#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_CAF	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_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	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
MID1	4281	genome.wustl.edu	37	X	10427745	10427745	+	Missense_Mutation	SNP	A	A	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chrX:10427745A>G	ENST00000317552.4	-	8	1788	c.1388T>C	c.(1387-1389)gTc>gCc	p.V463A	MID1_ENST00000380779.1_Missense_Mutation_p.V463A|MID1_ENST00000380782.2_Missense_Mutation_p.V463A|MID1_ENST00000380780.1_Missense_Mutation_p.V463A|MID1_ENST00000479925.1_5'UTR|MID1_ENST00000453318.2_Missense_Mutation_p.V463A|MID1_ENST00000380785.1_Missense_Mutation_p.V463A|MID1_ENST00000380787.1_Missense_Mutation_p.V463A	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	463	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						GATGGCCTTGACCATGAAGAT	0.517																																							0											0													235.0	169.0	191.0					X																	10427745		2203	4300	6503	SO:0001583	missense	0			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7095	protein-coding gene	gene with protein product	"""Opitz/BBB syndrome"""	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1388T>C	X.37:g.10427745A>G	ENSP00000312678:p.Val463Ala		B2RCG2|O75361|Q9BZX5	Missense_Mutation	SNP	pfam_SPRY_rcpt,pfam_Znf_B-box,pfam_Fibronectin_type3,superfamily_ConA-like_lec_gl_sf,superfamily_Fibronectin_type3,smart_Znf_RING,smart_Znf_B-box,smart_Bbox_C,smart_Fibronectin_type3,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY,pfscan_Fibronectin_type3,pfscan_Znf_B-box,pfscan_Znf_RING,prints_Butyrophylin	p.V463A	ENST00000317552.4	37	c.1388	CCDS14138.1	X	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796037	0.90453	.	.	ENSG00000101871	ENST00000453318;ENST00000317552;ENST00000380785;ENST00000380779;ENST00000380787;ENST00000380780;ENST00000380782;ENST00000454373;ENST00000413894	T;T;T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	5.34	5.34	0.76211	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84520	0.5490	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;0.999;0.998	D	0.86070	0.1537	10	0.66056	D	0.02	.	14.4277	0.67227	1.0:0.0:0.0:0.0	.	463;463;413	A8K5A0;O15344;B4DLX8	.;TRI18_HUMAN;.	A	463;463;463;463;463;463;463;413;463	ENSP00000414521:V463A;ENSP00000312678:V463A;ENSP00000370162:V463A;ENSP00000370156:V463A;ENSP00000370164:V463A;ENSP00000370157:V463A;ENSP00000370159:V463A;ENSP00000391154:V463A	ENSP00000312678:V463A	V	-	2	0	MID1	10387745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.772000	0.91757	1.787000	0.52448	0.481000	0.45027	GTC	0	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3		0.517	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	MID1	protein_coding	OTTHUMT00000055738.1	51	168	0	0.00	0	0	A		0	0		10427745	-1	no_errors	ENST00000317552	ensembl	human	known	74_37	missense	27	75	25	36.44	9	43	SNP	1	G
ARMCX2	9823	genome.wustl.edu	37	X	100911457	100911457	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chrX:100911457C>T	ENST00000328766.5	-	5	1571	c.1118G>A	c.(1117-1119)cGc>cAc	p.R373H	ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000330154.2_Missense_Mutation_p.R373H|ARMCX2_ENST00000356824.4_Missense_Mutation_p.R373H	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	373						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						AGGAAAGGGGCGCTTCTGCAT	0.537																																							0											0													91.0	79.0	83.0					X																	100911457		2203	4300	6503	SO:0001583	missense	0			AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"""Armadillo repeat containing"""	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.1118G>A	X.37:g.100911457C>T	ENSP00000331662:p.Arg373His		O60267|Q5H9D9	Missense_Mutation	SNP	pfam_ARM-rpt_dom,superfamily_ARM-type_fold,smart_Armadillo	p.R373H	ENST00000328766.5	37	c.1118	CCDS14490.1	X	.	.	.	.	.	.	.	.	.	.	C	15.04	2.714272	0.48622	.	.	ENSG00000184867	ENST00000328766;ENST00000330154;ENST00000356824	T;T;T	0.34667	1.35;1.35;1.35	3.77	3.77	0.43336	.	0.437146	0.20194	N	0.097257	T	0.24431	0.0592	N	0.19112	0.55	0.33792	D	0.625625	D	0.61080	0.989	B	0.43331	0.416	T	0.35699	-0.9778	10	0.51188	T	0.08	-4.9691	10.0786	0.42375	0.0:1.0:0.0:0.0	.	373	Q7L311	ARMX2_HUMAN	H	373	ENSP00000331662:R373H;ENSP00000328631:R373H;ENSP00000349281:R373H	ENSP00000331662:R373H	R	-	2	0	ARMCX2	100798113	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.861000	0.39438	2.131000	0.65755	0.422000	0.28245	CGC	0	NULL		0.537	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ARMCX2	protein_coding	OTTHUMT00000057586.1	81	155	0	0.00	0	0	C	NM_014782	0	0		100911457	-1	no_errors	ENST00000328766	ensembl	human	known	74_37	missense	26	74	37.21	36.97	16	44	SNP	1	T
AFF2	2334	genome.wustl.edu	37	X	148069069	148069069	+	Missense_Mutation	SNP	C	C	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chrX:148069069C>A	ENST00000370460.2	+	20	4275	c.3796C>A	c.(3796-3798)Ctg>Atg	p.L1266M	AFF2_ENST00000370457.5_Missense_Mutation_p.L1231M|AFF2_ENST00000286437.5_Missense_Mutation_p.L907M|AFF2_ENST00000342251.3_Missense_Mutation_p.L1233M	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1266					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GGCCGACAAACTGACAAGAGA	0.468																																							0											0													183.0	142.0	156.0					X																	148069069		2203	4300	6503	SO:0001583	missense	0			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3796C>A	X.37:g.148069069C>A	ENSP00000359489:p.Leu1266Met		A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	pfam_TF_AF4/FMR2	p.L1266M	ENST00000370460.2	37	c.3796	CCDS14684.1	X	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710157	0.89018	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000008	D	0.89812	0.6823	M	0.85859	2.78	0.80722	D	1	D;D;D;D;D;D	0.89917	0.99;0.999;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.986;0.998;0.999;0.999;0.999;1.0	D	0.91090	0.4906	10	0.87932	D	0	.	18.9513	0.92642	0.0:1.0:0.0:0.0	.	907;1231;1231;1227;1256;1266	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	M	1266;1231;1233;907	ENSP00000359489:L1266M;ENSP00000359486:L1231M;ENSP00000345459:L1233M;ENSP00000286437:L907M	ENSP00000286437:L907M	L	+	1	2	AFF2	147876775	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.040000	0.70980	2.423000	0.82170	0.600000	0.82982	CTG	0	pfam_TF_AF4/FMR2		0.468	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AFF2	protein_coding	OTTHUMT00000058673.2	10	268	0	0.00	0	0	C	NM_002025	0	0		148069069	1	no_errors	ENST00000370460	ensembl	human	known	74_37	missense	23	222	11.54	4.70	3	11	SNP	1	A
IDS	3423	genome.wustl.edu	37	X	148564527	148564527	+	Missense_Mutation	SNP	C	C	T	rs113993946		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chrX:148564527C>T	ENST00000340855.6	-	9	1612	c.1403G>A	c.(1402-1404)cGg>cAg	p.R468Q	IDS_ENST00000537071.1_Missense_Mutation_p.R71Q|IDS_ENST00000541269.1_Missense_Mutation_p.R257Q|IDS_ENST00000422081.2_Missense_Mutation_p.R257Q	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	468			R -> G (in MPS2; mild to severe forms).|R -> L (in MPS2; mild to severe forms). {ECO:0000269|PubMed:7581397, ECO:0000269|PubMed:9222763, ECO:0000269|PubMed:9501270}.|R -> Q (in MPS2; severe/intermediate form; greatly reduced activity; poor transport to lysosomes). {ECO:0000269|PubMed:11683780, ECO:0000269|PubMed:7581397, ECO:0000269|PubMed:8664909, ECO:0000269|PubMed:8940265, ECO:0000269|PubMed:9222763, ECO:0000269|PubMed:9266380, ECO:0000269|PubMed:9375851, ECO:0000269|PubMed:9501270, ECO:0000269|PubMed:9660053, ECO:0000269|PubMed:9921913, ECO:0000269|PubMed:9950361}.|R -> W (in MPS2; mild to severe forms). {ECO:0000269|PubMed:10447264, ECO:0000269|PubMed:11683780, ECO:0000269|PubMed:1284597, ECO:0000269|PubMed:7728156, ECO:0000269|PubMed:8664909, ECO:0000269|PubMed:9266380, ECO:0000269|PubMed:9501270, ECO:0000269|PubMed:9660053, ECO:0000269|PubMed:9950361}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GTCTGAAGGCCGGGGATACTG	0.468																																							0											0			GRCh37	CM930422|CM950672	IDS	M	rs113993946						108.0	100.0	103.0					X																	148564527		2203	4300	6503	SO:0001583	missense	0			M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.1403G>A	X.37:g.148564527C>T	ENSP00000339801:p.Arg468Gln		D3DWT4|Q14604|Q9BRM3	Missense_Mutation	SNP	pfam_Sulfatase,pfam_Phosphodiest/P_Trfase,superfamily_Alkaline_phosphatase_core	p.R468Q	ENST00000340855.6	37	c.1403	CCDS14685.1	X	.	.	.	.	.	.	.	.	.	.	C	24.9	4.576921	0.86645	.	.	ENSG00000010404	ENST00000340855;ENST00000537071;ENST00000541269	D;D;D	0.99760	-6.03;-6.33;-6.66	5.37	5.37	0.77165	Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99691	0.9883	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.988;0.999	D	0.97628	1.0140	10	0.72032	D	0.01	.	18.2398	0.89963	0.0:1.0:0.0:0.0	.	378;468	B4DGD7;P22304	.;IDS_HUMAN	Q	468;71;257	ENSP00000339801:R468Q;ENSP00000440324:R71Q;ENSP00000441261:R257Q	ENSP00000339801:R468Q	R	-	2	0	IDS	148372432	1.000000	0.71417	1.000000	0.80357	0.347000	0.29111	7.016000	0.76393	2.246000	0.74042	0.422000	0.28245	CGG	0	superfamily_Alkaline_phosphatase_core		0.468	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IDS	protein_coding	OTTHUMT00000058677.3	130	269	0	0.00	0	0	C		rs113993946	C->A,G,T		148564527	-1	no_errors	ENST00000340855	ensembl	human	known	74_37	missense	52	125	34.18	39.90	27	83	SNP	1	T
NOTCH2NL	388677	genome.wustl.edu	37	1	145281625	145281625	+	Silent	SNP	C	C	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr1:145281625C>G	ENST00000369340.3	+	5	999	c.555C>G	c.(553-555)ccC>ccG	p.P185P	RP11-458D21.5_ENST00000468030.1_Silent_p.P185P|NOTCH2NL_ENST00000362074.6_Silent_p.P185P|NOTCH2NL_ENST00000344859.3_Silent_p.P185P			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	185	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						TGTATGTGCCCTGTGCACCCT	0.582																																							0											0													173.0	174.0	174.0					1																	145281625		2203	4300	6503	SO:0001819	synonymous_variant	0				CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.555C>G	1.37:g.145281625C>G			Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Silent	SNP	pfam_EG-like_dom,pfam_EGF_extracell,pfam_EGF-like_Ca-bd_dom,smart_EGF-like_Ca-bd_dom,smart_EG-like_dom,pfscan_EG-like_dom	p.P185	ENST00000369340.3	37	c.555	CCDS909.1	1																																																																																			0	smart_EG-like_dom,pfscan_EG-like_dom		0.582	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ENSG00000255168	protein_coding	OTTHUMT00000038546.1	124	171	0	0.00	0	0	C	NM_203458	0	0		145281625	1	no_errors	ENST00000468030	ensembl	human	known	74_37	silent	130	188	11.56	8.29	17	17	SNP	0.997	G
BRINP3	339479	genome.wustl.edu	37	1	190449665	190449665	+	5'Flank	SNP	T	T	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr1:190449665T>C	ENST00000367462.3	-	0	0				RP11-161I10.1_ENST00000417409.1_lincRNA|RP11-547I7.2_ENST00000424735.1_lincRNA	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3						cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											ACCTTAACAATTGTGAGAGTT	0.348																																							0											0																																										SO:0001631	upstream_gene_variant	0			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533		1.37:g.190449665T>C	Exception_encountered		B3KVP1|B7Z260|O95726|Q2M330	RNA	SNP	0	NULL	ENST00000367462.3	37	NULL	CCDS1373.1	1																																																																																			0	0		0.348	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000237457	protein_coding	OTTHUMT00000086278.1	18	360	0	0.00	0	0	T	NM_199051	0	0		190449665	1	no_errors	ENST00000424735	ensembl	human	known	74_37	rna	7	256	35.71	27.68	5	98	SNP	0.003	C
RGS1	5996	genome.wustl.edu	37	1	192548271	192548271	+	Missense_Mutation	SNP	A	A	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr1:192548271A>G	ENST00000367459.3	+	5	515	c.449A>G	c.(448-450)aAt>aGt	p.N150S		NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	150	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|immune response (GO:0006955)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			kidney(8)|large_intestine(1)|lung(13)	22		Breast(1374;0.188)				TTTTAGATCAATATTGACTTC	0.318																																							0											0													67.0	73.0	71.0					1																	192548271		2203	4300	6503	SO:0001583	missense	0			AF493925	CCDS1375.2	1q31	2008-02-05	2007-08-14		ENSG00000090104	ENSG00000090104		"""Regulators of G-protein signaling"""	9991	protein-coding gene	gene with protein product		600323	"""regulator of G-protein signalling 1"""	IER1		8241276, 8602223	Standard	NM_002922		Approved	1R20, IR20, BL34	uc001gsi.1	Q08116	OTTHUMG00000035598	ENST00000367459.3:c.449A>G	1.37:g.192548271A>G	ENSP00000356429:p.Asn150Ser		B2RDM9|B4DZY0|Q07918|Q9H1W2	Missense_Mutation	SNP	pfam_RGS_dom,superfamily_Regulat_G_prot_signal_superfam,smart_Regulat_G_prot_signal_superfam,pfscan_Regulat_G_prot_signal_superfam,prints_RGS_dom	p.N150S	ENST00000367459.3	37	c.449	CCDS1375.2	1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.731795	0.89390	.	.	ENSG00000090104	ENST00000367459	T	0.36520	1.25	5.68	5.68	0.88126	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60881	0.2303	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.60777	-0.7196	10	0.37606	T	0.19	.	15.0466	0.71833	1.0:0.0:0.0:0.0	.	150	Q08116	RGS1_HUMAN	S	150	ENSP00000356429:N150S	ENSP00000356429:N150S	N	+	2	0	RGS1	190814894	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.289000	0.77006	0.482000	0.46254	AAT	0	pfam_RGS_dom,superfamily_Regulat_G_prot_signal_superfam,smart_Regulat_G_prot_signal_superfam,pfscan_Regulat_G_prot_signal_superfam,prints_RGS_dom		0.318	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RGS1	protein_coding	OTTHUMT00000086391.1	81	308	0	0.00	0	0	A	NM_002922	0	0		192548271	1	no_errors	ENST00000367459	ensembl	human	known	74_37	missense	140	270	30.54	29.13	62	111	SNP	1	G
CCSAP	126731	genome.wustl.edu	37	1	229478671	229478671	+	5'UTR	SNP	G	G	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr1:229478671G>A	ENST00000284617.2	-	0	64				CCSAP_ENST00000366686.1_5'Flank|CCSAP_ENST00000366687.1_5'Flank|CCSAP_ENST00000452552.1_5'Flank|CCSAP_ENST00000483092.1_5'UTR	NM_145257.3	NP_660300.3	Q6IQ19	CCSAP_HUMAN	centriole, cilia and spindle-associated protein						multicellular organismal development (GO:0007275)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of embryonic development (GO:0045995)	axon (GO:0030424)|axoneme (GO:0005930)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cilium (GO:0005929)|spindle (GO:0005819)											CCTTCCCGCCGCGCCCGGCCG	0.741																																							0											0																																										SO:0001623	5_prime_UTR_variant	0			BC071609	CCDS1577.1	1q42.13	2012-06-19	2012-06-19	2012-06-19	ENSG00000154429	ENSG00000154429			29578	protein-coding gene	gene with protein product	"""centriole and spindle-associated protein"""		"""chromosome 1 open reading frame 96"""	C1orf96		22493317	Standard	NM_145257		Approved	FLJ41471, CSAP	uc001htl.4	Q6IQ19	OTTHUMG00000037663	ENST00000284617.2:c.-61C>T	1.37:g.229478671G>A			A8K5X2|Q6P9G2|Q6ZW85|Q8IXU1|Q96BM2	RNA	SNP	0	NULL	ENST00000284617.2	37	NULL	CCDS1577.1	1																																																																																			0	0		0.741	CCSAP-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CCSAP	protein_coding		25	30	0	0.00	0	0	G	NM_145257	0	0		229478671	-1	no_errors	ENST00000483092	ensembl	human	known	74_37	rna	12	44	36.84	25.42	7	15	SNP	0	A
OR2W3	343171	genome.wustl.edu	37	1	248059455	248059455	+	Silent	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr1:248059455C>T	ENST00000360358.3	+	1	567	c.567C>T	c.(565-567)tgC>tgT	p.C189C	OR2W3_ENST00000537741.1_Silent_p.C189C	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGATGGCCTGCGTCAGCACTG	0.607																																							0											0													137.0	117.0	123.0					1																	248059455		2203	4300	6503	SO:0001819	synonymous_variant	0			N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.567C>T	1.37:g.248059455C>T			Q6IF06|Q8NG86	Silent	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.C189	ENST00000360358.3	37	c.567	CCDS31099.1	1																																																																																			0	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt		0.607	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2W3	protein_coding	OTTHUMT00000096861.1	34	129	0	0.00	0	0	C	NM_001001957	0	0		248059455	1	no_errors	ENST00000360358	ensembl	human	known	74_37	silent	27	103	25	36.02	9	58	SNP	0.024	T
ODC1	4953	genome.wustl.edu	37	2	10584662	10584662	+	Missense_Mutation	SNP	C	C	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:10584662C>A	ENST00000234111.4	-	4	724	c.214G>T	c.(214-216)Gat>Tat	p.D72Y	ODC1_ENST00000405333.1_Missense_Mutation_p.D72Y|SNORA80B_ENST00000383906.1_RNA|ODC1_ENST00000446285.1_5'UTR	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	72					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	GCTTTGCTATCATTACATTTG	0.473																																							0											0													97.0	92.0	94.0					2																	10584662		2203	4300	6503	SO:0001583	missense	0				CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.214G>T	2.37:g.10584662C>A	ENSP00000234111:p.Asp72Tyr		Q53TU3|Q6LDS9	Missense_Mutation	SNP	pfam_De-COase2_N,pfam_De-COase2_C,superfamily_Ala_racemase/Decarboxylase_C,prints_Orn_de-COase,prints_Orn/DAP/Arg_de-COase	p.D72Y	ENST00000234111.4	37	c.214	CCDS1672.1	2	.	.	.	.	.	.	.	.	.	.	C	16.34	3.094406	0.56075	.	.	ENSG00000115758	ENST00000234111;ENST00000405333	T;T	0.42900	0.96;0.96	5.37	5.37	0.77165	Orn/DAP/Arg decarboxylase 2, N-terminal (1);	0.044849	0.85682	D	0.000000	T	0.50871	0.1641	M	0.78637	2.42	0.58432	D	0.999998	P	0.43750	0.816	B	0.41271	0.352	T	0.59931	-0.7361	10	0.62326	D	0.03	.	19.1175	0.93348	0.0:1.0:0.0:0.0	.	72	P11926	DCOR_HUMAN	Y	72	ENSP00000234111:D72Y;ENSP00000385333:D72Y	ENSP00000234111:D72Y	D	-	1	0	ODC1	10502113	1.000000	0.71417	0.991000	0.47740	0.962000	0.63368	3.250000	0.51445	2.508000	0.84585	0.655000	0.94253	GAT	0	pfam_De-COase2_N,prints_Orn_de-COase,prints_Orn/DAP/Arg_de-COase		0.473	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ODC1	protein_coding	OTTHUMT00000206896.2	76	199	0	0.00	0	0	C		0	0		10584662	-1	no_errors	ENST00000234111	ensembl	human	known	74_37	missense	30	105	33.33	35.19	15	57	SNP	1	A
APLF	200558	genome.wustl.edu	37	2	68753274	68753274	+	Missense_Mutation	SNP	A	A	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:68753274A>G	ENST00000303795.4	+	6	875	c.704A>G	c.(703-705)cAa>cGa	p.Q235R		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	235					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGAAGAAGGCAATTAATTTCA	0.373																																							0											0													108.0	110.0	110.0					2																	68753274		2203	4300	6503	SO:0001583	missense	0			BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.704A>G	2.37:g.68753274A>G	ENSP00000307004:p.Gln235Arg		A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	pfam_Znf_C2H2_APLF-like,superfamily_SMAD_FHA_domain	p.Q235R	ENST00000303795.4	37	c.704	CCDS1888.1	2	.	.	.	.	.	.	.	.	.	.	a	0.007	-1.985923	0.00443	.	.	ENSG00000169621	ENST00000303795	T	0.18810	2.19	4.85	3.96	0.45880	.	0.764841	0.12264	N	0.484493	T	0.05273	0.0140	N	0.00707	-1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30357	-0.9981	10	0.02654	T	1	.	8.5827	0.33640	0.1074:0.0:0.8926:0.0	.	235;235	F8WET0;Q8IW19	.;APLF_HUMAN	R	235	ENSP00000307004:Q235R	ENSP00000307004:Q235R	Q	+	2	0	APLF	68606778	0.471000	0.25862	0.782000	0.31804	0.072000	0.16883	1.088000	0.30877	1.388000	0.46506	-0.473000	0.04963	CAA	0	NULL		0.373	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APLF	protein_coding	OTTHUMT00000251759.1	22	247	0	0.40	0	1	A	NM_173545	0	0		68753274	1	no_errors	ENST00000303795	ensembl	human	known	74_37	missense	28	120	36.96	39.70	17	79	SNP	0.671	G
SCN1A	6323	genome.wustl.edu	37	2	166868749	166868749	+	Missense_Mutation	SNP	G	G	A	rs140731963		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:166868749G>A	ENST00000303395.4	-	19	3748	c.3749C>T	c.(3748-3750)aCg>aTg	p.T1250M	AC010127.3_ENST00000597623.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.T1239M|SCN1A_ENST00000409050.1_Missense_Mutation_p.T1222M|SCN1A_ENST00000423058.2_Missense_Mutation_p.T1250M			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1250					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.T1239M(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCCAACATCGTCTTAATCGT	0.318																																							0											1	Substitution - Missense(1)	large_intestine(1)						G	MET/THR,MET/THR,MET/THR,MET/THR	0,4404		0,0,2202	78.0	73.0	75.0		3749,3665,3749,3716	4.4	1.0	2	dbSNP_134	75	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,missense,missense	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	81,81,81,81	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1250/2010,1222/1982,1250/2010,1239/1999	166868749	3,12999	2202	4299	6501	SO:0001583	missense	0			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3749C>T	2.37:g.166868749G>A	ENSP00000303540:p.Thr1250Met		E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_DUF3451,pfam_Na_trans_assoc,pfam_PKD1_2_channel,prints_Na_channel_a1su,prints_Na_channel_asu,prints_PKD_2	p.T1250M	ENST00000303395.4	37	c.3749	CCDS54413.1	2	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503404	0.44558	0.0	3.49E-4	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.5	4.42	0.53409	.	0.094690	0.45867	D	0.000326	D	0.95893	0.8663	M	0.76838	2.35	0.40706	D	0.982527	P;D;B	0.54601	0.601;0.967;0.013	B;B;B	0.39771	0.136;0.309;0.006	D	0.96407	0.9301	10	0.54805	T	0.06	.	15.1821	0.72968	0.0795:0.0:0.9205:0.0	.	1239;1222;1250	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	M	1250;1250;1239;1222	ENSP00000407030:T1250M;ENSP00000303540:T1250M;ENSP00000364554:T1239M;ENSP00000386312:T1222M	ENSP00000303540:T1250M	T	-	2	0	SCN1A	166576995	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	4.565000	0.60836	2.568000	0.86640	0.557000	0.71058	ACG	0	NULL		0.318	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	SCN1A	protein_coding	OTTHUMT00000102661.1	27	269	0	0.00	0	0	G	NM_006920	rs140731963	G->A		166868749	-1	no_errors	ENST00000303395	ensembl	human	known	74_37	missense	40	122	25.93	35.11	14	66	SNP	0.984	A
TTN	7273	genome.wustl.edu	37	2	179560833	179560833	+	Silent	SNP	G	G	A	rs587780979		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:179560833G>A	ENST00000591111.1	-	112	30239	c.30015C>T	c.(30013-30015)gaC>gaT	p.D10005D	TTN_ENST00000342992.6_Silent_p.D9078D|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.D10322D|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTCCAGTTCGTCATAAGGTT	0.378																																							0											0													128.0	108.0	114.0					2																	179560833		1772	3890	5662	SO:0001819	synonymous_variant	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30015C>T	2.37:g.179560833G>A			A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom	p.D9078	ENST00000591111.1	37	c.27234		2																																																																																			0	superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom		0.378	TTN-019	PUTATIVE	basic	protein_coding	TTN	protein_coding	OTTHUMT00000460310.1	69	306	0	0.33	0	1	G	NM_133378	rs587780979	G->A		179560833	-1	no_errors	ENST00000342992	ensembl	human	known	74_37	silent	46	195	20.69	39.32	12	127	SNP	0.021	A
HECW2	57520	genome.wustl.edu	37	2	197182045	197182045	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:197182045C>T	ENST00000260983.3	-	10	2569	c.2387G>A	c.(2386-2388)cGc>cAc	p.R796H	HECW2_ENST00000409111.1_Missense_Mutation_p.R440H	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	796	Interaction with TP73.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						AACATCCTGGCGCACTGAAGG	0.498																																							0											0													81.0	72.0	75.0					2																	197182045		2203	4300	6503	SO:0001583	missense	0			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.2387G>A	2.37:g.197182045C>T	ENSP00000260983:p.Arg796His		B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	pfam_HECT,pfam_WW_dom,pfam_C2_dom,superfamily_HECT,superfamily_WW_dom,superfamily_C2_dom,smart_C2_dom,smart_WW_dom,smart_HECT,pfscan_HECT,pfscan_C2_dom,pfscan_WW_dom	p.R796H	ENST00000260983.3	37	c.2387	CCDS33354.1	2	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233550	0.79688	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.36157	1.27;1.31	5.84	4.96	0.65561	.	0.695056	0.15369	N	0.265959	T	0.26810	0.0656	N	0.19112	0.55	0.80722	D	1	B	0.19445	0.036	B	0.12156	0.007	T	0.03784	-1.1004	10	0.39692	T	0.17	.	15.3556	0.74425	0.0:0.9322:0.0:0.0678	.	796	Q9P2P5	HECW2_HUMAN	H	440;796	ENSP00000386775:R440H;ENSP00000260983:R796H	ENSP00000260983:R796H	R	-	2	0	HECW2	196890290	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.597000	0.67577	2.771000	0.95319	0.655000	0.94253	CGC	0	NULL		0.498	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HECW2	protein_coding	OTTHUMT00000335199.3	75	157	0	0.00	0	0	C	NM_020760	0	0		197182045	-1	no_errors	ENST00000260983	ensembl	human	known	74_37	missense	42	85	32.26	38.57	20	54	SNP	1	T
SPEG	10290	genome.wustl.edu	37	2	220331922	220331922	+	Missense_Mutation	SNP	G	G	A	rs377353278		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:220331922G>A	ENST00000312358.7	+	10	3040	c.2908G>A	c.(2908-2910)Gtg>Atg	p.V970M	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	970	Ig-like 4.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GTCCCTGGCCGTGCTGGCCCC	0.677											OREG0004000	type=REGULATORY REGION|Gene=APEG1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																											0											0								G	MET/VAL	0,4046		0,0,2023	46.0	56.0	53.0		2908	4.8	1.0	2		53	1,8323		0,1,4161	no	missense	SPEG	NM_005876.4	21	0,1,6184	AA,AG,GG		0.012,0.0,0.0081	probably-damaging	970/3268	220331922	1,12369	2023	4162	6185	SO:0001583	missense	0			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2908G>A	2.37:g.220331922G>A	ENSP00000311684:p.Val970Met	2265	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom	p.V970M	ENST00000312358.7	37	c.2908	CCDS42824.1	2	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527827	0.44969	0.0	1.2E-4	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.67698	-0.28	4.75	4.75	0.60458	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.36268	N	0.002685	T	0.73992	0.3658	L	0.43923	1.385	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.75033	-0.3460	10	0.56958	D	0.05	.	12.3766	0.55283	0.083:0.0:0.917:0.0	.	970	Q15772	SPEG_HUMAN	M	970	ENSP00000311684:V970M	ENSP00000265327:V970M	V	+	1	0	SPEG	220040166	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.863000	0.62983	2.465000	0.83290	0.655000	0.94253	GTG	0	pfscan_Ig-like_dom		0.677	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SPEG	protein_coding	OTTHUMT00000130252.2	40	63	0	0.00	0	0	G	NM_005876	rs377353278	G->A		220331922	1	no_errors	ENST00000312358	ensembl	human	novel	74_37	missense	6	43	62.5	32.81	10	21	SNP	1	A
SNED1	25992	genome.wustl.edu	37	2	241992589	241992589	+	Silent	SNP	G	G	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:241992589G>A	ENST00000310397.8	+	16	2103	c.2103G>A	c.(2101-2103)ccG>ccA	p.P701P	SNED1_ENST00000342631.6_Silent_p.P701P|SNED1_ENST00000401884.1_Silent_p.P701P|SNED1_ENST00000405547.3_Silent_p.P701P|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000469006.1_3'UTR	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	701	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCGGCCCCCCGGAGGAGGTGA	0.716																																							0											0													15.0	20.0	19.0					2																	241992589		2072	4176	6248	SO:0001819	synonymous_variant	0			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2103G>A	2.37:g.241992589G>A			B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	pfam_EG-like_dom,pfam_Fibronectin_type3,pfam_Nidogen_extracell_dom,pfam_EGF_extracell,pfam_EGF-like_Ca-bd_dom,superfamily_Fibronectin_type3,superfamily_Sushi_SCR_CCP,smart_Nidogen_extracell_dom,smart_EG-like_dom,smart_EGF-like_Ca-bd_dom,smart_Sushi_SCR_CCP,smart_Fibronectin_type3,pfscan_EG-like_dom,pfscan_Fibronectin_type3,pfscan_Sushi_SCR_CCP	p.P701	ENST00000310397.8	37	c.2103	CCDS46562.1	2																																																																																			0	superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP		0.716	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SNED1	protein_coding	OTTHUMT00000323935.2	9	16	0	0.00	0	0	G	XM_059482	0	0		241992589	1	no_errors	ENST00000310397	ensembl	human	known	74_37	silent	12	19	29.41	44.12	5	15	SNP	0	A
HDLBP	3069	genome.wustl.edu	37	2	242192848	242192848	+	Missense_Mutation	SNP	T	T	C	rs7578199	byFrequency	TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:242192848T>C	ENST00000391975.1	-	10	1480	c.1253A>G	c.(1252-1254)aAt>aGt	p.N418S	HDLBP_ENST00000391976.2_Missense_Mutation_p.N418S|HDLBP_ENST00000427183.2_Missense_Mutation_p.N385S|HDLBP_ENST00000310931.4_Missense_Mutation_p.N418S|HDLBP_ENST00000476807.1_5'Flank	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	418	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.		N -> S (in dbSNP:rs7578199).		cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CTGGGCCACATTGACATCCTC	0.498													T|||	690	0.13778	0.1785	0.1916	5008	,	,		20669	0.001		0.2684	False		,,,				2504	0.0511						0											0								T	SER/ASN,SER/ASN	805,3601	322.9+/-297.8	65,675,1463	228.0	187.0	201.0		1253,1253	-11.9	0.0	2	dbSNP_116	201	2118,6482	364.2+/-333.4	261,1596,2443	yes	missense,missense	HDLBP	NM_005336.4,NM_203346.3	46,46	326,2271,3906	CC,CT,TT		24.6279,18.2705,22.4742	benign,benign	418/1269,418/1269	242192848	2923,10083	2203	4300	6503	SO:0001583	missense	0				CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.1253A>G	2.37:g.242192848T>C	ENSP00000375836:p.Asn418Ser		B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	pfam_KH_dom_type_1,smart_KH_dom,pfscan_KH_dom_type_1	p.N418S	ENST00000391975.1	37	c.1253	CCDS2547.1	2	356|356	0.163003663003663|0.163003663003663	76|76	0.15447154471544716|0.15447154471544716	79|79	0.21823204419889503|0.21823204419889503	1|1	0.0017482517482517483|0.0017482517482517483	200|200	0.2638522427440633|0.2638522427440633	T|T	6.318|6.318	0.426852|0.426852	0.11987|0.11987	0.182705|0.182705	0.246279|0.246279	ENSG00000115677|ENSG00000115677	ENST00000453141|ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183	.|T;T;T;T	.|0.29655	.|1.56;1.56;1.56;1.56	5.96|5.96	-11.9|-11.9	0.00025|0.00025	.|K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	.|0.573156	.|0.21521	.|N	.|0.073204	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.10296	.|0.0;0.003;0.0	.|B;B;B	.|0.11329	.|0.005;0.006;0.005	T|T	0.15809|0.15809	-1.0424|-1.0424	4|9	.|0.28530	.|T	.|0.3	-18.9169|-18.9169	10.2925|10.2925	0.43605|0.43605	0.0:0.389:0.3221:0.2889|0.0:0.389:0.3221:0.2889	rs7578199;rs60102099;rs7578199|rs7578199;rs60102099;rs7578199	.|418;385;418	.|B2R5V9;E7EM71;Q00341	.|.;.;VIGLN_HUMAN	V|S	296|418;418;418;385	.|ENSP00000375836:N418S;ENSP00000375837:N418S;ENSP00000312042:N418S;ENSP00000399139:N385S	.|ENSP00000312042:N418S	M|N	-|-	1|2	0|0	HDLBP|HDLBP	241841521|241841521	0.029000|0.029000	0.19370|0.19370	0.000000|0.000000	0.03702|0.03702	0.038000|0.038000	0.13279|0.13279	0.019000|0.019000	0.13444|0.13444	-2.653000|-2.653000	0.00423|0.00423	-2.181000|-2.181000	0.00316|0.00316	ATG|AAT	0	pfam_KH_dom_type_1,smart_KH_dom,pfscan_KH_dom_type_1		0.498	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HDLBP	protein_coding	OTTHUMT00000257245.5	52	224	0	0.00	0	0	T	NM_203346	rs7578199	T->C		242192848	-1	no_errors	ENST00000310931	ensembl	human	known	74_37	missense	27	128	25	30.05	9	55	SNP	0	C
KIT	3815	genome.wustl.edu	37	4	55593610	55593610	+	Missense_Mutation	SNP	T	T	G	rs121913517|rs121913685|rs121913511|rs121913510		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr4:55593610T>G	ENST00000288135.5	+	11	1773	c.1676T>G	c.(1675-1677)gTt>gGt	p.V559G		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	559			Missing (in GIST). {ECO:0000269|PubMed:9697690}.|Missing (in GIST; somatic mutation). {ECO:0000269|PubMed:9438854}.|V -> A (in GIST). {ECO:0000269|PubMed:11505412}.|V -> D (in GIST; somatic mutation). {ECO:0000269|PubMed:9438854}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V559D(58)|p.V559del(18)|p.W557_E561del(17)|p.V559A(16)|p.V559G(12)|p.K558_E562del(10)|p.W557_V559>C(9)|p.V559_E561del(8)|p.W557_V559del(7)|p.Q556_V560del(6)|p.V559_V560del(6)|p.K558_V560del(5)|p.K558_V559del(3)|p.W557_V560>C(3)|p.Y553_T574>S(3)|p.V559_G565del(3)|p.V555_I571del(3)|p.V555_V560del(3)|p.V555_P573del(3)|p.Q556_V560>H(3)|p.V555_V559del(3)|p.K558_V559>N(2)|p.Q556_L576del(2)|p.K550_V559del(2)|p.K558_V560>N(2)|p.K558_V559>SS(2)|p.W557_P573>S(2)|p.K558_N564del(2)|p.W557_Q575del(2)|p.V555_E562del(2)|p.W557_V560del(2)|p.Q556_V559del(2)|p.K558_V560>I(2)|p.V555_G565del(1)|p.Q556_N566>SNNLQLY(1)|p.Q556_V559>H(1)|p.V559K(1)|p.M552_E561>K(1)|p.V555_I563del(1)|p.K558_G565del(1)|p.E554_I571del(1)|p.K558_Q575del(1)|p.Q556_V560>F(1)|p.V555_Y570del(1)|p.M552_T574>TESA(1)|p.K558_D572del(1)|p.V559_I571del(1)|p.Q556_D572>PS(1)|p.Q556_D572del(1)|p.W557_E562del(1)|p.V555_N566>D(1)|p.V559_N564del(1)|p.V555_V560>V(1)|p.Q556_V560>HNLQLY(1)|p.Q556_E561del(1)|p.K558_L576>NV(1)|p.Q556_E561>HH(1)|p.W557_V560>F(1)|p.W557_I571del(1)|p.V559_L576del(1)|p.E554_N564del(1)|p.Q556_V560>TTF(1)|p.V559_E562del(1)|p.Q556_D572>H(1)|p.K558_Y570>N(1)|p.M552_D572del(1)|p.Y553_V559>E(1)|p.Q556_T574del(1)|p.P551_V559del>L(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.Q556_V559>HT(1)|p.E554_E562del(1)|p.Y553_V559del(1)|p.K558_G565>R(1)|p.V559_P573>A(1)|p.K558_V560>M(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGTGGAAGGTTGTTGAGGAG	0.388		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														0	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	267	Deletion - In frame(132)|Substitution - Missense(87)|Complex - deletion inframe(45)|Complex - compound substitution(2)|Complex - insertion inframe(1)	soft_tissue(257)|skin(8)|testis(1)|haematopoietic_and_lymphoid_tissue(1)	GRCh37	CM013551	KIT	M	rs121913517						80.0	82.0	82.0					4																	55593610		2203	4300	6503	SO:0001583	missense	0	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1676T>G	4.37:g.55593610T>G	ENSP00000288135:p.Val559Gly		B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	pirsf_Tyr_kinase_CSF1/PDGF_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_Ig_I-set,pfam_Immunoglobulin,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom	p.V559G	ENST00000288135.5	37	c.1676	CCDS3496.1	4	.	.	.	.	.	.	.	.	.	.	T	24.4	4.526245	0.85600	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.95272	-3.66;-3.66	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.56097	D	0.000032	D	0.97377	0.9142	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.999;0.998	D	0.97974	1.0345	10	0.87932	D	0	.	16.6003	0.84812	0.0:0.0:0.0:1.0	.	66;555;559	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	G	559;555	ENSP00000288135:V559G;ENSP00000390987:V555G	ENSP00000288135:V559G	V	+	2	0	KIT	55288367	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.880000	0.87243	2.319000	0.78375	0.533000	0.62120	GTT	0	pirsf_Tyr_kinase_CSF1/PDGF_rcpt,superfamily_Kinase-like_dom		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIT	protein_coding	OTTHUMT00000250618.1	40	408	0	0.00	0	0	T		rs121913517	T->A,C,G		55593610	1	no_errors	ENST00000288135	ensembl	human	known	74_37	missense	54	389	32.5	24.32	26	125	SNP	1	G
GPR98	84059	genome.wustl.edu	37	5	90059169	90059169	+	Silent	SNP	G	G	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr5:90059169G>C	ENST00000405460.2	+	59	12264	c.12168G>C	c.(12166-12168)gtG>gtC	p.V4056V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4056	Calx-beta 27. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATTCATATGTGACATTGACGG	0.418																																							0											0													68.0	64.0	65.0					5																	90059169		1862	4105	5967	SO:0001819	synonymous_variant	0			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12168G>C	5.37:g.90059169G>C			O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	pfam_Calx_beta,pfam_EPTP,pfam_GPCR_2_secretin-like,pfam_GPS_dom,superfamily_ConA-like_lec_gl_sf,superfamily_Gal_Oxase/kelch_b-propeller,smart_Calx_beta,pfscan_EAR,pfscan_GPS_dom,pfscan_GPCR_2-like	p.V4056	ENST00000405460.2	37	c.12168	CCDS47246.1	5																																																																																			0	pfam_Calx_beta,smart_Calx_beta		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR98	protein_coding	OTTHUMT00000369993.2	28	274	0	0.00	0	0	G	NM_032119	0	0		90059169	1	no_errors	ENST00000405460	ensembl	human	known	74_37	silent	24	147	29.41	29.38	10	62	SNP	1	C
SLC18B1	116843	genome.wustl.edu	37	6	133095445	133095445	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr6:133095445C>T	ENST00000275227.4	-	9	1001	c.905G>A	c.(904-906)aGg>aAg	p.R302K	SLC18B1_ENST00000538764.1_Missense_Mutation_p.R176K|SLC18B1_ENST00000367918.1_3'UTR	NM_052831.2	NP_439896.1	Q6NT16	S18B1_HUMAN	solute carrier family 18, subfamily B, member 1	302					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)											AAGCCATTTCCTTAGAGGCTG	0.383																																							0											0													93.0	97.0	95.0					6																	133095445		2203	4300	6503	SO:0001583	missense	0			AK124442	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409		"""Solute carriers"""	21573	protein-coding gene	gene with protein product		613361	"""chromosome 6 open reading frame 192"""	C6orf192		19697161	Standard	XM_006715328		Approved	dJ55C23.6	uc003qdw.1	Q6NT16	OTTHUMG00000015595	ENST00000275227.4:c.905G>A	6.37:g.133095445C>T	ENSP00000275227:p.Arg302Lys		A8K1K3|B3KW77|Q6ISF2	Missense_Mutation	SNP	pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom	p.R302K	ENST00000275227.4	37	c.905	CCDS5163.1	6	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033245	0.35893	.	.	ENSG00000146409	ENST00000275227;ENST00000538764	T;T	0.63255	-0.03;-0.03	5.32	5.32	0.75619	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.61476	0.2350	L	0.52011	1.625	0.80722	D	1	D;B	0.76494	0.999;0.083	D;B	0.80764	0.994;0.086	T	0.60239	-0.7302	10	0.02654	T	1	-15.633	18.1369	0.89622	0.0:1.0:0.0:0.0	.	176;302	B7Z1S5;Q6NT16	.;CF192_HUMAN	K	302;176	ENSP00000275227:R302K;ENSP00000444098:R176K	ENSP00000275227:R302K	R	-	2	0	C6orf192	133137138	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.268000	0.72552	2.625000	0.88918	0.655000	0.94253	AGG	0	pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom		0.383	SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC18B1	protein_coding	OTTHUMT00000042273.1	106	193	0	0.51	0	1	C	NM_052831	0	0		133095445	-1	no_errors	ENST00000275227	ensembl	human	known	74_37	missense	79	113	28.18	35.96	31	64	SNP	1	T
MCMDC2	157777	genome.wustl.edu	37	8	67790820	67790820	+	Missense_Mutation	SNP	A	A	G	rs200037793		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr8:67790820A>G	ENST00000422365.2	+	6	664	c.493A>G	c.(493-495)Ata>Gta	p.I165V	MCMDC2_ENST00000313616.5_Missense_Mutation_p.I165V|MCMDC2_ENST00000492775.1_Missense_Mutation_p.I165V|MCMDC2_ENST00000469823.1_3'UTR|MCMDC2_ENST00000541540.1_Missense_Mutation_p.I102V|MCMDC2_ENST00000396592.3_Missense_Mutation_p.I165V	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	165					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						ATTTCAGTATATAAGAGTGCA	0.308													A|||	1	0.000199681	0.0008	0.0	5008	,	,		13153	0.0		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0													126.0	130.0	128.0					8																	67790820		2203	4298	6501	SO:0001583	missense	0			BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.493A>G	8.37:g.67790820A>G	ENSP00000413632:p.Ile165Val		B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	pfam_MCM_DNA-dep_ATPase,superfamily_NA-bd_OB-fold,superfamily_P-loop_NTPase,smart_MCM_DNA-dep_ATPase	p.I165V	ENST00000422365.2	37	c.493	CCDS6197.2	8	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	12.80	2.046644	0.36085	.	.	ENSG00000178460	ENST00000379356;ENST00000396592;ENST00000422365;ENST00000492775;ENST00000313616;ENST00000541540	T;T;T;T;T	0.28895	3.69;3.69;3.69;3.69;1.59	5.36	2.89	0.33648	.	0.048726	0.85682	N	0.000000	T	0.22322	0.0538	L	0.39397	1.21	0.39998	D	0.975131	B;B;B;B	0.18863	0.031;0.018;0.018;0.031	B;B;B;B	0.19666	0.026;0.012;0.012;0.026	T	0.07028	-1.0794	10	0.15952	T	0.53	-3.1743	9.8747	0.41195	0.8579:0.0:0.1421:0.0	.	102;165;165;165	Q4G0Z9-4;Q4G0Z9;B4DXX4;G3XAN3	.;CH045_HUMAN;.;.	V	37;165;165;165;165;102	ENSP00000379837:I165V;ENSP00000413632:I165V;ENSP00000428037:I165V;ENSP00000317234:I165V;ENSP00000445629:I102V	ENSP00000317234:I165V	I	+	1	0	C8orf45	67953374	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.903000	0.56318	0.310000	0.22990	-0.353000	0.07706	ATA	0	superfamily_NA-bd_OB-fold,smart_MCM_DNA-dep_ATPase		0.308	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MCMDC2	protein_coding	OTTHUMT00000347350.1	37	304	0	0.00	0	0	A	NM_173518	rs200037793	A->G		67790820	1	no_errors	ENST00000422365	ensembl	human	known	74_37	missense	99	156	33.56	35.27	50	85	SNP	1	G
GDF6	392255	genome.wustl.edu	37	8	97157553	97157553	+	Silent	SNP	C	C	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr8:97157553C>G	ENST00000287020.5	-	2	705	c.606G>C	c.(604-606)ctG>ctC	p.L202L		NM_001001557.2	NP_001001557.1	Q6KF10	GDF6_HUMAN	growth differentiation factor 6	202					activin receptor signaling pathway (GO:0032924)|apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|growth (GO:0040007)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal cell apoptotic process (GO:1990009)	extracellular space (GO:0005615)				breast(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27	Breast(36;2.67e-05)					CCTGCGGGTCCAGGGTCCGCG	0.741																																							0											0													2.0	3.0	3.0					8																	97157553		1647	3446	5093	SO:0001819	synonymous_variant	0				CCDS34926.1	8q22.1	2014-01-29			ENSG00000156466	ENSG00000156466			4221	protein-coding gene	gene with protein product		601147	"""segmentation syndrome 1"""	SGM1		10022976, 18425797	Standard	NM_001001557		Approved	BMP13, KFS, KFS1	uc003yhp.3	Q6KF10	OTTHUMG00000164710	ENST00000287020.5:c.606G>C	8.37:g.97157553C>G			Q6PI58	Silent	SNP	pfam_TGF-b_C,pfam_TGF-b_N,smart_TGF-b_C	p.L202	ENST00000287020.5	37	c.606	CCDS34926.1	8																																																																																			0	pfam_TGF-b_N		0.741	GDF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GDF6	protein_coding	OTTHUMT00000379862.2	8	20	0	0.00	0	0	C	NM_001001557	0	0		97157553	-1	no_errors	ENST00000287020	ensembl	human	known	74_37	silent	2	21	66.67	40.00	4	14	SNP	0.998	G
POP1	10940	genome.wustl.edu	37	8	99169924	99169924	+	Missense_Mutation	SNP	G	G	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr8:99169924G>A	ENST00000401707.2	+	16	2581	c.2500G>A	c.(2500-2502)Ggc>Agc	p.G834S	POP1_ENST00000349693.3_Missense_Mutation_p.G834S	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	834					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GCGAGCTCCCGGCAGAGGCCA	0.587																																							0											0													36.0	41.0	40.0					8																	99169924		2203	4300	6503	SO:0001583	missense	0			D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.2500G>A	8.37:g.99169924G>A	ENSP00000385787:p.Gly834Ser		A8K5W9|Q15037	Missense_Mutation	SNP	pfam_RNase_P/MRP_POP1,pfam_POPLD	p.G834S	ENST00000401707.2	37	c.2500	CCDS6277.1	8	.	.	.	.	.	.	.	.	.	.	G	2.062	-0.415135	0.04766	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.10573	2.86;2.86	5.77	-8.53	0.00916	.	1.164950	0.05877	N	0.625723	T	0.04952	0.0133	L	0.31294	0.92	0.09310	N	1	B	0.17852	0.024	B	0.08055	0.003	T	0.39941	-0.9589	10	0.09084	T	0.74	-9.0474	3.511	0.07708	0.5326:0.0907:0.1151:0.2616	.	834	Q99575	POP1_HUMAN	S	834	ENSP00000385787:G834S;ENSP00000339529:G834S	ENSP00000339529:G834S	G	+	1	0	POP1	99239100	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.558000	0.05978	-1.684000	0.01443	-1.394000	0.01149	GGC	0	NULL		0.587	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POP1	protein_coding	OTTHUMT00000379470.1	58	123	1.64	0.00	1	0	G	NM_015029	0	0		99169924	1	no_errors	ENST00000349693	ensembl	human	known	74_37	missense	23	57	28.12	33.72	9	29	SNP	0	A
CARD17	440068	genome.wustl.edu	37	11	104970124	104970124	+	Missense_Mutation	SNP	G	G	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr11:104970124G>T	ENST00000375707.1	-	3	315	c.299C>A	c.(298-300)aCt>aAt	p.T100N	CASP1_ENST00000598974.1_Intron|CASP1_ENST00000593315.1_Intron|CASP1_ENST00000594519.1_Intron|CARD16_ENST00000525374.1_Intron|CASP1_ENST00000415981.2_Intron	NM_001007232.1	NP_001007233.1	Q5XLA6	CAR17_HUMAN	caspase recruitment domain family, member 17	100					regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	6						ATCTTGTGTAGTAAGGTGATT	0.383																																							0											0													126.0	119.0	121.0					11																	104970124		2202	4299	6501	SO:0001583	missense	0				CCDS31662.1	11q22.3	2009-01-13				ENSG00000255221			33827	protein-coding gene	gene with protein product	"""Inhibitory CARD"""	609490				15383541	Standard	NM_001007232		Approved	INCA	uc001pir.1	Q5XLA6		ENST00000375707.1:c.299C>A	11.37:g.104970124G>T	ENSP00000364859:p.Thr100Asn			Missense_Mutation	SNP	pfam_CARD,superfamily_DEATH-like_dom,smart_CARD,pfscan_CARD	p.T100N	ENST00000375707.1	37	c.299	CCDS31662.1	11	.	.	.	.	.	.	.	.	.	.	.	0	-2.596598	0.00125	.	.	ENSG00000255221	ENST00000375707	T	0.17854	2.25	1.6	-3.2	0.05156	.	.	.	.	.	T	0.05456	0.0144	N	0.04297	-0.235	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31668	-0.9935	9	0.08837	T	0.75	.	5.3838	0.16206	0.0:0.2862:0.4889:0.2249	.	100	Q5XLA6	CAR17_HUMAN	N	100	ENSP00000364859:T100N	ENSP00000364859:T100N	T	-	2	0	CARD17	104475334	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.349000	0.00069	-2.726000	0.00386	-0.687000	0.03738	ACT	0	NULL		0.383	CARD17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CARD17	protein_coding	OTTHUMT00000388181.1	47	210	0	0.94	0	2	G	NM_001007232	0	0		104970124	-1	no_errors	ENST00000375707	ensembl	human	known	74_37	missense	38	109	26.92	32.30	14	52	SNP	0	T
CRIP2	1397	genome.wustl.edu	37	14	105939835	105939835	+	5'Flank	SNP	A	A	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr14:105939835A>C	ENST00000329146.4	+	0	0				CRIP2_ENST00000483017.3_Missense_Mutation_p.Q84P|RP11-521B24.5_ENST00000552675.1_RNA	NM_001312.3	NP_001303.1	P52943	CRIP2_HUMAN	cysteine-rich protein 2						hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	cell cortex (GO:0005938)	zinc ion binding (GO:0008270)			lung(2)	2		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.235)		CTGGTGCACCAGGCAGAGGGA	0.627																																							0											0																																										SO:0001631	upstream_gene_variant	0				CCDS10003.1, CCDS59246.1	14q32.3	2008-08-11			ENSG00000182809	ENSG00000182809			2361	protein-coding gene	gene with protein product		601183				8843343, 10681529	Standard	NM_001312		Approved	CRP2, ESP1	uc031qqr.1	P52943	OTTHUMG00000029906		14.37:g.105939835A>C	Exception_encountered		A1A4U1|B7Z6C0|E9PD13	Missense_Mutation	SNP	pfam_Znf_LIM,smart_Znf_LIM,pfscan_Znf_LIM	p.Q84P	ENST00000329146.4	37	c.251	CCDS10003.1	14	.	.	.	.	.	.	.	.	.	.	A	5.699	0.313481	0.10789	.	.	ENSG00000182809	ENST00000483017	T	0.72051	-0.62	1.64	1.64	0.23874	.	.	.	.	.	T	0.71888	0.3393	.	.	.	0.20196	N	0.999928	P	0.52061	0.95	P	0.53490	0.727	T	0.60601	-0.7231	8	0.72032	D	0.01	.	5.3584	0.16073	1.0:0.0:0.0:0.0	.	84	B7Z6C0	.	P	84	ENSP00000426119:Q84P	ENSP00000426119:Q84P	Q	+	2	0	CRIP2	105010880	0.000000	0.05858	0.008000	0.14137	0.024000	0.10985	-0.327000	0.07955	1.022000	0.39626	0.329000	0.21502	CAG	0	pfscan_Znf_LIM		0.627	CRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CRIP2	protein_coding	OTTHUMT00000074597.3	58	66	0	0.00	0	0	A	NM_001312	0	0		105939835	1	no_errors	ENST00000483017	ensembl	human	putative	74_37	missense	12	44	40	44.44	8	36	SNP	0.008	C
ATP10A	57194	genome.wustl.edu	37	15	25971102	25971102	+	Silent	SNP	T	T	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr15:25971102T>G	ENST00000356865.6	-	5	1086	c.975A>C	c.(973-975)gcA>gcC	p.A325A		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	325					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ACTTACCGACTGCTGAAAACA	0.587																																							0											0													112.0	92.0	99.0					15																	25971102		2203	4300	6503	SO:0001819	synonymous_variant	0			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.975A>C	15.37:g.25971102T>G			Q4G0S9|Q969I4	Silent	SNP	pfam_ATPase_P-typ_transduc_dom_A,pfam_HAD-like_dom,superfamily_HAD-like_dom,superfamily_ATPase_P-typ_cyto_domN,prints_Cation_transp_P_typ_ATPase,tigrfam_ATPase_P-typ_Plipid-transp,tigrfam_Cation_transp_P_typ_ATPase	p.A325	ENST00000356865.6	37	c.975	CCDS32178.1	15																																																																																			0	pfam_ATPase_P-typ_transduc_dom_A,tigrfam_ATPase_P-typ_Plipid-transp		0.587	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP10A	protein_coding	OTTHUMT00000414830.1	19	73	0	0.00	0	0	T	NM_024490	0	0		25971102	-1	no_errors	ENST00000356865	ensembl	human	known	74_37	silent	8	37	33.33	37.29	4	22	SNP	0.001	G
ALPK3	57538	genome.wustl.edu	37	15	85405949	85405949	+	Nonsense_Mutation	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr15:85405949C>T	ENST00000258888.5	+	10	4986	c.4819C>T	c.(4819-4821)Cga>Tga	p.R1607*		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1607	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCTCTTTGGGCGACTGGTAAG	0.587																																							0											0													58.0	57.0	57.0					15																	85405949		2203	4299	6502	SO:0001587	stop_gained	0			AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4819C>T	15.37:g.85405949C>T	ENSP00000258888:p.Arg1607*		Q9P2L6	Nonsense_Mutation	SNP	pfam_MHCK_EF2_kinase,pfam_Ig_I-set,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_MHCK_EF2_kinase,pfscan_MHCK_EF2_kinase,pfscan_Ig-like_dom	p.R1607*	ENST00000258888.5	37	c.4819	CCDS10333.1	15	.	.	.	.	.	.	.	.	.	.	C	46	12.581377	0.99680	.	.	ENSG00000136383	ENST00000258888	.	.	.	4.97	4.04	0.47022	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.1525	10.4838	0.44708	0.3514:0.6486:0.0:0.0	.	.	.	.	X	1607	.	ENSP00000258888:R1607X	R	+	1	2	ALPK3	83206953	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.639000	0.46570	1.286000	0.44565	0.655000	0.94253	CGA	0	superfamily_Kinase-like_dom,pfscan_MHCK_EF2_kinase		0.587	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALPK3	protein_coding	OTTHUMT00000308997.1	50	196	0	1.01	0	2	C	NM_020778	0	0		85405949	1	no_errors	ENST00000258888	ensembl	human	known	74_37	nonsense	23	94	32.35	38.16	11	58	SNP	1	T
BRD7	29117	genome.wustl.edu	37	16	50357576	50357576	+	Nonsense_Mutation	SNP	A	A	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr16:50357576A>C	ENST00000394688.3	-	12	1524	c.1365T>G	c.(1363-1365)taT>taG	p.Y455*	BRD7_ENST00000394689.2_Nonsense_Mutation_p.Y455*			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	455					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TGACATACGGATAATCTTGGC	0.443																																							0											0													108.0	91.0	97.0					16																	50357576		2198	4300	6498	SO:0001587	stop_gained	0			AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1365T>G	16.37:g.50357576A>C	ENSP00000378180:p.Tyr455*		Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Nonsense_Mutation	SNP	pfam_DUF3512,pfam_Bromodomain,superfamily_Bromodomain,smart_Bromodomain,prints_Bromodomain,pfscan_Bromodomain	p.Y455*	ENST00000394688.3	37	c.1365	CCDS10742.1	16	.	.	.	.	.	.	.	.	.	.	A	37	6.084326	0.97267	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	.	.	.	5.53	-0.728	0.11162	.	0.187371	0.48767	D	0.000165	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.8448	7.115	0.25411	0.3973:0.0:0.4736:0.129	.	.	.	.	X	455	.	ENSP00000378180:Y455X	Y	-	3	2	BRD7	48915077	0.990000	0.36364	0.914000	0.36105	0.920000	0.55202	0.345000	0.19979	-0.161000	0.10983	0.533000	0.62120	TAT	0	pfam_DUF3512		0.443	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	BRD7	protein_coding	OTTHUMT00000256874.3	77	85	0	0.00	0	0	A	NM_013263	0	0		50357576	-1	no_errors	ENST00000394689	ensembl	human	known	74_37	nonsense	16	19	52.94	61.22	18	30	SNP	0.812	C
FOXN1	8456	genome.wustl.edu	37	17	26851036	26851036	+	Missense_Mutation	SNP	A	A	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr17:26851036A>G	ENST00000226247.2	+	1	78	c.49A>G	c.(49-51)Acc>Gcc	p.T17A	FOXN1_ENST00000579795.1_Missense_Mutation_p.T17A	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	17					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					GCCGGGCCCCACCAGACTGGA	0.677																																							0											0													23.0	25.0	24.0					17																	26851036		2203	4299	6502	SO:0001583	missense	0			Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"""Forkhead boxes"""	12765	protein-coding gene	gene with protein product		600838	"""winged-helix nude"", ""Rowett nude"""	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.49A>G	17.37:g.26851036A>G	ENSP00000226247:p.Thr17Ala		B2R9Q7|O15352	Missense_Mutation	SNP	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.T17A	ENST00000226247.2	37	c.49	CCDS11232.1	17	.	.	.	.	.	.	.	.	.	.	A	10.77	1.443388	0.25987	.	.	ENSG00000109101	ENST00000226247	D	0.92446	-3.04	5.03	-8.54	0.00912	.	1.196700	0.05895	N	0.628926	T	0.81351	0.4804	N	0.19112	0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.66472	-0.5915	10	0.26408	T	0.33	.	7.5555	0.27822	0.1782:0.1188:0.5865:0.1165	.	17	O15353	FOXN1_HUMAN	A	17	ENSP00000226247:T17A	ENSP00000226247:T17A	T	+	1	0	FOXN1	23875163	0.076000	0.21285	0.626000	0.29213	0.949000	0.60115	-0.007000	0.12810	-1.346000	0.02211	-0.488000	0.04728	ACC	0	NULL		0.677	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXN1	protein_coding	OTTHUMT00000255832.1	130	51	0	0.00	0	0	A		0	0		26851036	1	no_errors	ENST00000226247	ensembl	human	known	74_37	missense	79	58	20.2	27.50	20	22	SNP	0.071	G
USP32	84669	genome.wustl.edu	37	17	58289456	58289456	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr17:58289456C>T	ENST00000300896.4	-	19	2302	c.2108G>A	c.(2107-2109)cGc>cAc	p.R703H	USP32_ENST00000592339.1_Missense_Mutation_p.R373H	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	703					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ATCTTTGTTGCGAACTGGAAG	0.313																																							0											0													84.0	84.0	84.0					17																	58289456		2203	4297	6500	SO:0001583	missense	0			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2108G>A	17.37:g.58289456C>T	ENSP00000300896:p.Arg703His		Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	pfam_Peptidase_C19/C67,pfam_Pept_C19_DUSP,smart_EF_hand_dom,smart_Pept_C19_DUSP,pfscan_EF_hand_dom,pfscan_Peptidase_C19/C67,prints_Recoverin	p.R703H	ENST00000300896.4	37	c.2108	CCDS32697.1	17	.	.	.	.	.	.	.	.	.	.	C	32	5.119717	0.94385	.	.	ENSG00000170832	ENST00000300896	T	0.54279	0.58	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.66567	0.2802	L	0.55990	1.75	0.80722	D	1	D	0.69078	0.997	P	0.61003	0.882	T	0.69412	-0.5152	10	0.62326	D	0.03	.	18.5194	0.90947	0.0:1.0:0.0:0.0	.	703	Q8NFA0	UBP32_HUMAN	H	703	ENSP00000300896:R703H	ENSP00000300896:R703H	R	-	2	0	USP32	55644238	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.679000	0.84048	2.438000	0.82558	0.655000	0.94253	CGC	0	NULL		0.313	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP32	protein_coding	OTTHUMT00000449235.2	57	395	0	0.50	0	2	C	NM_032582	0	0		58289456	-1	no_errors	ENST00000300896	ensembl	human	known	74_37	missense	152	394	9.52	13.32	16	61	SNP	1	T
RP11-51L5.5	0	genome.wustl.edu	37	17	60366722	60366722	+	RNA	SNP	C	C	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr17:60366722C>T	ENST00000602493.1	-	0	358																											ATCTTTGTTGCGAACTGGAAG	0.308																																							0											0																																												0																															17.37:g.60366722C>T				RNA	SNP	0	NULL	ENST00000602493.1	37	NULL		17																																																																																			0	0		0.308	RP11-51L5.5-002	KNOWN	basic	processed_transcript	ENSG00000263887	pseudogene	OTTHUMT00000467668.1	39	229	0	0.87	0	2	C		0	0		60366722	-1	no_errors	ENST00000602493	ensembl	human	known	74_37	rna	100	268	16.53	24.08	20	85	SNP	1	T
CARD14	79092	genome.wustl.edu	37	17	78182112	78182112	+	Missense_Mutation	SNP	A	A	G			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr17:78182112A>G	ENST00000573882.1	+	23	3519	c.2983A>G	c.(2983-2985)Aag>Gag	p.K995E	RP11-334C17.5_ENST00000572730.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.K995E|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	995					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CGAGCAGAAGAAGGTGGTGTG	0.657																																							0											0													33.0	36.0	35.0					17																	78182112		2198	4298	6496	SO:0001583	missense	0			AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2983A>G	17.37:g.78182112A>G	ENSP00000458715:p.Lys995Glu		B8QQJ3|Q9BVB5	Missense_Mutation	SNP	pfam_CARD,superfamily_DEATH-like_dom,superfamily_P-loop_NTPase,superfamily_PDZ,pfscan_CARD,pfscan_PDZ,pfscan_Guanylate_kin-like	p.K995E	ENST00000573882.1	37	c.2983	CCDS11768.1	17	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060834	0.76074	.	.	ENSG00000141527	ENST00000344227	T	0.17528	2.27	3.92	3.92	0.45320	.	0.276135	0.33712	N	0.004634	T	0.31638	0.0803	M	0.70275	2.135	0.80722	D	1	D	0.61080	0.989	P	0.58331	0.837	T	0.03619	-1.1019	10	0.49607	T	0.09	-39.5438	8.4333	0.32771	0.8022:0.1978:0.0:0.0	.	995	Q9BXL6	CAR14_HUMAN	E	995	ENSP00000344549:K995E	ENSP00000344549:K995E	K	+	1	0	CARD14	75796707	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	3.371000	0.52379	1.651000	0.50673	0.528000	0.53228	AAG	0	superfamily_P-loop_NTPase		0.657	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CARD14	protein_coding	OTTHUMT00000437507.1	110	79	0	1.25	0	1	A		0	0		78182112	1	no_errors	ENST00000344227	ensembl	human	known	74_37	missense	56	77	33.33	28.70	28	31	SNP	1	G
MUC16	94025	genome.wustl.edu	37	19	9016675	9016675	+	Missense_Mutation	SNP	G	G	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr19:9016675G>T	ENST00000397910.4	-	28	38265	c.38062C>A	c.(38062-38064)Ctc>Atc	p.L12688I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12690					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGCTGGGGAGGGAGGATGGA	0.478																																							0											0													51.0	52.0	52.0					19																	9016675		1886	4125	6011	SO:0001583	missense	0			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38062C>A	19.37:g.9016675G>T	ENSP00000381008:p.Leu12688Ile		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	pfam_SEA_dom,smart_SEA_dom,pfscan_SEA_dom	p.L12688I	ENST00000397910.4	37	c.38062	CCDS54212.1	19	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.997781	0.00435	.	.	ENSG00000181143	ENST00000397910	T	0.02015	4.5	1.23	-2.46	0.06461	.	.	.	.	.	T	0.01730	0.0055	L	0.33189	0.99	.	.	.	B	0.16166	0.016	B	0.06405	0.002	T	0.47535	-0.9110	8	0.87932	D	0	.	0.0952	0.00043	0.2886:0.1604:0.2304:0.3206	.	12688	B5ME49	.	I	12688	ENSP00000381008:L12688I	ENSP00000381008:L12688I	L	-	1	0	MUC16	8877675	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-3.279000	0.00197	-2.750000	0.00124	CTC	0	NULL		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC16	protein_coding	OTTHUMT00000402806.1	130	51	0	0.00	0	0	G	NM_024690	0	0		9016675	-1	no_errors	ENST00000397910	ensembl	human	known	74_37	missense	46	20	35.21	25.93	25	7	SNP	0	T
MYBL2	4605	genome.wustl.edu	37	20	42331285	42331285	+	Silent	SNP	C	C	T	rs181688716	byFrequency	TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr20:42331285C>T	ENST00000217026.4	+	8	1234	c.1107C>T	c.(1105-1107)acC>acT	p.T369T	MYBL2_ENST00000396863.4_Silent_p.T345T	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	369					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCAGTGTGACCGAGTACCGCC	0.642													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18237	0.0		0.0	False		,,,				2504	0.0						0.9996,0.0003994											0								C		0,4406		0,0,2203	115.0	111.0	113.0		1107	-4.3	1.0	20		113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYBL2	NM_002466.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		369/701	42331285	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0				CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1107C>T	20.37:g.42331285C>T			B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	pfam_C-myb_C,pfam_SANT/Myb,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom	p.T369	ENST00000217026.4	37	c.1107	CCDS13322.1	20																																																																																			0	NULL		0.642	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYBL2	protein_coding	OTTHUMT00000080408.1	35	80	0	0.00	0	0	C	NM_002466	rs181688716	C->T		42331285	1	no_errors	ENST00000217026	ensembl	human	known	74_37	silent	23	79	30.3	28.83	10	32	SNP	0.962	T
CASS4	57091	genome.wustl.edu	37	20	55028090	55028090	+	Missense_Mutation	SNP	G	G	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr20:55028090G>A	ENST00000360314.3	+	6	2083	c.1858G>A	c.(1858-1860)Gaa>Aaa	p.E620K	CASS4_ENST00000434344.1_Intron|CASS4_ENST00000371336.3_Missense_Mutation_p.E620K	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	620					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AAGAGAAACTGAATCACACCA	0.413																																							0											0													58.0	61.0	60.0					20																	55028090		2203	4300	6503	SO:0001583	missense	0			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1858G>A	20.37:g.55028090G>A	ENSP00000353462:p.Glu620Lys		E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	pfam_Serine_rich,pfam_CAS_DUF3513,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain	p.E620K	ENST00000360314.3	37	c.1858	CCDS33492.1	20	.	.	.	.	.	.	.	.	.	.	G	34	5.400662	0.96030	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.25414	1.8;1.8	6.17	6.17	0.99709	CAS family, DUF3513 (1);	0.734154	0.13562	N	0.378746	T	0.52158	0.1717	M	0.68317	2.08	0.52501	D	0.999957	D;D;D	0.69078	0.961;0.997;0.993	P;P;D	0.63113	0.764;0.856;0.911	T	0.37502	-0.9703	10	0.52906	T	0.07	-12.9138	20.8794	0.99867	0.0:0.0:1.0:0.0	.	566;620;620	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	K	620	ENSP00000353462:E620K;ENSP00000360387:E620K	ENSP00000353462:E620K	E	+	1	0	CASS4	54461497	0.770000	0.28543	0.228000	0.23943	0.186000	0.23388	2.419000	0.44671	2.941000	0.99782	0.655000	0.94253	GAA	0	pfam_CAS_DUF3513		0.413	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CASS4	protein_coding	OTTHUMT00000079789.2	62	322	0	0.00	0	0	G	NM_020356	0	0		55028090	1	no_errors	ENST00000360314	ensembl	human	known	74_37	missense	52	260	35	23.08	28	78	SNP	0.961	A
CASS4	57091	genome.wustl.edu	37	20	55028092	55028092	+	Missense_Mutation	SNP	A	A	T			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr20:55028092A>T	ENST00000360314.3	+	6	2085	c.1860A>T	c.(1858-1860)gaA>gaT	p.E620D	CASS4_ENST00000434344.1_Intron|CASS4_ENST00000371336.3_Missense_Mutation_p.E620D	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	620					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						GAGAAACTGAATCACACCAAA	0.403																																							0											0													58.0	61.0	60.0					20																	55028092		2203	4300	6503	SO:0001583	missense	0			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1860A>T	20.37:g.55028092A>T	ENSP00000353462:p.Glu620Asp		E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	pfam_Serine_rich,pfam_CAS_DUF3513,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain	p.E620D	ENST00000360314.3	37	c.1860	CCDS33492.1	20	.	.	.	.	.	.	.	.	.	.	A	8.978	0.974509	0.18736	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.21932	1.98;1.98	6.17	-8.81	0.00813	CAS family, DUF3513 (1);	0.734154	0.13562	N	0.378746	T	0.10981	0.0268	L	0.41415	1.275	0.23107	N	0.998287	B;B;B	0.24882	0.031;0.113;0.053	B;B;B	0.25884	0.047;0.038;0.064	T	0.18209	-1.0344	10	0.26408	T	0.33	-12.9138	6.0965	0.20023	0.1194:0.2224:0.4994:0.1587	.	566;620;620	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	D	620	ENSP00000353462:E620D;ENSP00000360387:E620D	ENSP00000353462:E620D	E	+	3	2	CASS4	54461499	0.000000	0.05858	0.001000	0.08648	0.171000	0.22731	-0.456000	0.06754	-1.106000	0.03008	-0.250000	0.11733	GAA	0	pfam_CAS_DUF3513		0.403	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CASS4	protein_coding	OTTHUMT00000079789.2	61	322	0	0.00	0	0	A	NM_020356	0	0		55028092	1	no_errors	ENST00000360314	ensembl	human	known	74_37	missense	53	261	34.57	23.24	28	79	SNP	0	T
KLHL29	114818	genome.wustl.edu	37	2	23919269	23919270	+	Frame_Shift_Ins	INS	-	-	CCTCGTCT			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	-	-	-	CCTCGTCT	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr2:23919269_23919270insCCTCGTCT	ENST00000486442.1	+	11	2708_2709	c.1991_1992insCCTCGTCT	c.(1990-1995)aacctcfs	p.-667fs		NM_052920.1	NP_443152.1	Q96CT2	KLH29_HUMAN	kelch-like family member 29											breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|lung(1)|ovary(3)	10						GATAACTGGAACCTCGTCTCCA	0.599																																							0											0																																										SO:0001589	frameshift_variant	0				CCDS54335.1	2p23.3	2013-09-27	2013-02-22	2007-01-09	ENSG00000119771	ENSG00000119771		"""Kelch-like"", ""BTB/POZ domain containing"""	29404	protein-coding gene	gene with protein product			"""kelch repeat and BTB (POZ) domain containing 9"", ""kelch-like 29 (Drosophila)"""	KBTBD9		11572484	Standard	NM_052920		Approved	KIAA1921	uc010ykg.2	Q96CT2	OTTHUMG00000151899	ENST00000486442.1:c.1992_1999dupCCTCGTCT	2.37:g.23919270_23919277dupCCTCGTCT	ENSP00000420659:p.Ser667fs		Q8N388|Q96BF0|Q96PW7	Frame_Shift_Ins	INS	pfam_Kelch_1,pfam_BACK,pfam_Kelch_2,pfam_BTB_POZ,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,smart_BACK,smart_Kelch_1,pfscan_BTB/POZ-like	p.S668fs	ENST00000486442.1	37	c.1991_1992	CCDS54335.1	2																																																																																			0	smart_Kelch_1		0.599	KLHL29-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	KLHL29	protein_coding	OTTHUMT00000324315.3	46	164	0	0.00	0	0	0	NM_052920	0	0		23919270	1	no_errors	ENST00000486442	ensembl	human	known	74_37	frame_shift_ins	21	119	27.59	9.16	8	12	INS	1.000:1.000	CCTCGTCT
CHD8	57680	genome.wustl.edu	37	14	21868216	21868216	+	Frame_Shift_Del	DEL	C	C	-			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr14:21868216delC	ENST00000557364.1	-	25	5004	c.4741delG	c.(4741-4743)gtafs	p.V1581fs	SNORD8_ENST00000363915.1_RNA|CHD8_ENST00000555962.1_5'UTR|CHD8_ENST00000430710.3_Frame_Shift_Del_p.V1302fs|CHD8_ENST00000399982.2_Frame_Shift_Del_p.V1581fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1581					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		AGCATTCGTACCCGCAACAGT	0.438																																							0											0													212.0	205.0	207.0					14																	21868216		1916	4132	6048	SO:0001589	frameshift_variant	0			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.4741delG	14.37:g.21868216delC	ENSP00000451601:p.Val1581fs		Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	pfam_SNF2_N,pfam_Chromo_domain,pfam_BRK_domain,pfam_Helicase_C,pfam_Helicase/UvrB_dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,superfamily_P-loop_NTPase,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,smart_BRK_domain,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.V1581fs	ENST00000557364.1	37	c.4741	CCDS53885.1	14																																																																																			0	NULL		0.438	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CHD8	protein_coding	OTTHUMT00000410436.1	42	219	0	0.00	0	0	C	NM_020920	0	0		21868216	-1	no_errors	ENST00000399982	ensembl	human	known	74_37	frame_shift_del	30	137	40	31.50	20	63	DEL	1	0
QRICH2	84074	genome.wustl.edu	37	17	74273351	74273351	+	Frame_Shift_Del	DEL	G	G	-	rs367825841		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr17:74273351delG	ENST00000262765.5	-	16	4839	c.4660delC	c.(4660-4662)cggfs	p.R1555fs		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1555										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CCGCAGCGCCGGGGCACAGTT	0.607																																							0											0													42.0	50.0	47.0					17																	74273351		2203	4300	6503	SO:0001589	frameshift_variant	0			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.4660delC	17.37:g.74273351delG	ENSP00000262765:p.Arg1555fs		A2RRE1|Q96LM3	Frame_Shift_Del	DEL	NULL	p.R1554fs	ENST00000262765.5	37	c.4660	CCDS32741.1	17																																																																																			0	NULL		0.607	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	QRICH2	protein_coding	OTTHUMT00000395140.1	104	80	0	0.00	0	0	G	NM_032134	0	0		74273351	-1	no_errors	ENST00000262765	ensembl	human	known	74_37	frame_shift_del	57	61	20.83	33.70	15	31	DEL	0.91	0
HMGB1P5	10354	genome.wustl.edu	37	3	22424272	22424272	+	RNA	SNP	T	T	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr3:22424272T>C	ENST00000451497.1	+	0	837									high mobility group box 1 pseudogene 5																		TCATCTTCAGTTGTCTCTGAT	0.353																																							0											0																																												0			AF076677		3p24	2011-09-21	2011-04-05	2010-10-15	ENSG00000132967	ENSG00000132967		"""High mobility group / HMG-box pseudogenes"""	4997	pseudogene	pseudogene			"""high-mobility group (nonhistone chromosomal) protein 1-like 5"", ""high-mobility group (nonhistone chromosomal) protein 1-like 5 pseudogene"", ""high-mobility group box 1-like 5 pseudogene"", ""high-mobility group box 1-like 15"", ""high-mobility group box 1 pseudogene 2"", ""high-mobility group box 1-like 5"", ""high-mobility group box 1 pseudogene 5"""	HMG1L5, HMGB1L15, HMGB1P2, HMGB1L5		9925949	Standard	NG_000897		Approved				OTTHUMG00000155591		3.37:g.22424272T>C				RNA	SNP	0	NULL	ENST00000451497.1	37	NULL		3																																																																																			0	0		0.353	HMGB1P5-002	KNOWN	basic	processed_transcript	HMGB1P5	pseudogene	OTTHUMT00000340803.1	21	0	0	0.00	0	0	T	NG_000897	0	0		22424272	1	no_errors	ENST00000451497	ensembl	human	known	74_37	rna	40	0	13.04	0.00	6	0	SNP	0.995	C
RP11-93K22.13	0	genome.wustl.edu	37	3	129810213	129810213	+	lincRNA	SNP	C	C	T	rs557466292		TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr3:129810213C>T	ENST00000514010.1	-	0	248				ALG1L2_ENST00000507643.1_RNA																							GTTCAGGGCCCGGTAGGCCTC	0.617													c|||	1	0.000199681	0.0	0.0014	5008	,	,		17323	0.0		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0																																												0																															3.37:g.129810213C>T				RNA	SNP	0	NULL	ENST00000514010.1	37	NULL		3																																																																																			0	0		0.617	RP11-93K22.13-001	KNOWN	basic	lincRNA	ALG1L2	lincRNA	OTTHUMT00000358040.1	52	0	0	0.00	0	0	C		rs557466292	C->T		129810213	1	no_errors	ENST00000503500	ensembl	human	known	74_37	rna	19	0	26.92	0.00	7	0	SNP	0.97	T
PPIA	5478	genome.wustl.edu	37	7	44840986	44840986	+	Missense_Mutation	SNP	A	A	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr7:44840986A>C	ENST00000468812.1	+	5	508	c.463A>C	c.(463-465)Aag>Cag	p.K155Q	PPIA_ENST00000480603.1_3'UTR|PPIA_ENST00000489459.1_Missense_Mutation_p.K95Q|PPIA_ENST00000355968.6_Missense_Mutation_p.K95Q	NM_021130.3	NP_066953.1	P62937	PPIA_HUMAN	peptidylprolyl isomerase A (cyclophilin A)	155	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				blood coagulation (GO:0007596)|entry into host cell (GO:0030260)|establishment of integrated proviral latency (GO:0075713)|leukocyte migration (GO:0050900)|lipid particle organization (GO:0034389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of protein secretion (GO:0050714)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of viral genome replication (GO:0045069)|RNA-dependent DNA replication (GO:0006278)|uncoating of virus (GO:0019061)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral release from host cell (GO:0019076)|virion assembly (GO:0019068)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Cyclosporine(DB00091)|L-Proline(DB00172)	GACCAGCAAGAAGATCACCAT	0.478																																					Pancreas(95;605 727 734 1731 12572 23104 24406 38694 39103 44805)		0											0													44.0	38.0	40.0					7																	44840986		2202	4280	6482	SO:0001583	missense	0			X52851	CCDS5494.1, CCDS75592.1	7p13	2010-03-23			ENSG00000196262	ENSG00000196262	5.2.1.8		9253	protein-coding gene	gene with protein product		123840				1989998, 2197089	Standard	XM_005249791		Approved	CYPA	uc003tlw.3	P62937	OTTHUMG00000023687	ENST00000468812.1:c.463A>C	7.37:g.44840986A>C	ENSP00000419425:p.Lys155Gln		A8K220|P05092|Q3KQW3|Q567Q0|Q6IBU5|Q96IX3|Q9BRU4|Q9BTY9|Q9UC61	Missense_Mutation	SNP	pfam_Cyclophilin-like_PPIase_dom,superfamily_Cyclophilin-like_PPIase_dom,pfscan_Cyclophilin-like_PPIase_dom,prints_Cyclophilin-like_PPIase_dom	p.K155Q	ENST00000468812.1	37	c.463	CCDS5494.1	7	.	.	.	.	.	.	.	.	.	.	A	17.40	3.380359	0.61845	.	.	ENSG00000196262	ENST00000468812;ENST00000489459;ENST00000355968;ENST00000395070;ENST00000244636	T;T;T	0.45276	0.9;0.9;0.9	4.86	4.86	0.63082	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.053667	0.64402	U	0.000001	T	0.36276	0.0961	L	0.38953	1.18	0.44719	D	0.99771	B	0.16802	0.019	B	0.22386	0.039	T	0.19582	-1.0301	10	0.56958	D	0.05	.	14.1228	0.65201	1.0:0.0:0.0:0.0	.	155	P62937	PPIA_HUMAN	Q	155;95;95;119;95	ENSP00000419425:K155Q;ENSP00000427976:K95Q;ENSP00000430817:K95Q	ENSP00000442606:K95Q	K	+	1	0	PPIA	44807511	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.973000	0.76116	1.821000	0.53095	0.377000	0.23210	AAG	0	pfam_Cyclophilin-like_PPIase_dom,superfamily_Cyclophilin-like_PPIase_dom,pfscan_Cyclophilin-like_PPIase_dom		0.478	PPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPIA	protein_coding	OTTHUMT00000251293.1	45	0	2.17	0.00	1	0	A	NM_021130	0	0		44840986	1	no_errors	ENST00000468812	ensembl	human	known	74_37	missense	34	0	15	0.00	6	0	SNP	1	C
GLIDR	389741	genome.wustl.edu	37	9	66554510	66554510	+	lincRNA	SNP	C	C	A			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr9:66554510C>A	ENST00000305709.5	+	0	1123				RP11-262H14.3_ENST00000445604.2_lincRNA	NR_015363.1																						CCTTTGACCTCATTGTGGTCC	0.512																																							0											0																																												0																															9.37:g.66554510C>A				RNA	SNP	0	NULL	ENST00000305709.5	37	NULL		9																																																																																			0	0		0.512	RP11-262H14.4-001	KNOWN	basic	lincRNA	MGC21881	lincRNA	OTTHUMT00000037077.1	429	0	0	0.00	0	0	C		0	0		66554510	1	no_errors	ENST00000305709	ensembl	human	known	74_37	rna	252	0	11.76	0.00	34	0	SNP	0	A
GOLGA6L17P	642402	genome.wustl.edu	37	15	85053254	85053254	+	RNA	SNP	T	T	C			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr15:85053254T>C	ENST00000414190.2	-	0	198					NR_003246.2																						TACCAACAGCTTCTCCACTCA	0.577																																							0											0																																												0																															15.37:g.85053254T>C				RNA	SNP	0	NULL	ENST00000414190.2	37	NULL		15																																																																																			0	0		0.577	GOLGA6L5-003	KNOWN	mRNA_end_NF|basic	processed_transcript	GOLGA6L5	pseudogene	OTTHUMT00000418579.1	18	0	0	0.00	0	0	T		0	0		85053254	-1	no_errors	ENST00000414190	ensembl	human	known	74_37	rna	11	0	21.43	0.00	3	0	SNP	0.973	C
CTNND2	1501	genome.wustl.edu	37	5	11385097	11385112	+	Frame_Shift_Del	DEL	GCCGAGCCGCCGCGCT	GCCGAGCCGCCGCGCT	-			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	GCCGAGCCGCCGCGCT	GCCGAGCCGCCGCGCT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr5:11385097_11385112delGCCGAGCCGCCGCGCT	ENST00000304623.8	-	7	1031_1046	c.842_857delAGCGCGGCGGCTCGGC	c.(841-858)cagcgcggcggctcggccfs	p.QRGGSA281fs	CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000495388.2_5'Flank|CTNND2_ENST00000359640.2_Frame_Shift_Del_p.QRGGSA281fs|CTNND2_ENST00000511377.1_Frame_Shift_Del_p.QRGGSA190fs|CTNND2_ENST00000503622.1_Intron	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	281					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A286T(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						gccctcgggggccgagccgccgcgctgcagcttggt	0.778																																							0											1	Substitution - Missense(1)	endometrium(1)																																								SO:0001589	frameshift_variant	0			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.842_857delAGCGCGGCGGCTCGGC	5.37:g.11385097_11385112delGCCGAGCCGCCGCGCT	ENSP00000307134:p.Gln281fs		B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Frame_Shift_Del	DEL	pfam_Armadillo,superfamily_ARM-type_fold,smart_Armadillo,pfscan_Armadillo	p.Q281fs	ENST00000304623.8	37	c.857_842	CCDS3881.1	5																																																																																			0	NULL		0.778	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTNND2	protein_coding	OTTHUMT00000206999.1	57	12	0	0.00	0	0	GCCGAGCCGCCGCGCT	NM_001332	0	0		11385112	-1	no_errors	ENST00000304623	ensembl	human	known	74_37	frame_shift_del	24	8	22.58	0.00	7	0	DEL	1.000:1.000:0.994:1.000:1.000:0.999:1.000:1.000:0.996:1.000:1.000:1.000:1.000:1.000:1.000:1.000	0
MED15	51586	genome.wustl.edu	37	22	20918817	20918819	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-XU-A933-01A-11D-A423-09	TCGA-XU-A933-10A-01D-A426-09	CAG	CAG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	efc5c6fb-4660-49ff-acd5-ed6ae94a2881	11407dd0-5b1d-46b8-a640-3c2ae4071034	g.chr22:20918817_20918819delCAG	ENST00000263205.7	+	6	601_603	c.532_534delCAG	c.(532-534)cagdel	p.Q188del	MED15_ENST00000406969.1_In_Frame_Del_p.Q162del|MED15_ENST00000542773.1_5'UTR|MED15_ENST00000382974.2_In_Frame_Del_p.Q117del|MED15_ENST00000425759.2_In_Frame_Del_p.Q77del|MED15_ENST00000541476.1_In_Frame_Del_p.Q162del|MED15_ENST00000292733.7_In_Frame_Del_p.Q188del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	188	Poly-Gln.				gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			ggcggcgctacagcagcagcagc	0.626											OREG0026319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											0											0																																										SO:0001651	inframe_deletion	0			AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.532_534delCAG	22.37:g.20918826_20918828delCAG	ENSP00000263205:p.Gln188del	744	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Del	DEL	pfam_Mediator_Med15_met	p.Q181in_frame_del	ENST00000263205.7	37	c.532_534	CCDS33602.1	22																																																																																			0	pfam_Mediator_Med15_met		0.626	MED15-004	KNOWN	basic|CCDS	protein_coding	MED15	protein_coding	OTTHUMT00000320177.2	41	4	2.38	0.00	1	0	CAG	NM_015889	0	0		20918819	1	no_errors	ENST00000263205	ensembl	human	known	74_37	in_frame_del	20	4	13.04	0.00	3	0	DEL	0.686:0.761:0.805	0
