#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
DNAJC27	51277	genome.wustl.edu	37	2	25174396	25174396	+	Missense_Mutation	SNP	A	A	G			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr2:25174396A>G	ENST00000264711.2	-	6	745	c.556T>C	c.(556-558)Tgt>Cgt	p.C186R	DNAJC27_ENST00000534855.1_Missense_Mutation_p.C115R	NM_001198559.1|NM_016544.2	NP_001185488.1|NP_057628.1	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27	186					small GTPase mediated signal transduction (GO:0007264)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						CCATTTTCACATAAATCAACT	0.368																																							0											0													72.0	73.0	73.0					2																	25174396		2203	4300	6503	SO:0001583	missense	0				CCDS1716.1, CCDS74493.1	2p23.3	2011-09-02	2008-08-20	2008-08-20	ENSG00000115137	ENSG00000115137		"""Heat shock proteins / DNAJ (HSP40)"""	30290	protein-coding gene	gene with protein product		613527	"""rab and DnaJ domain containing"""	RBJ		14980719	Standard	NM_016544		Approved	RabJS	uc002rft.2	Q9NZQ0	OTTHUMG00000125524	ENST00000264711.2:c.556T>C	2.37:g.25174396A>G	ENSP00000264711:p.Cys186Arg		Q5JV88|Q86Y24	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_DnaJ_domain,pfam_EF_GTP-bd_dom,superfamily_P-loop_NTPase,superfamily_DnaJ_domain,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,smart_DnaJ_domain,pfscan_DnaJ_domain,prints_Small_GTPase,prints_DnaJ_domain,tigrfam_Small_GTP-bd_dom	p.C186R	ENST00000264711.2	37	c.556	CCDS1716.1	2	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599523	0.87055	.	.	ENSG00000115137	ENST00000264711;ENST00000534855	T;T	0.20598	2.06;2.06	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.22704	0.0548	L	0.50333	1.59	0.80722	D	1	P	0.51351	0.944	B	0.40165	0.321	T	0.02098	-1.1214	10	0.72032	D	0.01	-15.8812	15.2006	0.73132	1.0:0.0:0.0:0.0	.	186	Q9NZQ0	DJC27_HUMAN	R	186;115	ENSP00000264711:C186R;ENSP00000440086:C115R	ENSP00000264711:C186R	C	-	1	0	DNAJC27	25027900	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.103000	0.94232	2.263000	0.75096	0.533000	0.62120	TGT	0	superfamily_P-loop_NTPase,smart_Ran_GTPase		0.368	DNAJC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAJC27	protein_coding	OTTHUMT00000246855.3	92	182	0	0.00	0	0	A	NM_016544	0	0		25174396	-1	no_errors	ENST00000264711	ensembl	human	known	74_37	missense	94	170	22.31	24.11	27	54	SNP	1	G
SF3B1	23451	genome.wustl.edu	37	2	198273163	198273163	+	Silent	SNP	G	G	A			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr2:198273163G>A	ENST00000335508.6	-	8	1138	c.1047C>T	c.(1045-1047)agC>agT	p.S349S		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	349	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GAACTGGAGTGCTTCCACCCA	0.488			Mis		myelodysplastic syndrome																																		0		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	0													123.0	118.0	120.0					2																	198273163		2203	4300	6503	SO:0001819	synonymous_variant	0			AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1047C>T	2.37:g.198273163G>A			E9PCH3	Silent	SNP	pfam_SF3b_su1,superfamily_ARM-type_fold	p.S349	ENST00000335508.6	37	c.1047	CCDS33356.1	2																																																																																			0	pfam_SF3b_su1		0.488	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SF3B1	protein_coding	OTTHUMT00000335245.2	86	253	0	0.00	0	0	G		0	0		198273163	-1	no_errors	ENST00000335508	ensembl	human	known	74_37	silent	36	129	43.75	36.76	28	75	SNP	1	A
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr7:74146970T>A	ENST00000324896.4	+	15	1660	c.1271T>A	c.(1270-1272)cTt>cAt	p.L424H	GTF2I_ENST00000353920.4_Missense_Mutation_p.L404H|GTF2I_ENST00000346152.4_Missense_Mutation_p.L403H|GTF2I_ENST00000416070.1_Missense_Mutation_p.L383H	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	424					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATATTACTTGCAAAGGAA	0.378																																							0											0													13.0	13.0	13.0					7																	74146970		1741	3768	5509	SO:0001583	missense	0			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1271T>A	7.37:g.74146970T>A	ENSP00000322542:p.Leu424His		O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	p.L424H	ENST00000324896.4	37	c.1271	CCDS5573.1	7	.	.	.	.	.	.	.	.	.	.	T	18.18	3.565904	0.65651	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.72	4.72	0.59763	.	0.110120	0.39544	N	0.001322	T	0.37019	0.0988	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.999	D;D;P;D;D	0.74348	0.983;0.979;0.874;0.971;0.963	T	0.36089	-0.9762	10	0.56958	D	0.05	-16.5588	13.3771	0.60745	0.0:0.0:0.0:1.0	.	402;383;404;403;424	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	H	424;419;404;403;383	ENSP00000322542:L424H;ENSP00000322671:L404H;ENSP00000322599:L403H;ENSP00000387651:L383H	ENSP00000322542:L424H	L	+	2	0	GTF2I	73784906	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.342000	0.65970	1.753000	0.51906	0.477000	0.44152	CTT	0	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I		0.378	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GTF2I	protein_coding	OTTHUMT00000252708.1	298	122	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	208	80	40.57	35.48	142	44	SNP	1	A
STRIP2	57464	genome.wustl.edu	37	7	129098231	129098231	+	Missense_Mutation	SNP	C	C	A			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr7:129098231C>A	ENST00000249344.2	+	10	1254	c.1214C>A	c.(1213-1215)gCa>gAa	p.A405E	STRIP2_ENST00000435494.2_Missense_Mutation_p.A405E	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	405					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											CCCTCACAGGCACCCCTCTCT	0.602																																							0											0													44.0	41.0	42.0					7																	129098231		2203	4300	6503	SO:0001583	missense	0			AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.1214C>A	7.37:g.129098231C>A	ENSP00000249344:p.Ala405Glu		Q8WUZ4	Missense_Mutation	SNP	pfam_DUF3402,pfam_N1221	p.A405E	ENST00000249344.2	37	c.1214	CCDS34752.1	7	.	.	.	.	.	.	.	.	.	.	C	10.32	1.317895	0.23994	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.42513	0.97;0.97	5.37	3.48	0.39840	.	0.732884	0.13648	N	0.372517	T	0.25717	0.0626	N	0.08118	0	0.25358	N	0.988808	B;B	0.11235	0.004;0.0	B;B	0.13407	0.009;0.0	T	0.15122	-1.0448	10	0.29301	T	0.29	0.511	14.6531	0.68811	0.0:0.7227:0.2773:0.0	.	405;405	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	E	405	ENSP00000249344:A405E;ENSP00000392393:A405E	ENSP00000249344:A405E	A	+	2	0	FAM40B	128885467	1.000000	0.71417	0.955000	0.39395	0.973000	0.67179	3.108000	0.50337	0.679000	0.31345	0.655000	0.94253	GCA	0	NULL		0.602	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STRIP2	protein_coding	OTTHUMT00000349418.1	46	126	0	0.00	0	0	C	NM_001134336	0	0		129098231	1	no_errors	ENST00000249344	ensembl	human	known	74_37	missense	24	64	41.46	35.64	17	36	SNP	0.998	A
C10orf90	118611	genome.wustl.edu	37	10	128149995	128149995	+	Missense_Mutation	SNP	G	G	A	rs375267781		TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr10:128149995G>A	ENST00000284694.7	-	5	1814	c.1694C>T	c.(1693-1695)aCg>aTg	p.T565M	C10orf90_ENST00000544758.1_Missense_Mutation_p.T662M|C10orf90_ENST00000480379.1_De_novo_Start_InFrame|C10orf90_ENST00000454341.1_Missense_Mutation_p.T468M|C10orf90_ENST00000356858.3_Missense_Mutation_p.T518M	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	565					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TCTTGCAGGCGTTTGCTGAGA	0.592																																							0											0								A	MET/THR	0,4406		0,0,2203	76.0	73.0	74.0		1694	-4.3	0.0	10		74	5,8595	4.3+/-15.6	0,5,4295	no	missense	C10orf90	NM_001004298.2	81	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	benign	565/700	128149995	5,13001	2203	4300	6503	SO:0001583	missense	0			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1694C>T	10.37:g.128149995G>A	ENSP00000284694:p.Thr565Met		B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	NULL	p.T662M	ENST00000284694.7	37	c.1985	CCDS31310.1	10	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	5.903|5.903	0.350693|0.350693	0.11182|0.11182	0.0|0.0	5.81E-4|5.81E-4	ENSG00000154493|ENSG00000154493	ENST00000424927|ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642	.|T;T;T;T	.|0.18657	.|2.21;2.2;2.21;2.23	5.01|5.01	-4.29|-4.29	0.03721|0.03721	.|.	.|1.916440	.|0.02445	.|N	.|0.085007	T|T	0.07683|0.07683	0.0193|0.0193	N|N	0.01482|0.01482	-0.84|-0.84	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.13145	.|0.007;0.007;0.007	.|B;B;B	.|0.10450	.|0.002;0.005;0.005	T|T	0.27400|0.27400	-1.0075|-1.0075	5|10	.|0.26408	.|T	.|0.33	1.3857|1.3857	7.6243|7.6243	0.28204|0.28204	0.4959:0.1999:0.3042:0.0|0.4959:0.1999:0.3042:0.0	.|.	.|662;565;468	.|F5GZL2;Q96M02;Q96M02-2	.|.;CJ090_HUMAN;.	C|M	108|518;565;468;662;565	.|ENSP00000284694:T565M;ENSP00000398786:T468M;ENSP00000444369:T662M;ENSP00000405995:T565M	.|ENSP00000284694:T565M	R|T	-|-	1|2	0|0	C10orf90|C10orf90	128139985|128139985	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-2.254000|-2.254000	0.01183|0.01183	-1.097000|-1.097000	0.03042|0.03042	-2.271000|-2.271000	0.00274|0.00274	CGC|ACG	0	NULL		0.592	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	C10orf90	protein_coding		90	148	0	0.67	0	1	G	NM_001004298	rs375267781	G->A		128149995	-1	no_errors	ENST00000544758	ensembl	human	known	74_37	missense	51	66	42.7	40.54	38	45	SNP	0	A
RDH5	5959	genome.wustl.edu	37	12	56115574	56115574	+	Missense_Mutation	SNP	A	A	G			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr12:56115574A>G	ENST00000257895.5	+	3	564	c.412A>G	c.(412-414)Atg>Gtg	p.M138V	RDH5_ENST00000547072.1_Missense_Mutation_p.M41V|RP11-644F5.10_ENST00000550412.1_3'UTR|RP11-644F5.10_ENST00000549424.1_3'UTR|RDH5_ENST00000548082.1_Missense_Mutation_p.M138V|RDH5_ENST00000553160.1_Intron	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	138					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	TGTGAACACAATGGGTCCCAT	0.607																																							0											0													51.0	48.0	49.0					12																	56115574		2203	4300	6503	SO:0001583	missense	0			U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	9940	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 5"""	601617	"""retinol dehydrogenase 5 (11-cis and 9-cis)"""	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.412A>G	12.37:g.56115574A>G	ENSP00000257895:p.Met138Val		O00179|Q8TAI2	Missense_Mutation	SNP	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR,prints_DHB_DH	p.M138V	ENST00000257895.5	37	c.412	CCDS31829.1	12	.	.	.	.	.	.	.	.	.	.	A	3.767	-0.048324	0.07407	.	.	ENSG00000135437	ENST00000547072;ENST00000552930;ENST00000257895;ENST00000548082	D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07	5.36	-4.8	0.03190	NAD(P)-binding domain (1);	0.675505	0.15310	N	0.269132	T	0.71913	0.3396	N	0.02334	-0.595	0.09310	N	1	B	0.14012	0.009	B	0.18263	0.021	T	0.62618	-0.6816	10	0.44086	T	0.13	.	0.9125	0.01298	0.1676:0.2072:0.2145:0.4106	.	138	Q92781	RDH1_HUMAN	V	41;41;138;138	ENSP00000449927:M41V;ENSP00000448014:M41V;ENSP00000257895:M138V;ENSP00000447128:M138V	ENSP00000257895:M138V	M	+	1	0	RDH5	54401841	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-1.952000	0.01528	-1.264000	0.02452	-1.740000	0.00687	ATG	0	pfam_DH_sc/Rdtase_SDR,prints_DHB_DH		0.607	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RDH5	protein_coding	OTTHUMT00000407493.1	141	90	0	0.00	0	0	A	NM_002905	0	0		56115574	1	no_errors	ENST00000257895	ensembl	human	known	74_37	missense	69	56	39.47	29.11	45	23	SNP	0.003	G
ABCC4	10257	genome.wustl.edu	37	13	95696021	95696021	+	Missense_Mutation	SNP	T	T	C			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr13:95696021T>C	ENST00000376887.4	-	29	3764	c.3650A>G	c.(3649-3651)aAa>aGa	p.K1217R	ABCC4_ENST00000412704.1_Missense_Mutation_p.K1170R	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1217	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CCGGATTTTTTTTTGTATTAA	0.363																																							0											0													96.0	96.0	96.0					13																	95696021		2203	4300	6503	SO:0001583	missense	0			U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3650A>G	13.37:g.95696021T>C	ENSP00000366084:p.Lys1217Arg		A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_ABC1_TM_dom,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC1_TM_dom,prints_CysFib_conduc_TM	p.K1217R	ENST00000376887.4	37	c.3650	CCDS9474.1	13	.	.	.	.	.	.	.	.	.	.	T	16.63	3.178042	0.57692	.	.	ENSG00000125257	ENST00000412704;ENST00000376887	T;T	0.77750	-1.12;-1.12	5.81	5.81	0.92471	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.198585	0.51477	D	0.000093	T	0.73071	0.3540	L	0.31207	0.915	0.80722	D	1	B;B	0.32781	0.009;0.384	B;B	0.40864	0.055;0.342	T	0.69986	-0.4996	10	0.27082	T	0.32	.	16.1668	0.81768	0.0:0.0:0.0:1.0	.	1170;1217	O15439-2;O15439	.;MRP4_HUMAN	R	1170;1217	ENSP00000388657:K1170R;ENSP00000366084:K1217R	ENSP00000366084:K1217R	K	-	2	0	ABCC4	94494022	1.000000	0.71417	0.037000	0.18230	0.971000	0.66376	5.955000	0.70306	2.210000	0.71456	0.533000	0.62120	AAA	0	superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like		0.363	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCC4	protein_coding	OTTHUMT00000045478.2	54	176	0	0.00	0	0	T	NM_005845	0	0		95696021	-1	no_errors	ENST00000376887	ensembl	human	known	74_37	missense	39	94	35	44.05	21	74	SNP	0.954	C
CHD3	1107	genome.wustl.edu	37	17	7798460	7798460	+	Nonsense_Mutation	SNP	C	C	T			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr17:7798460C>T	ENST00000330494.7	+	9	1645	c.1495C>T	c.(1495-1497)Cga>Tga	p.R499*	CHD3_ENST00000380358.4_Nonsense_Mutation_p.R558*|CHD3_ENST00000358181.4_Nonsense_Mutation_p.R499*	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	499	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GCTGTGTCCCCGATGCACAGT	0.552																																							0											0													222.0	166.0	185.0					17																	7798460		2203	4300	6503	SO:0001587	stop_gained	0			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.1495C>T	17.37:g.7798460C>T	ENSP00000332628:p.Arg499*		D3DTQ9|E9PG89|Q9Y4I0	Nonsense_Mutation	SNP	pfam_CHD_C2,pfam_SNF2_N,pfam_DUF1086,pfam_CHD_N,pfam_DUF1087,pfam_Znf_PHD-finger,pfam_Chromo_domain,pfam_Helicase_C,pfam_HDA_complex_subunit-2/3,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,superfamily_Chromodomain-like,superfamily_Znf_FYVE_PHD,superfamily_HMG_box_dom,smart_Znf_PHD,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Znf_PHD-finger,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.R499*	ENST00000330494.7	37	c.1495	CCDS32554.1	17	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.675191|6.675191	0.97755|0.97755	.|.	.|.	ENSG00000170004|ENSG00000170004	ENST00000452447|ENST00000380358;ENST00000358181;ENST00000330494	T|.	0.64618|.	-0.11|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	.|0.000000	.|0.33180	.|N	.|0.005184	T|.	0.46308|.	0.1386|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.38478|.	-0.9659|.	5|.	0.87932|0.02654	D|T	0|1	-6.7131|-6.7131	18.5172|18.5172	0.90939|0.90939	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	369|558;499;499	ENSP00000405861:P369L|.	ENSP00000405861:P369L|ENSP00000332628:R499X	P|R	+|+	2|1	0|2	CHD3|CHD3	7739185|7739185	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.674000|4.674000	0.61612|0.61612	2.611000|2.611000	0.88343|0.88343	0.561000|0.561000	0.74099|0.74099	CCG|CGA	0	pfam_Znf_PHD-finger,superfamily_Chromodomain-like,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,pfscan_Znf_PHD-finger		0.552	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CHD3	protein_coding	OTTHUMT00000318050.1	41	180	0	0.00	0	0	C	NM_001005273	0	0		7798460	1	no_errors	ENST00000330494	ensembl	human	known	74_37	nonsense	26	113	38.1	35.80	16	63	SNP	1	T
FOXN1	8456	genome.wustl.edu	37	17	26851557	26851557	+	Missense_Mutation	SNP	G	G	A	rs200888774		TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr17:26851557G>A	ENST00000226247.2	+	2	189	c.160G>A	c.(160-162)Gac>Aac	p.D54N	FOXN1_ENST00000579795.1_Missense_Mutation_p.D54N	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	54					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)					ATTTGTGTCCGACGGCCCTCC	0.672													g|||	0	0.0	0.0	0.0	5008	,	,		14357	0.0		0.0	False		,,,				2504	0.0						1,0											0													53.0	58.0	56.0					17																	26851557		2203	4300	6503	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.160G>A	17.37:g.26851557G>A	ENSP00000226247:p.Asp54Asn		B2R9Q7|O15352	Missense_Mutation	SNP	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.D54N	ENST00000226247.2	37	c.160	CCDS11232.1	17	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	11.82	1.751915	0.31046	.	.	ENSG00000109101	ENST00000226247	D	0.94758	-3.51	5.54	4.57	0.56435	.	0.076424	0.56097	N	0.000039	D	0.89269	0.6667	L	0.29908	0.895	0.09310	N	0.999999	P	0.44478	0.836	B	0.37650	0.255	D	0.83641	0.0150	10	0.56958	D	0.05	.	11.9959	0.53204	0.0811:0.0:0.9189:0.0	.	54	O15353	FOXN1_HUMAN	N	54	ENSP00000226247:D54N	ENSP00000226247:D54N	D	+	1	0	FOXN1	23875684	0.210000	0.23517	0.041000	0.18516	0.012000	0.07955	2.132000	0.42083	1.496000	0.48567	-0.215000	0.12644	GAC	0	NULL		0.672	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXN1	protein_coding	OTTHUMT00000255832.1	19	67	0	0.00	0	0	G		rs200888774	G->A		26851557	1	no_errors	ENST00000226247	ensembl	human	known	74_37	missense	16	43	51.52	31.25	17	20	SNP	0.242	A
CLTC	1213	genome.wustl.edu	37	17	57743887	57743887	+	Missense_Mutation	SNP	G	G	C			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr17:57743887G>C	ENST00000269122.3	+	12	2103	c.1829G>C	c.(1828-1830)cGg>cCg	p.R610P	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Missense_Mutation_p.R610P	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	610	Distal segment.|Heavy chain arm.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CATTATGACCGGGCTCATATT	0.413			T	"""ALK, TFE3"""	"""ALCL, renal """																																		0		Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	0													117.0	110.0	112.0					17																	57743887		2203	4300	6503	SO:0001583	missense	0			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.1829G>C	17.37:g.57743887G>C	ENSP00000269122:p.Arg610Pro		D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	pfam_Clathrin_H-chain/VPS_repeat,pfam_Clathrin_H-chain_propeller_rpt,pfam_Clathrin_H-chain_linker_core,superfamily_Clathrin_H-chain_propeller_N,superfamily_ARM-type_fold,smart_Clathrin_H-chain/VPS_repeat,pirsf_Clathrin_heavy_chain	p.R610P	ENST00000269122.3	37	c.1829	CCDS32696.1	17	.	.	.	.	.	.	.	.	.	.	G	33	5.254186	0.95336	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.18502	2.21;2.21	5.84	5.84	0.93424	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	M	0.91612	3.225	0.80722	D	1	D;D	0.67145	0.996;0.971	D;D	0.71414	0.935;0.973	T	0.62305	-0.6882	10	0.87932	D	0	.	20.1535	0.98095	0.0:0.0:1.0:0.0	.	610;610	Q00610;Q00610-2	CLH1_HUMAN;.	P	610	ENSP00000269122:R610P;ENSP00000376763:R610P	ENSP00000269122:R610P	R	+	2	0	CLTC	55098669	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.869000	0.99810	2.764000	0.94973	0.650000	0.86243	CGG	0	pfam_Clathrin_H-chain/VPS_repeat,superfamily_ARM-type_fold,smart_Clathrin_H-chain/VPS_repeat,pirsf_Clathrin_heavy_chain		0.413	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLTC	protein_coding	OTTHUMT00000258859.1	34	292	0	0.68	0	2	G	NM_004859	0	0		57743887	1	no_errors	ENST00000269122	ensembl	human	known	74_37	missense	43	166	24.56	23.98	14	53	SNP	1	C
MRPS7	51081	genome.wustl.edu	37	17	73258007	73258007	+	Missense_Mutation	SNP	C	C	G			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr17:73258007C>G	ENST00000245539.6	+	1	253	c.26C>G	c.(25-27)gCc>gGc	p.A9G	MRPS7_ENST00000579761.1_Missense_Mutation_p.A9G|GGA3_ENST00000351904.7_5'Flank|GGA3_ENST00000582486.1_Intron|GGA3_ENST00000537686.1_5'Flank|GGA3_ENST00000579743.1_Intron|MRPS7_ENST00000579002.1_5'UTR|GGA3_ENST00000538886.1_5'Flank|GGA3_ENST00000582717.1_Intron|GGA3_ENST00000245541.6_5'Flank|GGA3_ENST00000578348.1_Intron	NM_015971.3	NP_057055.2	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7	9					translation (GO:0006412)	cytosolic small ribosomal subunit (GO:0022627)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)	6	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			GTGAAGGTTGCCCGAGGATGG	0.697																																							0											0													21.0	30.0	27.0					17																	73258007		2200	4298	6498	SO:0001583	missense	0			AB051348	CCDS11718.1	17q25.1	2012-09-13				ENSG00000125445		"""Mitochondrial ribosomal proteins / small subunits"""	14499	protein-coding gene	gene with protein product		611974					Standard	NM_015971		Approved	MRP-S, RP-S7, RPMS7	uc002jnm.4	Q9Y2R9		ENST00000245539.6:c.26C>G	17.37:g.73258007C>G	ENSP00000245539:p.Ala9Gly		B2R9N5|Q53GD6	Missense_Mutation	SNP	pfam_Ribosomal_S7_dom,superfamily_Ribosomal_S7_dom	p.A9G	ENST00000245539.6	37	c.26	CCDS11718.1	17	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901204	0.33535	.	.	ENSG00000125445	ENST00000245539	T	0.47177	0.85	5.72	-7.9	0.01169	.	0.941813	0.08896	N	0.877946	T	0.29256	0.0728	L	0.34521	1.04	0.20403	N	0.999908	B	0.06786	0.001	B	0.04013	0.001	T	0.26985	-1.0087	10	0.23302	T	0.38	-0.8785	10.596	0.45338	0.0:0.1891:0.1094:0.7015	.	9	Q9Y2R9	RT07_HUMAN	G	9	ENSP00000245539:A9G	ENSP00000245539:A9G	A	+	2	0	MRPS7	70769602	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.837000	0.04377	-0.979000	0.03529	-0.345000	0.07892	GCC	0	NULL		0.697	MRPS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MRPS7	protein_coding	OTTHUMT00000446666.1	180	56	0	0.00	0	0	C	NM_015971	0	0		73258007	1	no_errors	ENST00000245539	ensembl	human	known	74_37	missense	91	18	33.58	40.00	46	12	SNP	0	G
OR1I1	126370	genome.wustl.edu	37	19	15198335	15198335	+	Missense_Mutation	SNP	C	C	A			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr19:15198335C>A	ENST00000209540.2	+	1	545	c.459C>A	c.(457-459)aaC>aaA	p.N153K		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						TGATCACCAACCTCCAGTCTC	0.567																																							0											0													95.0	86.0	89.0					19																	15198335		2203	4300	6503	SO:0001583	missense	0			AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.459C>A	19.37:g.15198335C>A	ENSP00000209540:p.Asn153Lys		Q96R92	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.N153K	ENST00000209540.2	37	c.459	CCDS32937.1	19	.	.	.	.	.	.	.	.	.	.	c	7.016	0.557804	0.13436	.	.	ENSG00000094661	ENST00000209540	T	0.00084	8.75	4.61	1.14	0.20703	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33875	U	0.004480	T	0.00271	0.0008	M	0.76170	2.325	0.09310	N	1	D	0.54397	0.966	P	0.54965	0.765	T	0.46162	-0.9211	10	0.34782	T	0.22	.	6.5276	0.22309	0.0:0.547:0.0:0.453	.	153	O60431	OR1I1_HUMAN	K	153	ENSP00000209540:N153K	ENSP00000209540:N153K	N	+	3	2	OR1I1	15059335	0.000000	0.05858	0.463000	0.27130	0.090000	0.18270	-1.476000	0.02333	0.492000	0.27815	0.555000	0.69702	AAC	0	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM		0.567	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR1I1	protein_coding	OTTHUMT00000465665.1	35	155	0	0.00	0	0	C		0	0		15198335	1	no_errors	ENST00000209540	ensembl	human	known	74_37	missense	12	75	40	40.00	8	50	SNP	0	A
RPL18	6141	genome.wustl.edu	37	19	49120073	49120073	+	Silent	SNP	C	C	T			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr19:49120073C>T	ENST00000549920.1	-	4	599	c.207G>A	c.(205-207)aaG>aaA	p.K69K	RPL18_ENST00000549273.1_Silent_p.K69K|RPL18_ENST00000552588.1_Silent_p.K40K|SPHK2_ENST00000245222.4_5'Flank|AC022154.7_ENST00000598735.1_RNA|SPHK2_ENST00000340932.3_5'Flank|RPL18_ENST00000550645.1_Silent_p.K69K|AC022154.7_ENST00000600303.1_RNA|SPHK2_ENST00000600537.1_5'Flank|SPHK2_ENST00000601712.1_5'Flank|SPHK2_ENST00000598088.1_5'Flank|FAM83E_ENST00000595110.1_5'Flank	NM_000979.3	NP_000970.1	Q07020	RL18_HUMAN	ribosomal protein L18	69					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|kidney(2)	3		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.89e-05)|all cancers(93;0.00011)|GBM - Glioblastoma multiforme(486;0.0061)|Epithelial(262;0.0154)		GAAGCTTCATCTTCCGGATCT	0.572																																							0											0													79.0	74.0	75.0					19																	49120073		2203	4300	6503	SO:0001819	synonymous_variant	0			L11566	CCDS12726.1, CCDS58669.1	19q13	2011-04-06				ENSG00000063177		"""L ribosomal proteins"""	10310	protein-coding gene	gene with protein product	"""60S ribosomal protein L18"""	604179				8218404	Standard	NM_000979		Approved	L18	uc002pjq.2	Q07020	OTTHUMG00000169760	ENST00000549920.1:c.207G>A	19.37:g.49120073C>T			F8VWC5|Q8WTZ6	Missense_Mutation	SNP	NULL	p.D67N	ENST00000549920.1	37	c.199	CCDS12726.1	19	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220176	0.58560	.	.	ENSG00000063177	ENST00000084795;ENST00000546623	.	.	.	4.34	3.3	0.37823	.	.	.	.	.	T	0.53899	0.1825	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50215	-0.8854	4	.	.	.	-21.2038	5.9382	0.19177	0.0:0.793:0.0:0.207	.	.	.	.	N	71;42	.	.	D	-	1	0	RPL18	53811885	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.425000	0.34859	2.426000	0.82243	0.478000	0.44815	GAT	0	NULL		0.572	RPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPL18	protein_coding	OTTHUMT00000405732.2	51	157	0	0.00	0	0	C	NM_000979	0	0		49120073	-1	no_errors	ENST00000549370	ensembl	human	known	74_37	missense	32	81	38.46	35.71	20	45	SNP	1	T
FLNA	2316	genome.wustl.edu	37	X	153591113	153591114	+	Frame_Shift_Ins	INS	-	-	T			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chrX:153591113_153591114insT	ENST00000369850.3	-	16	2555_2556	c.2319_2320insA	c.(2317-2322)aaagtafs	p.V774fs	FLNA_ENST00000422373.1_Frame_Shift_Ins_p.V774fs|FLNA_ENST00000360319.4_Frame_Shift_Ins_p.V774fs|FLNA_ENST00000344736.4_Frame_Shift_Ins_p.V774fs	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	774					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGGCCGTATACTTTGACCTTGT	0.634																																							0											0																																										SO:0001589	frameshift_variant	0			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.2320dupA	X.37:g.153591116_153591116dupT	ENSP00000358866:p.Val774fs		E9KL45|Q5HY53|Q5HY55|Q8NF52	Frame_Shift_Ins	INS	pfam_Filamin/ABP280_repeat-like,pfam_CH-domain,superfamily_CH-domain,superfamily_Ig_E-set,smart_CH-domain,smart_Filamin,pfscan_CH-domain,pfscan_Filamin/ABP280_repeat-like	p.V773fs	ENST00000369850.3	37	c.2320_2319	CCDS48194.1	X																																																																																			0	pfam_Filamin/ABP280_repeat-like,superfamily_Ig_E-set,smart_Filamin,pfscan_Filamin/ABP280_repeat-like		0.634	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FLNA	protein_coding	OTTHUMT00000058942.3	88	77	0	0.00	0	0	0		0	0		153591114	-1	no_errors	ENST00000369850	ensembl	human	known	74_37	frame_shift_ins	62	41	22.5	26.79	18	15	INS	1.000:1.000	T
SNORD3C	780853	genome.wustl.edu	37	17	19091344	19091344	+	lincRNA	DEL	G	G	-			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr17:19091344delG	ENST00000362428.1	-	0	432				SNORD3A_ENST00000365494.1_lincRNA					small nucleolar RNA, C/D box 3C																		tatactttcagggatcatttc	0.468																																							0											0													2.0	1.0	1.0					17																	19091344		212	138	350			0					17p11.2	2013-09-05			ENSG00000199298	ENSG00000264940			33191	non-coding RNA	RNA, small nucleolar						9365252	Standard	NR_006881		Approved	U3-3					17.37:g.19091344delG				RNA	DEL	0	NULL	ENST00000362428.1	37	NULL		17																																																																																			0	0		0.468	SNORD3C-201	KNOWN	basic	snoRNA	SNORD3A	lincRNA		253	89	0	0.00	0	0	G	NR_006881	0	0		19091344	1	no_errors	ENST00000365494	ensembl	human	known	74_37	rna	227	98	10.28	6.67	26	7	DEL	1	0
PLXNB2	23654	genome.wustl.edu	37	22	50722370	50722371	+	In_Frame_Ins	INS	-	-	CGG			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	-	-	-	CGG	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr22:50722370_50722371insCGG	ENST00000449103.1	-	14	2452_2453	c.2312_2313insCCG	c.(2311-2313)cgg>cgCCGg	p.771_771R>RR	PLXNB2_ENST00000359337.4_In_Frame_Ins_p.771_771R>RR|PLXNB2_ENST00000496720.1_5'UTR			O15031	PLXB2_HUMAN	plexin B2	771					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGTTAGCGGCCCGGCACAGGCT	0.698																																							0											0																																										SO:0001652	inframe_insertion	0				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2310_2312dupCCG	22.37:g.50722371_50722373dupCGG	ENSP00000409171:p.Arg771dup		A6QRH0|Q7KZU3|Q9BSU7	In_Frame_Ins	INS	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Semap_dom,pfam_Plexin_repeat,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.772in_frame_insR	ENST00000449103.1	37	c.2313_2312	CCDS43035.1	22																																																																																			0	superfamily_Plexin-like_fold,smart_Plexin-like_fold		0.698	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNB2	protein_coding	OTTHUMT00000316874.3	56	18	0	0.00	0	0	0	NM_012401	0	0		50722371	-1	no_errors	ENST00000359337	ensembl	human	known	74_37	in_frame_ins	51	6	20.31	40.00	13	4	INS	1.000:1.000	CGG
FOXD4L5	653427	genome.wustl.edu	37	9	70177486	70177486	+	Silent	SNP	G	G	A	rs199726212	byFrequency	TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr9:70177486G>A	ENST00000377420.1	-	1	1329	c.498C>T	c.(496-498)ttC>ttT	p.F166F		NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5	166					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						GGATCTTAACGAAGCAGTCGT	0.627																																							0											0													1.0	1.0	1.0					9																	70177486		1	16	17	SO:0001819	synonymous_variant	0				CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	ENST00000377420.1:c.498C>T	9.37:g.70177486G>A				Silent	SNP	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.F166	ENST00000377420.1	37	c.498	CCDS47977.1	9																																																																																			0	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head		0.627	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXD4L5	protein_coding	OTTHUMT00000037122.1	20	0	4.76	0.00	1	0	G	NM_001126334	rs199726212	G->A		70177486	-1	no_errors	ENST00000377420	ensembl	human	known	74_37	silent	13	0	35	0.00	7	0	SNP	1	A
NDN	4692	genome.wustl.edu	37	15	23932210	23932210	+	Missense_Mutation	SNP	G	G	A			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr15:23932210G>A	ENST00000331837.4	-	1	240	c.155C>T	c.(154-156)cCg>cTg	p.P52L		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	52					axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		CGCGGCCTGCGGAGCGGCCGT	0.761									Prader-Willi syndrome																														0											0													4.0	6.0	5.0					15																	23932210		1468	2838	4306	SO:0001583	missense	0	Familial Cancer Database	Prader-Labhart-Willi syndrome	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"""Prader-Willi syndrome chromosome region"""	602117	"""necdin (mouse) homolog"", ""necdin homolog (mouse)"""			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.155C>T	15.37:g.23932210G>A	ENSP00000332643:p.Pro52Leu		B2R6Z5	Missense_Mutation	SNP	pfam_MAGE,pfscan_MAGE	p.P52L	ENST00000331837.4	37	c.155	CCDS10014.1	15	.	.	.	.	.	.	.	.	.	.	G	12.24	1.880072	0.33162	.	.	ENSG00000182636	ENST00000331837	T	0.02301	4.35	3.32	1.26	0.21427	.	0.000000	0.45606	D	0.000347	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.31519	0.327	B	0.17433	0.018	T	0.51482	-0.8700	10	0.26408	T	0.33	.	6.3621	0.21435	0.0:0.2019:0.5904:0.2077	.	52	Q99608	NECD_HUMAN	L	52	ENSP00000332643:P52L	ENSP00000332643:P52L	P	-	2	0	NDN	21483303	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-0.388000	0.07352	0.159000	0.19401	0.561000	0.74099	CCG	0	NULL		0.761	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDN	protein_coding	OTTHUMT00000251226.2	12	12	0	0.00	0	0	G	NM_002487	0	0		23932210	-1	no_errors	ENST00000331837	ensembl	human	known	74_37	missense	10	2	23.08	0.00	3	0	SNP	0	A
RUNX2	860	genome.wustl.edu	37	6	45390446	45390448	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	CAG	CAG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr6:45390446_45390448delCAG	ENST00000371438.1	+	2	533_535	c.175_177delCAG	c.(175-177)cagdel	p.Q71del	RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000465038.2_In_Frame_Del_p.Q71del|RUNX2_ENST00000352853.5_In_Frame_Del_p.Q139del|RUNX2_ENST00000359524.5_In_Frame_Del_p.Q57del|RUNX2_ENST00000576263.1_In_Frame_Del_p.Q71del|RUNX2_ENST00000371436.6_In_Frame_Del_p.Q71del|RUNX2_ENST00000541979.1_In_Frame_Del_p.Q139del|RUNX2_ENST00000371432.3_In_Frame_Del_p.Q57del	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						gcagcagcaacagcagcagcagc	0.729																																							0											0																																										SO:0001651	inframe_deletion	0			AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.175_177delCAG	6.37:g.45390455_45390457delCAG	ENSP00000360493:p.Gln71del		O14614|O14615|O95181	In_Frame_Del	DEL	pfam_Runt_dom,pfam_RunxI_C_dom,superfamily_p53-like_TF_DNA-bd,pfscan_Runt_dom,prints_AML1_Runt	p.Q130in_frame_del	ENST00000371438.1	37	c.379_381	CCDS43467.2	6																																																																																			0	NULL		0.729	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	RUNX2	protein_coding	OTTHUMT00000040755.2	77	7	0	0.00	0	0	CAG	NM_004348	0	0		45390448	1	no_errors	ENST00000352853	ensembl	human	known	74_37	in_frame_del	50	2	9.09	0.00	5	0	DEL	0.995:0.993:0.990	0
EIF2B2	8892	genome.wustl.edu	37	14	75471420	75471422	+	Intron	DEL	TTG	TTG	-			TCGA-3G-AB0Q-01A-11D-A423-09	TCGA-3G-AB0Q-11A-21D-A426-09	TTG	TTG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ef4fa790-c453-4568-bb03-76ae3d5931d4	126fc753-1f18-4013-8285-ed49ed76bc87	g.chr14:75471420_75471422delTTG	ENST00000266126.5	+	4	513				RP11-950C14.3_ENST00000554430.1_RNA	NM_014239.3	NP_055054.1	P49770	EI2BB_HUMAN	eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa						cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|central nervous system development (GO:0007417)|gene expression (GO:0010467)|myelination (GO:0042552)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|translation initiation factor activity (GO:0003743)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.00661)		ttttttttttttGCAAAACCGTT	0.34																																							0											0																																										SO:0001627	intron_variant	0				CCDS9836.1	14q24.3	2008-08-11	2002-08-29			ENSG00000119718			3258	protein-coding gene	gene with protein product		606454	"""eukaryotic translation initiation factor 2B, subunit 2 (beta, 39kD)"""			8887689	Standard	NM_014239		Approved	EIF2B, EIF-2Bbeta	uc001xrc.2	P49770		ENST00000266126.5:c.434-18TTG>-	14.37:g.75471420_75471422delTTG			O43201	RNA	DEL	0	NULL	ENST00000266126.5	37	NULL	CCDS9836.1	14																																																																																			0	0		0.340	EIF2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000258646	protein_coding	OTTHUMT00000414993.1	10	13	0	0.00	0	0	TTG	NM_014239	0	0		75471422	-1	no_errors	ENST00000554430	ensembl	human	known	74_37	rna	4	7	33.33	0.00	2	0	DEL	0.001:0.001:0.000	0
