#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ABCA5	23461	genome.wustl.edu	37	17	67246096	67246096	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr17:67246096G>A	ENST00000392676.3	-	37	4779	c.4715C>T	c.(4714-4716)cCt>cTt	p.P1572L	ABCA5_ENST00000392677.2_Missense_Mutation_p.P1573L|ABCA5_ENST00000588877.1_Missense_Mutation_p.P1572L			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1572					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	ATCTTCCTTAGGAATTTTATA	0.274																																						dbGAP											0													25.0	27.0	26.0					17																	67246096		2183	4274	6457	-	-	-	SO:0001583	missense	0			U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.4715C>T	17.37:g.67246096G>A	ENSP00000376443:p.Pro1572Leu		Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.P1573L	ENST00000392676.3	37	c.4718	CCDS11685.1	17	.	.	.	.	.	.	.	.	.	.	g	25.7	4.663003	0.88251	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.91180	-2.8;-2.8	5.51	4.52	0.55395	.	0.111023	0.40385	N	0.001103	D	0.96747	0.8938	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97464	1.0036	10	0.87932	D	0	.	15.2404	0.73465	0.0712:0.0:0.9288:0.0	.	1572	Q8WWZ7	ABCA5_HUMAN	L	1573;1572	ENSP00000376444:P1573L;ENSP00000376443:P1572L	ENSP00000376443:P1572L	P	-	2	0	ABCA5	64757691	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.992000	0.76238	2.746000	0.94184	0.650000	0.86243	CCT	ABCA5	-	NULL	ENSG00000154265		0.274	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	ABCA5	HGNC	protein_coding	OTTHUMT00000450654.1	32	0.00	0	G	NM_018672		67246096	67246096	-1	no_errors	ENST00000392677	ensembl	human	known	69_37n	missense	86	21.82	24	SNP	1.000	A
ABHD1	84696	genome.wustl.edu	37	2	27351965	27351965	+	Missense_Mutation	SNP	T	T	C			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr2:27351965T>C	ENST00000316470.4	+	3	542	c.428T>C	c.(427-429)cTa>cCa	p.L143P		NM_032604.3	NP_115993	Q96SE0	ABHD1_HUMAN	abhydrolase domain containing 1	143						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			endometrium(1)|kidney(1)|lung(3)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCTTGCACCTAGTTAACCAA	0.552																																						dbGAP											0													72.0	68.0	69.0					2																	27351965		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK093447	CCDS1736.1	2p23.3	2011-01-21			ENSG00000143994	ENSG00000143994		"""Abhydrolase domain containing"""	17553	protein-coding gene	gene with protein product		612195				11922611	Standard	NM_032604		Approved	LABH1, FLJ36128	uc002rit.3	Q96SE0	OTTHUMG00000097072	ENST00000316470.4:c.428T>C	2.37:g.27351965T>C	ENSP00000326491:p.Leu143Pro		B3KSF6|E9PDR9|Q05BY3|Q53SZ1|Q8IXQ7	Missense_Mutation	SNP	pfam_AB_hydrolase_1,pirsf_AB-Hydro_YheT	p.L143P	ENST00000316470.4	37	c.428	CCDS1736.1	2	.	.	.	.	.	.	.	.	.	.	T	10.73	1.431586	0.25813	.	.	ENSG00000143994	ENST00000316470;ENST00000416071	T;T	0.10192	2.9;2.9	4.95	3.78	0.43462	.	0.190807	0.36200	N	0.002735	T	0.30665	0.0772	M	0.80746	2.51	0.53005	D	0.99996	D	0.76494	0.999	D	0.83275	0.996	T	0.01909	-1.1249	10	0.62326	D	0.03	-28.3937	7.8352	0.29365	0.1844:0.0:0.0:0.8156	.	143	Q96SE0	ABHD1_HUMAN	P	143;80	ENSP00000326491:L143P;ENSP00000397522:L80P	ENSP00000326491:L143P	L	+	2	0	ABHD1	27205469	0.305000	0.24481	0.046000	0.18839	0.032000	0.12392	1.595000	0.36708	0.887000	0.36136	-0.333000	0.08304	CTA	ABHD1	-	pirsf_AB-Hydro_YheT	ENSG00000143994		0.552	ABHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABHD1	HGNC	protein_coding	OTTHUMT00000214188.1	38	0.00	0	T	NM_032604		27351965	27351965	+1	no_errors	ENST00000316470	ensembl	human	known	69_37n	missense	45	22.41	13	SNP	0.802	C
ANKRD35	148741	genome.wustl.edu	37	1	145556634	145556634	+	Silent	SNP	A	A	G			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr1:145556634A>G	ENST00000355594.4	+	3	291	c.204A>G	c.(202-204)gaA>gaG	p.E68E	ANKRD35_ENST00000544626.1_Silent_p.E68E	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	68										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCCTGACAGAATGTCTGACTA	0.547																																					Melanoma(9;127 754 22988 51047)	dbGAP											0													39.0	34.0	36.0					1																	145556634		2201	4295	6496	-	-	-	SO:0001819	synonymous_variant	0			AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.204A>G	1.37:g.145556634A>G			A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,prints_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.E68	ENST00000355594.4	37	c.204	CCDS919.1	1																																																																																			ANKRD35	-	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	ENSG00000198483		0.547	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD35	HGNC	protein_coding	OTTHUMT00000038515.1	41	0.00	0	A	NM_144698		145556634	145556634	+1	no_errors	ENST00000355594	ensembl	human	known	69_37n	silent	86	12.24	12	SNP	0.997	G
ATP11A	23250	genome.wustl.edu	37	13	113512469	113512469	+	Silent	SNP	C	C	G			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr13:113512469C>G	ENST00000487903.1	+	22	2620	c.2532C>G	c.(2530-2532)ggC>ggG	p.G844G	ATP11A_ENST00000283558.8_Silent_p.G844G|ATP11A_ENST00000375630.2_Silent_p.G844G|ATP11A_ENST00000375645.3_Silent_p.G844G			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	844					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				GTGTCATCGGCAAGGAAGGCC	0.493																																						dbGAP											0													105.0	98.0	100.0					13																	113512469		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.2532C>G	13.37:g.113512469C>G			Q5VXT2	Missense_Mutation	SNP	pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,tigrfam_ATPase_P-typ_ion-transptr	p.A265G	ENST00000487903.1	37	c.794	CCDS32011.1	13	.	.	.	.	.	.	.	.	.	.	C	8.013	0.758021	0.15846	.	.	ENSG00000068650	ENST00000418678	.	.	.	5.62	-4.35	0.03656	.	.	.	.	.	T	0.53981	0.1830	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52771	-0.8531	4	.	.	.	.	10.6357	0.45563	0.3831:0.5241:0.0927:0.0	.	.	.	.	G	819	.	.	A	+	2	0	ATP11A	112560470	0.983000	0.35010	0.566000	0.28421	0.765000	0.43378	0.206000	0.17375	-1.135000	0.02895	-0.165000	0.13383	GCA	ATP11A	-	superfamily_HAD-like_dom,tigrfam_ATPase_P-typ_ion-transptr	ENSG00000068650		0.493	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	ATP11A	HGNC	protein_coding	OTTHUMT00000045834.3	46	0.00	0	C	NM_015205		113512469	113512469	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000471555	ensembl	human	known	69_37n	missense	100	22.48	29	SNP	0.958	G
C17orf104	284071	genome.wustl.edu	37	17	42744021	42744021	+	Missense_Mutation	SNP	C	C	A			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr17:42744021C>A	ENST00000409122.2	+	5	884	c.742C>A	c.(742-744)Cac>Aac	p.H248N	C17orf104_ENST00000359945.3_Missense_Mutation_p.H248N|C17orf104_ENST00000409464.1_Missense_Mutation_p.H82N	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	248										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						TTCTAACTGTCACAATATTCA	0.358																																						dbGAP											0													77.0	68.0	71.0					17																	42744021		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.742C>A	17.37:g.42744021C>A	ENSP00000386452:p.His248Asn		B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	NULL	p.H248N	ENST00000409122.2	37	c.742	CCDS45703.2	17	.	.	.	.	.	.	.	.	.	.	C	7.057	0.565564	0.13560	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000456912;ENST00000409464	T;T;T;T;T	0.29655	1.56;1.56;1.61;1.61;1.56	5.54	4.41	0.53225	.	0.281914	0.31199	N	0.008067	T	0.16385	0.0394	N	0.08118	0	0.22975	N	0.998485	B;B;B	0.22909	0.077;0.022;0.022	B;B;B	0.21708	0.036;0.036;0.036	T	0.16748	-1.0392	10	0.32370	T	0.25	-15.7379	11.5276	0.50588	0.0:0.0713:0.0:0.9287	.	248;248;82	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	N	248;248;82;82;82	ENSP00000353028:H248N;ENSP00000386452:H248N;ENSP00000399809:H82N;ENSP00000397957:H82N;ENSP00000386586:H82N	ENSP00000353028:H248N	H	+	1	0	C17orf104	40099547	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.930000	0.48924	1.020000	0.39573	-0.423000	0.05987	CAC	C17orf104	-	NULL	ENSG00000180336		0.358	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	C17orf104	HGNC	protein_coding	OTTHUMT00000329171.2	30	0.00	0	C	NM_001145080		42744021	42744021	+1	no_errors	ENST00000409122	ensembl	human	known	69_37n	missense	115	29.88	49	SNP	1.000	A
CATSPER3	347732	genome.wustl.edu	37	5	134347257	134347257	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr5:134347257C>G	ENST00000282611.6	+	8	1227	c.1141C>G	c.(1141-1143)Ctg>Gtg	p.L381V		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	381					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GAGCCTAATGCTGGAAGACTT	0.542																																						dbGAP											0													88.0	76.0	80.0					5																	134347257		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.1141C>G	5.37:g.134347257C>G	ENSP00000282611:p.Leu381Val		Q86XS6	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_PKD1_2_channel	p.L381V	ENST00000282611.6	37	c.1141	CCDS4181.1	5	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741524	0.30865	.	.	ENSG00000152705	ENST00000282611	D	0.97279	-4.32	4.71	2.88	0.33553	.	0.149302	0.29369	N	0.012348	D	0.97155	0.9070	L	0.56769	1.78	0.29201	N	0.875201	D	0.76494	0.999	D	0.78314	0.991	D	0.92715	0.6186	10	0.62326	D	0.03	-20.6292	7.0461	0.25046	0.0:0.795:0.0:0.205	.	381	Q86XQ3	CTSR3_HUMAN	V	381	ENSP00000282611:L381V	ENSP00000282611:L381V	L	+	1	2	CATSPER3	134375156	0.997000	0.39634	0.987000	0.45799	0.152000	0.21847	1.083000	0.30815	1.329000	0.45376	0.561000	0.74099	CTG	CATSPER3	-	NULL	ENSG00000152705		0.542	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CATSPER3	HGNC	protein_coding	OTTHUMT00000251191.2	20	0.00	0	C	NM_178019		134347257	134347257	+1	no_errors	ENST00000282611	ensembl	human	known	69_37n	missense	106	31.85	50	SNP	0.970	G
PDXDC2P	283970	genome.wustl.edu	37	16	70010517	70010519	+	RNA	DEL	TGT	TGT	-	rs372253115		TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	TGT	TGT					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr16:70010517_70010519delTGT	ENST00000531894.1	-	0	3864_3866				RP11-419C5.2_ENST00000525562.1_RNA	NR_003610.1		Q6P474	PDXD2_HUMAN	pyridoxal-dependent decarboxylase domain containing 2, pseudogene						carboxylic acid metabolic process (GO:0019752)		carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)	p.Q253delQ(2)									AGTTATAGAATGTTGTTGAGTTG	0.507																																						dbGAP											2	Deletion - In frame(2)	breast(2)																																								-	-	-			0					16q22.1	2014-03-20	2010-09-02	2010-09-02	ENSG00000196696	ENSG00000196696			27559	pseudogene	pseudogene			"""pyridoxal-dependent decarboxylase domain containing 2"""	PDXDC2			Standard	NR_003610		Approved	DKFZp761H1120	uc010vlq.1	Q6P474	OTTHUMG00000167595		16.37:g.70010520_70010522delTGT			A8K9Z5	In_Frame_Del	DEL	pfam_NPIP	p.Q253in_frame_del	ENST00000531894.1	37	c.761_759		16																																																																																			RP11-419C5.2	-	pfam_NPIP	ENSG00000226232		0.507	PDXDC2P-001	KNOWN	basic|readthrough_transcript	processed_transcript	ENSG00000226232	Clone_based_vega_gene	processed_transcript	OTTHUMT00000395258.1	9	0.00	0	TGT			70010517	70010519	-1	no_errors	ENST00000532298	ensembl	human	novel	69_37n	in_frame_del	8	38.46	5	DEL	0.600:0.610:0.620	-
EPB41	2035	genome.wustl.edu	37	1	29344886	29344886	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr1:29344886delT	ENST00000343067.4	+	7	1183	c.1056delT	c.(1054-1056)gatfs	p.D352fs	EPB41_ENST00000398863.2_Frame_Shift_Del_p.D352fs|EPB41_ENST00000356093.2_Frame_Shift_Del_p.D352fs|EPB41_ENST00000373798.1_Frame_Shift_Del_p.D352fs|EPB41_ENST00000347529.3_Frame_Shift_Del_p.D317fs|EPB41_ENST00000373797.1_Frame_Shift_Del_p.D352fs|EPB41_ENST00000373800.3_Frame_Shift_Del_p.D143fs|EPB41_ENST00000349460.4_Frame_Shift_Del_p.D143fs	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	352	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		ATGTTAGTGATTTTAAACTGG	0.448																																						dbGAP											0													148.0	136.0	140.0					1																	29344886		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"""elliptocytosis 1, RH-linked"""	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.1056delT	1.37:g.29344886delT	ENSP00000345259:p.Asp352fs		B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Frame_Shift_Del	DEL	pirsf_Band_41_protein,pfam_Band_4.1_C,pfam_SAB,pfam_FERM_PH-like_C,pfam_FERM_N,pfam_FERM_central,pfam_FERM-adjacent,superfamily_FERM_central,smart_Band_41_domain,prints_Band_41_fam,prints_Ez/rad/moesin,pfscan_FERM_domain	p.F353fs	ENST00000343067.4	37	c.1056	CCDS53288.1	1																																																																																			EPB41	-	pirsf_Band_41_protein,pfam_FERM_central,superfamily_FERM_central,smart_Band_41_domain,pfscan_FERM_domain	ENSG00000159023		0.448	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	EPB41	HGNC	protein_coding	OTTHUMT00000010312.1	34	0.00	0	T	NM_203342		29344886	29344886	+1	no_errors	ENST00000343067	ensembl	human	known	69_37n	frame_shift_del	96	27.07	36	DEL	0.951	-
GPX2	2877	genome.wustl.edu	37	14	65406536	65406536	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr14:65406536C>G	ENST00000389614.5	-	2	329	c.243G>C	c.(241-243)gaG>gaC	p.E81D	FNTB_ENST00000447296.2_Intron|CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000542227.1_Intron	NM_002083.3	NP_002074.2	P18283	GPX2_HUMAN	glutathione peroxidase 2 (gastrointestinal)	81					interaction with symbiont (GO:0051702)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|response to oxidative stress (GO:0006979)|response to symbiotic bacterium (GO:0009609)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|glutathione peroxidase activity (GO:0004602)			large_intestine(2)|ovary(1)|skin(1)	4				all cancers(60;0.00117)|OV - Ovarian serous cystadenocarcinoma(108;0.00557)|BRCA - Breast invasive adenocarcinoma(234;0.00971)	Glutathione(DB00143)	TGTTCAGGATCTCCTCATTCT	0.512																																						dbGAP											0													56.0	52.0	53.0					14																	65406536		1963	4138	6101	-	-	-	SO:0001583	missense	0				CCDS41964.1	14q23.3	2012-05-22			ENSG00000176153	ENSG00000176153	1.11.1.9		4554	protein-coding gene	gene with protein product		138319				8428933, 8287691	Standard	NM_002083		Approved	GSHPX-GI	uc021ruq.2	P18283	OTTHUMG00000171677	ENST00000389614.5:c.243G>C	14.37:g.65406536C>G	ENSP00000374265:p.Glu81Asp		Q6PJ52|Q8WWI7|Q9NRP9	Missense_Mutation	SNP	pfam_Glutathione_peroxidase,superfamily_Thioredoxin-like_fold,pirsf_Glutathione_peroxidase,prints_Glutathione_peroxidase	p.E81D	ENST00000389614.5	37	c.243	CCDS41964.1	14	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778410	0.90195	.	.	ENSG00000176153	ENST00000389614;ENST00000557049	T;T	0.11495	2.77;2.77	6.06	6.06	0.98353	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.37679	0.1012	M	0.77820	2.39	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.03296	-1.1051	10	0.87932	D	0	-0.6872	19.3923	0.94587	0.0:1.0:0.0:0.0	.	81	P18283	GPX2_HUMAN	D	81;25	ENSP00000374265:E81D;ENSP00000451721:E25D	ENSP00000374265:E81D	E	-	3	2	GPX2	64476289	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.299000	0.51826	2.882000	0.98803	0.655000	0.94253	GAG	GPX2	-	pfam_Glutathione_peroxidase,superfamily_Thioredoxin-like_fold,pirsf_Glutathione_peroxidase	ENSG00000176153		0.512	GPX2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	GPX2	HGNC	protein_coding	OTTHUMT00000414708.1	37	0.00	0	C			65406536	65406536	-1	pseudogene	ENST00000389614	ensembl	human	known	69_37n	missense	37	15.91	7	SNP	1.000	G
RGL4	266747	genome.wustl.edu	37	22	24037232	24037232	+	Intron	SNP	G	G	A	rs539191534		TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr22:24037232G>A	ENST00000290691.5	+	6	2256				AP000347.2_ENST00000417194.1_RNA|GUSBP11_ENST00000455485.1_RNA|RGL4_ENST00000401461.1_Intron|KB-1572G7.2_ENST00000421064.1_RNA	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4						small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						GGAGATGCAGGACAAGTGTTT	0.433																																						dbGAP											0													91.0	82.0	85.0					22																	24037232		2203	4300	6503	-	-	-	SO:0001627	intron_variant	0				CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"""RalGDS related oncogene"""	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.1086+26G>A	22.37:g.24037232G>A			Q495L8	RNA	SNP	-	NULL	ENST00000290691.5	37	NULL	CCDS13811.1	22																																																																																			GUSBP11	-	-	ENSG00000228315		0.433	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GUSBP11	HGNC	protein_coding	OTTHUMT00000319711.1	25	0.00	0	G	NM_153615		24037232	24037232	-1	no_errors	ENST00000421064	ensembl	human	known	69_37n	rna	121	19.33	29	SNP	0.000	A
KLF4	9314	genome.wustl.edu	37	9	110249348	110249348	+	Missense_Mutation	SNP	T	T	G			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr9:110249348T>G	ENST00000374672.4	-	4	1698	c.1225A>C	c.(1225-1227)Aag>Cag	p.K409Q		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	443	Pro-rich.				cellular response to cycloheximide (GO:0071409)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|epidermal cell differentiation (GO:0009913)|epidermis morphogenesis (GO:0048730)|fat cell differentiation (GO:0045444)|mesodermal cell fate determination (GO:0007500)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of muscle hyperplasia (GO:0014740)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic camera-type eye development (GO:0031077)|post-embryonic hemopoiesis (GO:0035166)|regulation of cell differentiation (GO:0045595)|response to retinoic acid (GO:0032526)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001010)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.K400Q(1)		breast(1)|central_nervous_system(3)|endometrium(5)|large_intestine(1)|lung(3)|pancreas(1)|prostate(2)	16						TGGGAACTCTTTGTGTAGGTT	0.597																																						dbGAP											1	Substitution - Missense(1)	pancreas(1)											292.0	261.0	272.0					9																	110249348		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF022184	CCDS6770.2	9q31	2013-01-08			ENSG00000136826	ENSG00000136826		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6348	protein-coding gene	gene with protein product		602253				9422764, 16372018	Standard	NM_004235		Approved	EZF, GKLF	uc004bdg.3	O43474	OTTHUMG00000020449	ENST00000374672.4:c.1225A>C	9.37:g.110249348T>G	ENSP00000363804:p.Lys409Gln		B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Missense_Mutation	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.K409Q	ENST00000374672.4	37	c.1225	CCDS6770.2	9	.	.	.	.	.	.	.	.	.	.	T	24.9	4.578042	0.86645	.	.	ENSG00000136826	ENST00000374672	T	0.36157	1.27	5.33	4.2	0.49525	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.554792	0.15210	N	0.274523	T	0.58637	0.2136	M	0.89601	3.045	0.58432	D	0.999997	D;P	0.54397	0.966;0.89	P;P	0.54346	0.543;0.749	T	0.63804	-0.6554	10	0.87932	D	0	.	10.7368	0.46130	0.0:0.0756:0.0:0.9244	.	443;409	O43474;O43474-1	KLF4_HUMAN;.	Q	409	ENSP00000363804:K409Q	ENSP00000363804:K409Q	K	-	1	0	KLF4	109289169	1.000000	0.71417	0.984000	0.44739	0.967000	0.64934	8.005000	0.88553	0.876000	0.35872	-0.250000	0.11733	AAG	KLF4	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000136826		0.597	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	KLF4	HGNC	protein_coding	OTTHUMT00000053556.2	91	0.00	0	T	NM_004235		110249348	110249348	-1	no_errors	ENST00000374672	ensembl	human	known	69_37n	missense	195	54.55	234	SNP	1.000	G
MAGI2	9863	genome.wustl.edu	37	7	77789414	77789414	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr7:77789414G>A	ENST00000354212.4	-	16	3026	c.2773C>T	c.(2773-2775)Cgc>Tgc	p.R925C	MAGI2_ENST00000419488.1_Missense_Mutation_p.R911C|MAGI2_ENST00000522391.1_Missense_Mutation_p.R925C	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	925	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TTCTCTTTGCGGTGAATGACC	0.532																																						dbGAP											0													110.0	98.0	102.0					7																	77789414		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.2773C>T	7.37:g.77789414G>A	ENSP00000346151:p.Arg925Cys		A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	pfam_PDZ,pfam_WW_Rsp5_WWP,pfam_Guanylate_kin,superfamily_PDZ,superfamily_WW_Rsp5_WWP,smart_PDZ,smart_Guanylate_kin/L-typ_Ca_channel,smart_WW_Rsp5_WWP,pfscan_PDZ,pfscan_WW_Rsp5_WWP,pfscan_Guanylate_kin	p.R925C	ENST00000354212.4	37	c.2773	CCDS5594.1	7	.	.	.	.	.	.	.	.	.	.	G	31	5.084146	0.94100	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.31247	1.5;1.5;1.5	5.39	5.39	0.77823	PDZ/DHR/GLGF (3);	0.000000	0.37178	U	0.002215	T	0.61751	0.2372	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.67205	-0.5729	10	0.87932	D	0	.	19.1358	0.93428	0.0:0.0:1.0:0.0	.	925;911;925	E7EWI0;Q86UL8-2;Q86UL8	.;.;MAGI2_HUMAN	C	911;925;925;925	ENSP00000405766:R911C;ENSP00000346151:R925C;ENSP00000428389:R925C	ENSP00000346151:R925C	R	-	1	0	MAGI2	77627350	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.471000	0.97696	2.519000	0.84933	0.585000	0.79938	CGC	MAGI2	-	pfam_PDZ,superfamily_PDZ,pfscan_PDZ	ENSG00000187391		0.532	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAGI2	HGNC	protein_coding	OTTHUMT00000253197.3	39	0.00	0	G	NM_012301		77789414	77789414	-1	no_errors	ENST00000354212	ensembl	human	known	69_37n	missense	96	27.82	37	SNP	1.000	A
MAP3K1	4214	genome.wustl.edu	37	5	56176938	56176938	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr5:56176938delT	ENST00000399503.3	+	13	2208	c.2208delT	c.(2206-2208)tatfs	p.Y736fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	736					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GTGTTGATTATGTCTTAAATT	0.303																																						dbGAP											0													110.0	96.0	100.0					5																	56176938		1822	4079	5901	-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2208delT	5.37:g.56176938delT	ENSP00000382423:p.Tyr736fs			Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.Y736fs	ENST00000399503.3	37	c.2208	CCDS43318.1	5																																																																																			MAP3K1	-	superfamily_ARM-type_fold	ENSG00000095015		0.303	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	99	0.00	0	T	XM_042066		56176938	56176938	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	178	30.57	81	DEL	1.000	-
MUC5B	727897	genome.wustl.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	byFrequency	TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr11:1268064C>T	ENST00000529681.1	+	31	10012	c.9954C>T	c.(9952-9954)gcC>gcT	p.A3318A	MUC5B_ENST00000447027.1_Silent_p.A3321A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3318	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCTTCACAGCCACCCCCTCCT	0.652													c|||	1636	0.326677	0.2156	0.3256	5008	,	,		19867	0.5387		0.2853	False		,,,				2504	0.3016					dbGAP											0													15.0	28.0	24.0					11																	1268064		1776	4009	5785	-	-	-	SO:0001819	synonymous_variant	0			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.9954C>T	11.37:g.1268064C>T			O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,pfam_VWF_C,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_VWF_C,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_VWF_C	p.A3321	ENST00000529681.1	37	c.9963	CCDS44515.2	11	.	.	.	.	.	.	.	.	.	.	C	3.753	-0.051234	0.07407	.	.	ENSG00000117983	ENST00000538459	.	.	.	3.18	0.963	0.19649	.	.	.	.	.	T	0.15392	0.0371	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.38908	-0.9639	4	0.02654	T	1	.	6.2137	0.20644	0.3708:0.4477:0.1814:0.0	.	.	.	.	Y	201	.	ENSP00000442622:H201Y	H	+	1	0	MUC5B	1224640	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.998000	0.03701	-0.041000	0.13558	0.305000	0.20034	CAC	MUC5B	-	NULL	ENSG00000117983		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	MUC5B	HGNC	protein_coding	OTTHUMT00000390041.2	9	0.00	0	C	XM_001126093		1268064	1268064	+1	no_errors	ENST00000447027	ensembl	human	known	69_37n	silent	100	32.43	48	SNP	0.000	T
OR8K3	219473	genome.wustl.edu	37	11	56085814	56085814	+	Missense_Mutation	SNP	A	A	T			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr11:56085814A>T	ENST00000312711.1	+	1	32	c.32A>T	c.(31-33)gAa>gTa	p.E11V		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					ACGGTGAATGAATTCATTCTT	0.423																																						dbGAP											0													138.0	126.0	130.0					11																	56085814		2201	4295	6496	-	-	-	SO:0001583	missense	0			AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"""GPCR / Class A : Olfactory receptors"""	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.32A>T	11.37:g.56085814A>T	ENSP00000323555:p.Glu11Val		Q6IFC4	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.E11V	ENST00000312711.1	37	c.32	CCDS31527.1	11	.	.	.	.	.	.	.	.	.	.	A	15.61	2.885337	0.51908	.	.	ENSG00000181689	ENST00000312711	T	0.11604	2.76	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000013	T	0.27594	0.0678	M	0.73598	2.24	0.32707	N	0.512128	D	0.54601	0.967	P	0.56343	0.796	T	0.41980	-0.9478	10	0.72032	D	0.01	.	13.5997	0.62011	1.0:0.0:0.0:0.0	.	11	Q8NH51	OR8K3_HUMAN	V	11	ENSP00000323555:E11V	ENSP00000323555:E11V	E	+	2	0	OR8K3	55842390	0.971000	0.33674	0.655000	0.29622	0.110000	0.19582	5.479000	0.66813	2.154000	0.67381	0.519000	0.50382	GAA	OR8K3	-	NULL	ENSG00000181689		0.423	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR8K3	HGNC	protein_coding	OTTHUMT00000391602.1	44	0.00	0	A	NM_001005202		56085814	56085814	+1	no_errors	ENST00000312711	ensembl	human	known	69_37n	missense	107	23.57	33	SNP	0.896	T
PCDHGA2	56113	genome.wustl.edu	37	5	140720953	140720953	+	Silent	SNP	G	G	A			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr5:140720953G>A	ENST00000394576.2	+	1	2415	c.2415G>A	c.(2413-2415)acG>acA	p.T805T	PCDHGA3_ENST00000253812.6_5'Flank|PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	805					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T805T(2)		breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGAAGAAACGTTTTCTCAGG	0.388																																						dbGAP											2	Substitution - coding silent(2)	large_intestine(2)											60.0	65.0	63.0					5																	140720953		2201	4300	6501	-	-	-	SO:0001819	synonymous_variant	0			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2415G>A	5.37:g.140720953G>A			Q52LL6|Q9Y5D5	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	p.T805	ENST00000394576.2	37	c.2415	CCDS47289.1	5																																																																																			PCDHGA2	-	NULL	ENSG00000081853		0.388	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGA2	HGNC	protein_coding	OTTHUMT00000374738.1	42	0.00	0	G	NM_018915		140720953	140720953	+1	no_errors	ENST00000394576	ensembl	human	known	69_37n	silent	82	18.81	19	SNP	0.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178936095	178936095	+	Missense_Mutation	SNP	A	A	C	rs397517201		TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr3:178936095A>C	ENST00000263967.3	+	10	1794	c.1637A>C	c.(1636-1638)cAg>cCg	p.Q546P		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	546	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		Q -> E (in BC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> K (in OC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> P (found in an anaplastic astrocytoma sample; unknown pathological significance). {ECO:0000269|PubMed:15289301}.|Q -> R (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q546R(30)|p.Q546P(18)|p.Q546L(5)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATCACTGAGCAGGAGAAAGAT	0.363		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	53	Substitution - Missense(53)	endometrium(18)|breast(17)|large_intestine(10)|central_nervous_system(3)|prostate(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)											61.0	61.0	61.0					3																	178936095		1813	4072	5885	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1637A>C	3.37:g.178936095A>C	ENSP00000263967:p.Gln546Pro		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.Q546P	ENST00000263967.3	37	c.1637	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	20.7	4.039935	0.75732	.	.	ENSG00000121879	ENST00000263967	T	0.64260	-0.09	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76673	0.4020	M	0.64404	1.975	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.78687	-0.2107	10	0.66056	D	0.02	-14.2064	16.1026	0.81194	1.0:0.0:0.0:0.0	.	546	P42336	PK3CA_HUMAN	P	546	ENSP00000263967:Q546P	ENSP00000263967:Q546P	Q	+	2	0	PIK3CA	180418789	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	CAG	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	31	0.00	0	A			178936095	178936095	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	75	32.43	36	SNP	1.000	C
RET	5979	genome.wustl.edu	37	10	43609956	43609956	+	Silent	SNP	G	G	A	rs121913310		TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr10:43609956G>A	ENST00000355710.3	+	11	2140	c.1908G>A	c.(1906-1908)acG>acA	p.T636T	RET_ENST00000340058.5_Silent_p.T636T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	636			T -> TCRT (in MEN2A). {ECO:0000269|PubMed:9452064}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D631_I638>A(1)|p.E632_A640>VRP(1)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TGTGCCGCACGGTGATCGCAG	0.617		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	dbGAP	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	2	Complex - deletion inframe(2)	thyroid(2)	GRCh37	CI983210	RET	I							145.0	88.0	107.0					10																	43609956		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.1908G>A	10.37:g.43609956G>A			A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	pirsf_Tyr_kinase_Ret_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Cadherin,superfamily_Kinase-like_dom,superfamily_Cadherin-like,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,pfscan_Cadherin	p.T636	ENST00000355710.3	37	c.1908	CCDS7200.1	10																																																																																			RET	-	pirsf_Tyr_kinase_Ret_rcpt	ENSG00000165731		0.617	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RET	HGNC	protein_coding	OTTHUMT00000047694.2	25	0.00	0	G	NM_020975		43609956	43609956	+1	no_errors	ENST00000355710	ensembl	human	known	69_37n	silent	40	20.00	10	SNP	0.628	A
TLE3	7090	genome.wustl.edu	37	15	70347454	70347454	+	Silent	SNP	G	G	A			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr15:70347454G>A	ENST00000558939.1	-	15	2898	c.1521C>T	c.(1519-1521)ggC>ggT	p.G507G	TLE3_ENST00000560939.1_Silent_p.G509G|TLE3_ENST00000539550.1_Silent_p.G434G|TLE3_ENST00000317509.8_Silent_p.G495G|TLE3_ENST00000558379.1_Silent_p.G502G|TLE3_ENST00000559048.1_Silent_p.G507G|TLE3_ENST00000557997.1_Silent_p.G499G|TLE3_ENST00000451782.2_Silent_p.G504G|TLE3_ENST00000558201.1_Silent_p.G513G|TLE3_ENST00000560589.1_Silent_p.G451G|TLE3_ENST00000559929.1_Silent_p.G517G|TLE3_ENST00000557907.1_Silent_p.G499G|TLE3_ENST00000442299.2_Silent_p.G499G|TLE3_ENST00000559191.1_Silent_p.G88G|TLE3_ENST00000440567.3_Silent_p.G497G	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	507					Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TCTTCACGCAGCCCTTGCCAC	0.652																																						dbGAP											0													55.0	58.0	57.0					15																	70347454		2199	4298	6497	-	-	-	SO:0001819	synonymous_variant	0			M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1521C>T	15.37:g.70347454G>A			B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	pfam_Groucho/TLE_N,superfamily_WD40_repeat_dom	p.A578V	ENST00000558939.1	37	c.1733	CCDS45293.1	15																																																																																			TLE3	-	superfamily_WD40_repeat_dom	ENSG00000140332		0.652	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TLE3	HGNC	protein_coding	OTTHUMT00000416913.1	68	0.00	0	G	NM_005078		70347454	70347454	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000560525	ensembl	human	known	69_37n	missense	39	31.58	18	SNP	1.000	A
XXYLT1	152002	genome.wustl.edu	37	3	194877239	194877239	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A1KI-01A-11D-A14K-09	TCGA-B6-A1KI-10A-01W-A16I-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d9374702-8fc6-48c0-bec5-5c1105e641dc	12983a0c-2f74-4c87-af64-048fbfea9ddd	g.chr3:194877239A>G	ENST00000310380.6	-	3	832	c.724T>C	c.(724-726)Ttt>Ctt	p.F242L	XXYLT1_ENST00000437101.1_Missense_Mutation_p.F39L|XXYLT1_ENST00000355729.4_Missense_Mutation_p.F39L|XXYLT1_ENST00000429994.1_Missense_Mutation_p.F96L	NM_152531.4	NP_689744.3	Q8NBI6	XXLT1_HUMAN	xyloside xylosyltransferase 1	242						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring pentosyl groups (GO:0016763)										AAACTGTCAAATTCCTCAAAC	0.547																																						dbGAP											0													75.0	80.0	79.0					3																	194877239		1929	4144	6073	-	-	-	SO:0001583	missense	0			AK075551	CCDS43188.1	3q29	2013-02-22	2011-10-19	2011-10-19	ENSG00000173950	ENSG00000173950		"""Glycosyltransferase family 8 domain containing"""	26639	protein-coding gene	gene with protein product		614552	"""chromosome 3 open reading frame 21"""	C3orf21		22117070	Standard	NM_152531		Approved	FLJ35155	uc003fum.4	Q8NBI6	OTTHUMG00000155915	ENST00000310380.6:c.724T>C	3.37:g.194877239A>G	ENSP00000309640:p.Phe242Leu		D3DNW5|Q8NAL3|Q8WV03|Q96ME0	Missense_Mutation	SNP	pfam_Glyco_trans_8	p.F242L	ENST00000310380.6	37	c.724	CCDS43188.1	3	.	.	.	.	.	.	.	.	.	.	A	32	5.180013	0.94846	.	.	ENSG00000173950	ENST00000310380;ENST00000437101;ENST00000355729;ENST00000429994;ENST00000458652	T	0.66995	-0.24	5.48	5.48	0.80851	.	0.048981	0.85682	D	0.000000	T	0.77605	0.4155	L	0.58510	1.815	0.80722	D	1	D;D;D	0.76494	0.999;0.992;0.999	D;D;P	0.77004	0.989;0.939;0.863	T	0.76735	-0.2850	10	0.38643	T	0.18	-5.5457	13.5272	0.61601	1.0:0.0:0.0:0.0	.	96;242;39	C9JV19;Q8NBI6;Q8NBI6-2	.;XXLT1_HUMAN;.	L	242;39;39;96;96	ENSP00000309640:F242L	ENSP00000309640:F242L	F	-	1	0	C3orf21	196358528	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	8.838000	0.92115	2.077000	0.62373	0.460000	0.39030	TTT	XXYLT1	-	pfam_Glyco_trans_8	ENSG00000173950		0.547	XXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XXYLT1	HGNC	protein_coding	OTTHUMT00000342290.1	70	0.00	0	A	NM_152531		194877239	194877239	-1	no_errors	ENST00000310380	ensembl	human	known	69_37n	missense	68	12.82	10	SNP	1.000	G
