9BXJ4	.;C1QT3_HUMAN	L	115;235;162	ENSP00000371497:V235L;ENSP00000231338:V162L	ENSP00000231338:V162L	V	-	1	0	C1QTNF3	34059868	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	3.649000	0.54417	2.572000	0.86782	0.563000	0.77884	GTG	C1QTNF3	-	pfam_C1q,superfamily_Tumour_necrosis_fac-like,smart_C1q,pfscan_C1q,prints_C1q	ENSG00000082196		0.408	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	C1QTNF3	HGNC	protein_coding	OTTHUMT00000207469.1	53	0.00	0	C	NM_030945		34024111	34024111	-1	no_errors	ENST00000382065	ensembl	human	known	69_37n	missense	51	17.74	11	SNP	1.000	A
COL4A5	1287	genome.wustl.edu	37	X	107823802	107823802	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chrX:107823802A>G	ENST00000361603.2	+	14	1064	c.820A>G	c.(820-822)Ata>Gta	p.I274V	COL4A5_ENST00000328300.6_Missense_Mutation_p.I274V	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	274	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						ACCTCCAGGGATACGTGGTCC	0.413									Alport syndrome with Diffuse Leiomyomatosis																													dbGAP											0													133.0	118.0	123.0					X																	107823802		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.820A>G	X.37:g.107823802A>G	ENSP00000354505:p.Ile274Val		Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.I274V	ENST00000361603.2	37	c.820	CCDS14543.1	X	.	.	.	.	.	.	.	.	.	.	A	10.35	1.327267	0.24080	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.95756	-3.8;-3.8	5.7	1.99	0.26369	.	0.624529	0.17011	N	0.190509	D	0.84306	0.5443	N	0.03608	-0.345	0.23731	N	0.996993	B;B	0.11235	0.004;0.004	B;B	0.08055	0.003;0.003	T	0.73701	-0.3900	10	0.21540	T	0.41	.	4.9628	0.14076	0.3743:0.3919:0.0:0.2338	.	274;274	E7EVY4;P29400	.;CO4A5_HUMAN	V	274	ENSP00000331902:I274V;ENSP00000354505:I274V	ENSP00000331902:I274V	I	+	1	0	COL4A5	107710458	0.831000	0.29352	0.970000	0.41538	0.976000	0.68499	1.381000	0.34362	0.751000	0.32900	0.486000	0.48141	ATA	COL4A5	-	NULL	ENSG00000188153		0.413	COL4A5-001	KNOWN	basic|CCDS	protein_coding	COL4A5	HGNC	protein_coding	OTTHUMT00000057880.2	96	0.00	0	A			107823802	107823802	+1	no_errors	ENST00000328300	ensembl	human	known	69_37n	missense	95	15.93	18	SNP	0.789	G
DYRK4	8798	genome.wustl.edu	37	12	4708239	4708239	+	Missense_Mutation	SNP	C	C	A			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr12:4708239C>A	ENST00000540757.2	+	7	766	c.606C>A	c.(604-606)ttC>ttA	p.F202L	DYRK4_ENST00000543431.1_Missense_Mutation_p.F202L|DYRK4_ENST00000010132.5_Missense_Mutation_p.F202L	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	202	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTCAAGGCTTCAGTCTGTCCA	0.408																																						dbGAP											0													159.0	153.0	155.0					12																	4708239		2203	4300	6503	-	-	-	SO:0001583	missense	0			Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.606C>A	12.37:g.4708239C>A	ENSP00000441755:p.Phe202Leu		A8K8F7|Q8NEF2|Q92631	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.F202L	ENST00000540757.2	37	c.606	CCDS8530.1	12	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939125	0.52972	.	.	ENSG00000010219	ENST00000542744;ENST00000540757;ENST00000010132;ENST00000543431	T;T;T;T	0.15487	2.42;2.42;2.42;2.42	5.29	4.41	0.53225	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.054204	0.85682	D	0.000000	T	0.07279	0.0184	N	0.01454	-0.855	0.80722	D	1	P;B;B	0.47962	0.903;0.297;0.106	B;B;B	0.43867	0.434;0.16;0.135	T	0.31806	-0.9930	10	0.72032	D	0.01	.	8.3572	0.32338	0.0:0.7604:0.0:0.2396	.	317;202;202	F5H6L9;Q9NR20-2;Q9NR20	.;.;DYRK4_HUMAN	L	317;202;202;202	ENSP00000437534:F317L;ENSP00000441755:F202L;ENSP00000010132:F202L;ENSP00000439697:F202L	ENSP00000010132:F202L	F	+	3	2	DYRK4	4578500	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	0.890000	0.28295	1.232000	0.43678	0.555000	0.69702	TTC	DYRK4	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000010219		0.408	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DYRK4	HGNC	protein_coding	OTTHUMT00000398780.2	82	0.00	0	C			4708239	4708239	+1	no_errors	ENST00000010132	ensembl	human	known	69_37n	missense	75	11.76	10	SNP	1.000	A
NCAPG	64151	genome.wustl.edu	37	4	17819064	17819064	+	Missense_Mutation	SNP	A	A	T			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr4:17819064A>T	ENST00000251496.2	+	6	1132	c.956A>T	c.(955-957)aAc>aTc	p.N319I		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	319					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		CTCTGTAAAAACAATGATGGC	0.363																																						dbGAP											0													89.0	89.0	89.0					4																	17819064		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.956A>T	4.37:g.17819064A>T	ENSP00000251496:p.Asn319Ile		Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.N319I	ENST00000251496.2	37	c.956	CCDS3424.1	4	.	.	.	.	.	.	.	.	.	.	A	6.448	0.450742	0.12223	.	.	ENSG00000109805	ENST00000251496	T	0.33216	1.42	5.74	1.8	0.24995	Armadillo-type fold (1);	0.780131	0.13049	N	0.417869	T	0.19725	0.0474	L	0.33137	0.985	0.09310	N	0.999994	B	0.14012	0.009	B	0.13407	0.009	T	0.27905	-1.0060	10	0.18710	T	0.47	-4.2608	6.9539	0.24560	0.7413:0.1257:0.133:0.0	.	319	Q9BPX3	CND3_HUMAN	I	319	ENSP00000251496:N319I	ENSP00000251496:N319I	N	+	2	0	NCAPG	17428162	0.008000	0.16893	0.832000	0.32986	0.189000	0.23516	0.376000	0.20535	0.449000	0.26747	0.528000	0.53228	AAC	NCAPG	-	superfamily_ARM-type_fold	ENSG00000109805		0.363	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NCAPG	HGNC	protein_coding	OTTHUMT00000250375.1	66	0.00	0	A	NM_022346		17819064	17819064	+1	no_errors	ENST00000251496	ensembl	human	known	69_37n	missense	42	10.64	5	SNP	0.205	T
OPLAH	26873	genome.wustl.edu	37	8	145106682	145106682	+	Frame_Shift_Del	DEL	T	T	-			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr8:145106682delT	ENST00000426825.1	-	27	3749	c.3668delA	c.(3667-3669)aacfs	p.N1223fs	CTD-3065J16.6_ENST00000528912.1_RNA|CTD-3065J16.6_ENST00000561181.1_RNA|OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	1223					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGTCCGGCCGTTTTTGCGGAT	0.736																																						dbGAP											0													16.0	19.0	18.0					8																	145106682		1835	4079	5914	-	-	-	SO:0001589	frameshift_variant	0			AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.3668delA	8.37:g.145106682delT	ENSP00000475943:p.Asn1223fs		A5PKY8|Q75W65|Q9Y4Q0	RNA	DEL	-	NULL	ENST00000426825.1	37	NULL		8																																																																																			OPLAH	-	-	ENSG00000178814		0.736	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	OPLAH	HGNC	protein_coding		19	0.00	0	T	NM_017570		145106682	145106682	-1	no_errors	ENST00000426825	ensembl	human	known	69_37n	rna	9	18.18	2	DEL	1.000	-
PHF12	57649	genome.wustl.edu	37	17	27239625	27239625	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr17:27239625G>A	ENST00000332830.4	-	9	2774	c.1964C>T	c.(1963-1965)aCa>aTa	p.T655I	PHF12_ENST00000577226.1_Missense_Mutation_p.T655I|PHF12_ENST00000582655.1_5'UTR|PHF12_ENST00000268756.3_Missense_Mutation_p.T655I	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			CCTTGAATCTGTCAACGGAGG	0.572																																						dbGAP											0													82.0	88.0	86.0					17																	27239625		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"""Zinc fingers, PHD-type"""	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.1964C>T	17.37:g.27239625G>A	ENSP00000329933:p.Thr655Ile			Missense_Mutation	SNP	pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,superfamily_SMAD_FHA_domain,smart_Znf_PHD,pfscan_FHA_dom,pfscan_Znf_PHD-finger	p.T655I	ENST00000332830.4	37	c.1964	CCDS32598.1	17	.	.	.	.	.	.	.	.	.	.	G	15.38	2.815732	0.50527	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94931	-3.4;-3.56;-3.56	5.65	5.65	0.86999	.	0.369778	0.29587	N	0.011734	D	0.91071	0.7190	L	0.29908	0.895	0.37993	D	0.933965	B;B;P;P;B	0.44877	0.281;0.403;0.845;0.627;0.281	B;B;B;B;B	0.39379	0.077;0.161;0.298;0.255;0.077	D	0.93158	0.6555	10	0.66056	D	0.02	-26.9987	18.2796	0.90094	0.0:0.0:1.0:0.0	.	637;655;655;655;655	B4DFE2;Q96QT6-2;Q2TAK2;C9J9G2;Q96QT6	.;.;.;.;PHF12_HUMAN	I	655	ENSP00000329933:T655I;ENSP00000368157:T655I;ENSP00000268756:T655I	ENSP00000268756:T655I	T	-	2	0	PHF12	24263751	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.862000	0.69560	2.669000	0.90835	0.591000	0.81541	ACA	PHF12	-	NULL	ENSG00000109118		0.572	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHF12	HGNC	protein_coding	OTTHUMT00000255941.1	46	0.00	0	G	NM_020889		27239625	27239625	-1	no_errors	ENST00000332830	ensembl	human	known	69_37n	missense	44	12.00	6	SNP	1.000	A
PPP1R17	10842	genome.wustl.edu	37	7	31735165	31735165	+	Missense_Mutation	SNP	T	T	A			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr7:31735165T>A	ENST00000342032.3	+	3	793	c.165T>A	c.(163-165)aaT>aaA	p.N55K	PPP1R17_ENST00000409146.3_Intron	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	55					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										CCACCCTGAATGTTGAGTCAG	0.428																																						dbGAP											0													136.0	133.0	134.0					7																	31735165		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16973	protein-coding gene	gene with protein product	"""G-substrate"""	604088	"""chromosome 7 open reading frame 16"""	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.165T>A	7.37:g.31735165T>A	ENSP00000340125:p.Asn55Lys		B4DE58|Q9UDQ0	Missense_Mutation	SNP	NULL	p.N55K	ENST00000342032.3	37	c.165	CCDS5436.1	7	.	.	.	.	.	.	.	.	.	.	T	13.22	2.171833	0.38315	.	.	ENSG00000106341	ENST00000342032	T	0.29917	1.55	5.45	-2.05	0.07321	.	0.193299	0.45867	D	0.000336	T	0.24774	0.0601	M	0.62723	1.935	0.09310	N	0.999999	B	0.15930	0.015	B	0.18871	0.023	T	0.22277	-1.0221	10	0.32370	T	0.25	-21.9225	8.058	0.30617	0.1431:0.5905:0.0:0.2664	.	55	O96001	PPR17_HUMAN	K	55	ENSP00000340125:N55K	ENSP00000340125:N55K	N	+	3	2	C7orf16	31701690	0.000000	0.05858	0.052000	0.19188	0.989000	0.77384	-1.318000	0.02705	-0.156000	0.11079	0.533000	0.62120	AAT	PPP1R17	-	NULL	ENSG00000106341		0.428	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP1R17	HGNC	protein_coding	OTTHUMT00000250498.1	70	0.00	0	T	NM_006658		31735165	31735165	+1	no_errors	ENST00000342032	ensembl	human	known	69_37n	missense	74	11.90	10	SNP	0.005	A
PSG1	5669	genome.wustl.edu	37	19	43382212	43382212	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1QZ-01A-21D-A167-09	TCGA-E9-A1QZ-10A-01D-A167-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	2d47b244-e5e4-4645-91cb-71de1d685a95	7258e638-3291-484b-9c13-ffed4d7e747a	g.chr19:43382212A>G	ENST00000436291.2	-	2	399	c.283T>C	c.(283-285)Tat>Cat	p.Y95H	PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000595124.1_Missense_Mutation_p.Y95H|PSG1_ENST00000244296.2_Missense_Mutation_p.Y95H|PSG1_ENST00000595356.1_Missense_Mutation_p.Y95H|PSG1_ENST00000312439.6_Missense_Mutation_p.Y95H|PSG1_ENST00000403380.3_Missense_Mutation_p.Y95H	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	95	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				CGTCCACTATATGCAGGCCCA	0.448																																						dbGAP											0													292.0	280.0	284.0					19																	43382212		2202	4298	6500	-	-	-	SO:0001583	missense	0				CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.283T>C	19.37:g.43382212A>G	ENSP00000413041:p.Tyr95His		O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	pfam_Ig_V-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	p.Y95H	ENST00000436291.2	37	c.283	CCDS54275.1	19	.	.	.	.	.	.	.	.	.	.	N	1.030	-0.682282	0.03353	.	.	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	1.64	-2.68	0.06041	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.66733	0.2819	L	0.37897	1.145	0.09310	N	1	B;B;B;B;B;B;B;D;B	0.67145	0.152;0.004;0.019;0.005;0.03;0.01;0.015;0.996;0.004	B;B;B;B;B;B;B;D;B	0.70716	0.297;0.052;0.048;0.055;0.117;0.083;0.077;0.97;0.085	T	0.57802	-0.7748	9	0.39692	T	0.17	.	6.0472	0.19766	0.488:0.0:0.512:0.0	.	95;95;95;95;95;95;95;95;95	O75238;P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.;.	H	95	ENSP00000413041:Y95H;ENSP00000385386:Y95H;ENSP00000308970:Y95H;ENSP00000244296:Y95H	ENSP00000244296:Y95H	Y	-	1	0	PSG1	48074052	0.000000	0.05858	0.003000	0.11579	0.026000	0.11368	-2.547000	0.00931	-0.855000	0.04125	0.155000	0.16302	TAT	PSG1	-	pfam_Ig_V-set,smart_Ig_sub	ENSG00000231924		0.448	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PSG1	HGNC	protein_coding	OTTHUMT00000321426.1	124	0.00	0	A			43382212	43382212	-1	no_errors	ENST00000312439	ensembl	human	known	69_37n	missense	92	18.58	21	SNP	0.003	G
