#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
ACSS3	79611	genome.wustl.edu	37	12	81503342	81503342	+	Silent	SNP	T	T	C			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr12:81503342T>C	ENST00000548058.1	+	2	1225	c.315T>C	c.(313-315)ttT>ttC	p.F105F	ACSS3_ENST00000261206.3_Silent_p.F104F|RP11-543H12.1_ENST00000547123.1_RNA			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	105						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						TTTTCAGGTTTGTGGAAGGAA	0.323																																						dbGAP											0													84.0	83.0	83.0					12																	81503342		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0				CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.315T>C	12.37:g.81503342T>C			Q8NC66	Silent	SNP	pfam_AMP-dep_Synth/Lig,pfam_Acyl-CoA_synth_DUF3448	p.F105	ENST00000548058.1	37	c.315	CCDS9022.1	12																																																																																			ACSS3	-	pfam_Acyl-CoA_synth_DUF3448	ENSG00000111058		0.323	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ACSS3	HGNC	protein_coding	OTTHUMT00000407794.1	166	0.00	0	T	NM_024560		81503342	81503342	+1	no_errors	ENST00000548058	ensembl	human	known	69_37n	silent	228	21.38	62	SNP	1.000	C
APBA2	321	genome.wustl.edu	37	15	29397755	29397756	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	CA	CA					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr15:29397755_29397756delCA	ENST00000558402.1	+	12	2297_2298	c.1698_1699delCA	c.(1696-1701)tgcaagfs	p.CK566fs	APBA2_ENST00000561069.1_Frame_Shift_Del_p.CK566fs|APBA2_ENST00000411764.1_Frame_Shift_Del_p.CK554fs|APBA2_ENST00000558330.1_Frame_Shift_Del_p.CK554fs|APBA2_ENST00000558259.1_Frame_Shift_Del_p.CK566fs			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	566					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGGAGAACTGCAAGGAGGTAAG	0.569																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1698_1699delCA	15.37:g.29397755_29397756delCA	ENSP00000453293:p.Cys566fs		E9PGI4|O60571|Q5XKC0	Frame_Shift_Del	DEL	pfam_PTyr_interaction_dom,pfam_PDZ,superfamily_PDZ,smart_PTyr_interaction_dom,smart_PDZ,pfscan_PDZ,pfscan_PTyr_interaction_dom	p.C566fs	ENST00000558402.1	37	c.1698_1699	CCDS10022.1	15																																																																																			APBA2	-	superfamily_PDZ	ENSG00000034053		0.569	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APBA2	HGNC	protein_coding	OTTHUMT00000251362.3	14	0.00	0	CA	NM_005503		29397755	29397756	+1	no_errors	ENST00000558259	ensembl	human	known	69_37n	frame_shift_del	8	25.00	3	DEL	1.000:1.000	-
ATG2B	55102	genome.wustl.edu	37	14	96783628	96783628	+	Missense_Mutation	SNP	T	T	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr14:96783628T>A	ENST00000359933.4	-	20	3957	c.3064A>T	c.(3064-3066)Act>Tct	p.T1022S		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1022					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TACTGCAAAGTCTCCTCCTCA	0.338																																						dbGAP											0													61.0	57.0	58.0					14																	96783628		1813	4085	5898	-	-	-	SO:0001583	missense	0			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3064A>T	14.37:g.96783628T>A	ENSP00000353010:p.Thr1022Ser		Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	pfam_Autophagy-rel_C	p.T1022S	ENST00000359933.4	37	c.3064	CCDS9944.2	14	.	.	.	.	.	.	.	.	.	.	T	15.27	2.782334	0.49891	.	.	ENSG00000066739	ENST00000359933	T	0.42900	0.96	5.66	4.52	0.55395	.	0.257492	0.30723	U	0.009013	T	0.34048	0.0884	L	0.51422	1.61	0.43099	D	0.994783	P	0.40083	0.702	B	0.34418	0.182	T	0.11060	-1.0603	10	0.34782	T	0.22	.	11.5805	0.50889	0.0:0.0695:0.0:0.9305	.	1022	Q96BY7	ATG2B_HUMAN	S	1022	ENSP00000353010:T1022S	ENSP00000353010:T1022S	T	-	1	0	ATG2B	95853381	1.000000	0.71417	0.986000	0.45419	0.963000	0.63663	5.576000	0.67437	1.093000	0.41377	0.528000	0.53228	ACT	ATG2B	-	NULL	ENSG00000066739		0.338	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATG2B	HGNC	protein_coding	OTTHUMT00000314037.1	133	0.00	0	T	NM_018036		96783628	96783628	-1	no_errors	ENST00000359933	ensembl	human	known	69_37n	missense	141	30.20	61	SNP	1.000	A
CHRD	8646	genome.wustl.edu	37	3	184102997	184102997	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr3:184102997C>T	ENST00000204604.1	+	14	2035	c.1789C>T	c.(1789-1791)Cgg>Tgg	p.R597W	CHRD_ENST00000450923.1_Missense_Mutation_p.R597W|CHRD_ENST00000545352.1_Missense_Mutation_p.R227W|CHRD_ENST00000348986.3_Missense_Mutation_p.R557W|EIF2B5_ENST00000444495.1_Intron	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	597	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGGGCCTCGGCGGCTGCTGAA	0.572																																						dbGAP											0													56.0	60.0	58.0					3																	184102997		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1789C>T	3.37:g.184102997C>T	ENSP00000204604:p.Arg597Trp		O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	pfam_CHRD,pfam_VWF_C,smart_VWF_C,smart_CHRD,pirsf_Chordin,pfscan_CHRD,pfscan_VWF_C	p.R597W	ENST00000204604.1	37	c.1789	CCDS3266.1	3	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783636	0.70222	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.29	5.29	0.74685	CHRD (3);	0.000000	0.85682	D	0.000000	T	0.62938	0.2469	M	0.74881	2.28	0.51767	D	0.999937	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.991;0.993;0.992;0.996	T	0.65874	-0.6062	10	0.87932	D	0	-27.6398	11.8499	0.52405	0.1747:0.8253:0.0:0.0	.	227;557;597;597	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	W	597;597;557;227;310	ENSP00000204604:R597W;ENSP00000408972:R597W;ENSP00000334036:R557W;ENSP00000442948:R227W	ENSP00000204604:R597W	R	+	1	2	CHRD	185585691	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.045000	0.49838	2.662000	0.90505	0.655000	0.94253	CGG	CHRD	-	pfam_CHRD,smart_CHRD,pirsf_Chordin,pfscan_CHRD	ENSG00000090539		0.572	CHRD-001	KNOWN	basic|CCDS	protein_coding	CHRD	HGNC	protein_coding	OTTHUMT00000280432.1	58	0.00	0	C	NM_003741		184102997	184102997	+1	no_errors	ENST00000204604	ensembl	human	known	69_37n	missense	13	68.29	28	SNP	1.000	T
CIZ1	25792	genome.wustl.edu	37	9	130931780	130931780	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr9:130931780G>A	ENST00000393608.1	-	13	2252	c.2050C>T	c.(2050-2052)Cga>Tga	p.R684*	CIZ1_ENST00000325721.8_Nonsense_Mutation_p.R655*|CIZ1_ENST00000372954.1_Nonsense_Mutation_p.R604*|CIZ1_ENST00000541172.1_Nonsense_Mutation_p.R583*|CIZ1_ENST00000372948.3_Nonsense_Mutation_p.R628*|CIZ1_ENST00000277465.4_Nonsense_Mutation_p.R656*|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Nonsense_Mutation_p.R710*|CIZ1_ENST00000372938.5_Nonsense_Mutation_p.R684*|CIZ1_ENST00000357558.5_Nonsense_Mutation_p.R656*	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	684					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R684*(2)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CAGAAGGGTCGCAAGGATTGT	0.567																																						dbGAP											2	Substitution - Nonsense(2)	large_intestine(1)|lung(1)											106.0	96.0	100.0					9																	130931780		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.2050C>T	9.37:g.130931780G>A	ENSP00000377232:p.Arg684*		A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Nonsense_Mutation	SNP	pfam_Znf_C2H2_jaz,smart_Znf_U1,smart_Znf_C2H2-like,pfscan_Znf_C2H2_matrin	p.R710*	ENST00000393608.1	37	c.2128	CCDS6894.1	9	.	.	.	.	.	.	.	.	.	.	G	40	8.351770	0.98772	.	.	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	.	.	.	5.34	2.01	0.26516	.	0.000000	0.38548	N	0.001650	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.3476	14.4788	0.67564	0.0:0.0:0.4026:0.5974	.	.	.	.	X	604;684;710;656;655;623;583;656;628;684;606	.	.	R	-	1	2	CIZ1	129971601	1.000000	0.71417	0.997000	0.53966	0.866000	0.49608	1.560000	0.36331	0.148000	0.19059	0.462000	0.41574	CGA	CIZ1	-	smart_Znf_U1	ENSG00000148337		0.567	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CIZ1	HGNC	protein_coding	OTTHUMT00000054399.1	27	0.00	0	G	NM_012127		130931780	130931780	-1	no_errors	ENST00000538431	ensembl	human	known	69_37n	nonsense	26	13.33	4	SNP	0.994	A
DDX47	51202	genome.wustl.edu	37	12	12974215	12974215	+	Silent	SNP	A	A	G	rs560886374		TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr12:12974215A>G	ENST00000358007.3	+	3	277	c.255A>G	c.(253-255)gcA>gcG	p.A85A	DDX47_ENST00000392155.2_3'UTR|DDX47_ENST00000352940.4_Silent_p.A85A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	85	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		TTCTAAACGCACTGCTGGAGA	0.512													A|||	1	0.000199681	0.0	0.0	5008	,	,		17638	0.0		0.0	False		,,,				2504	0.001					dbGAP											0													135.0	132.0	133.0					12																	12974215		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.255A>G	12.37:g.12974215A>G			B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Silent	SNP	pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase_C,pfam_Helicase/UvrB_dom,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_RNA_helicase_DEAD_Q_motif	p.A85	ENST00000358007.3	37	c.255	CCDS8655.1	12																																																																																			DDX47	-	pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase/UvrB_dom,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd	ENSG00000213782		0.512	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DDX47	HGNC	protein_coding	OTTHUMT00000400674.1	276	0.36	1	A	NM_016355		12974215	12974215	+1	no_errors	ENST00000358007	ensembl	human	known	69_37n	silent	300	26.21	108	SNP	0.001	G
EEA1	8411	genome.wustl.edu	37	12	93195436	93195436	+	Silent	SNP	C	C	T			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr12:93195436C>T	ENST00000322349.8	-	20	2976	c.2712G>A	c.(2710-2712)caG>caA	p.Q904Q		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	904					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TGTTTTCCATCTGCACTTGAA	0.259																																						dbGAP											0													96.0	94.0	95.0					12																	93195436		2201	4293	6494	-	-	-	SO:0001819	synonymous_variant	0			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.2712G>A	12.37:g.93195436C>T			Q14221	Silent	SNP	pfam_Znf_FYVE,superfamily_Znf_FYVE_PHD,smart_Znf_FYVE,pfscan_Znf_FYVE-rel,pfscan_Znf_C2H2	p.Q904	ENST00000322349.8	37	c.2712	CCDS31874.1	12																																																																																			EEA1	-	NULL	ENSG00000102189		0.259	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EEA1	HGNC	protein_coding	OTTHUMT00000407304.1	78	0.00	0	C	NM_003566		93195436	93195436	-1	no_errors	ENST00000322349	ensembl	human	known	69_37n	silent	72	34.55	38	SNP	0.135	T
FLII	2314	genome.wustl.edu	37	17	18158120	18158120	+	Missense_Mutation	SNP	C	C	G			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr17:18158120C>G	ENST00000327031.4	-	5	601	c.376G>C	c.(376-378)Gcc>Ccc	p.A126P	FLII_ENST00000379450.4_Missense_Mutation_p.A95P|FLII_ENST00000584444.1_5'UTR|FLII_ENST00000579294.1_Missense_Mutation_p.A115P|FLII_ENST00000578558.1_Missense_Mutation_p.A126P|FLII_ENST00000545457.2_Missense_Mutation_p.A126P	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	126	Interaction with LRRFIP1 and LRRFIP2.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					ATGTTCTTGGCGTTCTCCAGC	0.662																																						dbGAP											0													90.0	82.0	85.0					17																	18158120		2203	4300	6503	-	-	-	SO:0001583	missense	0			U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.376G>C	17.37:g.18158120C>G	ENSP00000324573:p.Ala126Pro		B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	pfam_Gelsolin_dom,pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Gelsolin,prints_Gelsolin	p.A126P	ENST00000327031.4	37	c.376	CCDS11192.1	17	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361853	0.82353	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T;T	0.25250	1.81;1.84;1.87	5.8	4.83	0.62350	.	0.216114	0.48286	D	0.000191	T	0.45915	0.1366	M	0.73962	2.25	0.58432	D	0.999993	D;D;D;P	0.64830	0.966;0.966;0.994;0.923	P;P;P;P	0.55391	0.627;0.627;0.775;0.759	T	0.52704	-0.8540	10	0.72032	D	0.01	-26.9707	16.0594	0.80830	0.1354:0.8646:0.0:0.0	.	95;95;126;126	E7EPM0;B4DIL0;F5H407;Q13045	.;.;.;FLII_HUMAN	P	126;126;95	ENSP00000324573:A126P;ENSP00000438536:A126P;ENSP00000368763:A95P	ENSP00000324573:A126P	A	-	1	0	FLII	18098845	1.000000	0.71417	0.967000	0.41034	0.936000	0.57629	2.617000	0.46385	1.464000	0.47987	-0.152000	0.13540	GCC	FLII	-	smart_Leu-rich_rpt_typical-subtyp	ENSG00000177731		0.662	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLII	HGNC	protein_coding	OTTHUMT00000132032.2	23	0.00	0	C	NM_002018		18158120	18158120	-1	no_errors	ENST00000327031	ensembl	human	known	69_37n	missense	9	30.77	4	SNP	0.997	G
FREM1	158326	genome.wustl.edu	37	9	14746441	14746441	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr9:14746441G>A	ENST00000380880.3	-	35	6947	c.6164C>T	c.(6163-6165)gCc>gTc	p.A2055V	FREM1_ENST00000380881.4_Missense_Mutation_p.A2056V|FREM1_ENST00000422223.2_Missense_Mutation_p.A2055V|FREM1_ENST00000380894.1_Missense_Mutation_p.A591V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	2055					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GTGCCACCCGGCTGGACAGGA	0.498																																						dbGAP											0													127.0	128.0	128.0					9																	14746441		1973	4154	6127	-	-	-	SO:0001583	missense	0			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.6164C>T	9.37:g.14746441G>A	ENSP00000370262:p.Ala2055Val		B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	pfam_C-type_lectin,pfam_Calx_beta,superfamily_C-type_lectin_fold,superfamily_Cadherin-like,smart_C-type_lectin,pfscan_C-type_lectin	p.A2056V	ENST00000380880.3	37	c.6167	CCDS47952.1	9	.	.	.	.	.	.	.	.	.	.	G	12.22	1.874020	0.33069	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380894;ENST00000380880	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	6.03	1.02	0.19986	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	1.228390	0.05241	N	0.512172	T	0.15132	0.0365	L	0.44542	1.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33497	-0.9866	10	0.27785	T	0.31	-0.7941	6.2107	0.20628	0.3192:0.1164:0.5644:0.0	.	2055;591	Q5H8C1;B7ZBX4	FREM1_HUMAN;.	V	2056;2055;591;2055	ENSP00000370263:A2056V;ENSP00000412940:A2055V;ENSP00000370278:A591V;ENSP00000370262:A2055V	ENSP00000370262:A2055V	A	-	2	0	FREM1	14736441	0.806000	0.28996	0.868000	0.34077	0.959000	0.62525	1.400000	0.34577	0.142000	0.18901	0.557000	0.71058	GCC	FREM1	-	superfamily_C-type_lectin_fold,smart_C-type_lectin	ENSG00000164946		0.498	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FREM1	HGNC	protein_coding	OTTHUMT00000339474.2	126	0.00	0	G	NM_144966		14746441	14746441	-1	no_errors	ENST00000380881	ensembl	human	known	69_37n	missense	111	46.63	97	SNP	0.064	A
HPS1	3257	genome.wustl.edu	37	10	100185607	100185607	+	Missense_Mutation	SNP	A	A	G	rs541655491		TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr10:100185607A>G	ENST00000325103.6	-	12	1356	c.1123T>C	c.(1123-1125)Tgg>Cgg	p.W375R	HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Missense_Mutation_p.W375R	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	375					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		ATGCCCTGCCACAGGGGCAGG	0.637									Hermansky-Pudlak syndrome		OREG0020430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													89.0	92.0	91.0					10																	100185607		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	HPS, HPS1-8	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1123T>C	10.37:g.100185607A>G	ENSP00000326649:p.Trp375Arg	1349	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	NULL	p.W375R	ENST00000325103.6	37	c.1123	CCDS7475.1	10	.	.	.	.	.	.	.	.	.	.	A	24.1	4.491198	0.84962	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891;ENST00000359632	T;T;T	0.29397	1.57;1.57;1.57	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.57140	0.2033	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;1.0	T	0.61202	-0.7110	10	0.54805	T	0.06	.	15.2177	0.73281	1.0:0.0:0.0:0.0	.	25;375;375	Q658M9;Q8WXE5;D3DR62	.;.;.	R	375;375;342;170	ENSP00000326649:W375R;ENSP00000355310:W375R;ENSP00000352652:W170R	ENSP00000326649:W375R	W	-	1	0	HPS1	100175597	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.794000	0.91867	1.997000	0.58415	0.459000	0.35465	TGG	HPS1	-	NULL	ENSG00000107521		0.637	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	HPS1	HGNC	protein_coding	OTTHUMT00000049776.1	26	0.00	0	A	NM_000195, NM_182637, NM_182638, NM_182639		100185607	100185607	-1	no_errors	ENST00000325103	ensembl	human	known	69_37n	missense	16	42.86	12	SNP	1.000	G
IL1RAPL1	11141	genome.wustl.edu	37	X	29935618	29935618	+	Silent	SNP	G	G	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chrX:29935618G>A	ENST00000378993.1	+	7	1489	c.816G>A	c.(814-816)ggG>ggA	p.G272G	IL1RAPL1_ENST00000302196.4_Silent_p.G272G	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	272	Ig-like C2-type 3.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						CTTTCTTTGGGTACAGCGGAG	0.368																																						dbGAP											0													57.0	52.0	54.0					X																	29935618		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5996	protein-coding gene	gene with protein product		300206	"""mental retardation, X-linked 34"", ""mental retardation, X-linked 21"", ""mental retardation, X-linked 10"""	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.816G>A	X.37:g.29935618G>A			A0AVG4|Q9UJ53	Silent	SNP	pfam_TIR_dom,pfam_Ig_I-set,pfam_Immunoglobulin,superfamily_TIR_dom,smart_Ig_sub,smart_Ig_sub2,smart_TIR_dom,prints_IL1_rcpt_1,pfscan_TIR_dom,pfscan_Ig-like	p.G272	ENST00000378993.1	37	c.816	CCDS14218.1	X																																																																																			IL1RAPL1	-	pfam_Ig_I-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	ENSG00000169306		0.368	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL1RAPL1	HGNC	protein_coding	OTTHUMT00000056155.1	89	0.00	0	G	NM_014271		29935618	29935618	+1	no_errors	ENST00000302196	ensembl	human	known	69_37n	silent	84	46.50	73	SNP	0.977	A
MAP2K4	6416	genome.wustl.edu	37	17	11998993	11998993	+	Nonsense_Mutation	SNP	T	T	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr17:11998993T>A	ENST00000353533.5	+	4	558	c.495T>A	c.(493-495)taT>taA	p.Y165*	MAP2K4_ENST00000415385.3_Nonsense_Mutation_p.Y176*|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TTCAGTTTTATGGTGCACTCT	0.368			"""D, Mis, N"""		"""pancreatic, breast, colorectal"""																																	dbGAP		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)											178.0	168.0	171.0					17																	11998993		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.495T>A	17.37:g.11998993T>A	ENSP00000262445:p.Tyr165*		B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Nonsense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.Y176*	ENST00000353533.5	37	c.528	CCDS11162.1	17	.	.	.	.	.	.	.	.	.	.	T	35	5.446102	0.96187	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	.	.	.	5.9	2.57	0.30868	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8862	0.29651	0.0:0.3077:0.0:0.6923	.	.	.	.	X	165;176;142;37	.	ENSP00000262445:Y165X	Y	+	3	2	MAP2K4	11939718	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.356000	0.34079	0.510000	0.28216	0.533000	0.62120	TAT	MAP2K4	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000065559		0.368	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP2K4	HGNC	protein_coding	OTTHUMT00000441226.1	305	0.00	0	T			11998993	11998993	+1	no_errors	ENST00000415385	ensembl	human	known	69_37n	nonsense	133	44.81	108	SNP	1.000	A
MEX3C	51320	genome.wustl.edu	37	18	48703431	48703431	+	5'UTR	SNP	C	C	T			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr18:48703431C>T	ENST00000591040.1	-	0	558							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		GAGAGCCACGCAGAGCCAAGA	0.443																																						dbGAP											0													93.0	88.0	90.0					18																	48703431		2203	4300	6503	-	-	-	SO:0001623	5_prime_UTR_variant	0			BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	28040	protein-coding gene	gene with protein product		611005	"""ring finger and KH domain containing 2"", ""mex-3 homolog C (C. elegans)"""	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.-241G>A	18.37:g.48703431C>T			A1L022|Q9NZE3	Missense_Mutation	SNP	pfam_KH_dom_type_1,smart_KH_dom,smart_Znf_RING,pfscan_Znf_RING,pfscan_KH_dom_type_1	p.A424T	ENST00000591040.1	37	c.1270		18	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560456	0.65538	.	.	ENSG00000176624	ENST00000406189	T	0.33216	1.42	5.97	5.97	0.96955	.	0.111821	0.64402	D	0.000011	T	0.37999	0.1024	L	0.29908	0.895	0.52501	D	0.99995	D	0.62365	0.991	P	0.53593	0.73	T	0.01889	-1.1253	10	0.38643	T	0.18	-7.8678	19.2102	0.93751	0.0:1.0:0.0:0.0	.	424	Q5U5Q3	MEX3C_HUMAN	T	424	ENSP00000385610:A424T	ENSP00000385610:A424T	A	-	1	0	MEX3C	46957429	0.999000	0.42202	1.000000	0.80357	0.987000	0.75469	2.691000	0.47010	2.836000	0.97738	0.655000	0.94253	GCG	MEX3C	-	NULL	ENSG00000176624		0.443	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	MEX3C	HGNC	protein_coding	OTTHUMT00000449559.1	148	0.00	0	C	NM_016626		48703431	48703431	-1	no_errors	ENST00000406189	ensembl	human	known	69_37n	missense	50	76.44	172	SNP	1.000	T
KMT2C	58508	genome.wustl.edu	37	7	151849846	151849846	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr7:151849846delA	ENST00000262189.6	-	49	12688	c.12470delT	c.(12469-12471)ttafs	p.L4157fs	KMT2C_ENST00000485241.1_5'Flank|KMT2C_ENST00000355193.2_Frame_Shift_Del_p.L4214fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4157					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AGAGCTCACTAATCTGGGAGG	0.493																																						dbGAP											0													120.0	113.0	115.0					7																	151849846		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.12470delT	7.37:g.151849846delA	ENSP00000262189:p.Leu4157fs		Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	pfam_Znf_PHD-finger,pfam_SET_dom,pfam_FYrich_C,pfam_FYrich_N,superfamily_Znf_FYVE_PHD,superfamily_HMG_superfamily,smart_Znf_PHD,smart_Znf_RING,smart_HMG_superfamily,smart_FYrich_N,smart_FYrich_C,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_Znf_DHHC_palmitoyltrfase,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.L4214fs	ENST00000262189.6	37	c.12641	CCDS5931.1	7																																																																																			MLL3	-	NULL	ENSG00000055609		0.493	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MLL3	HGNC	protein_coding	OTTHUMT00000318887.3	196	0.00	0	A			151849846	151849846	-1	no_errors	ENST00000355193	ensembl	human	known	69_37n	frame_shift_del	79	71.14	212	DEL	0.012	-
OR10C1	442194	genome.wustl.edu	37	6	29408425	29408425	+	Silent	SNP	C	C	T	rs553886447		TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr6:29408425C>T	ENST00000444197.2	+	1	1343	c.633C>T	c.(631-633)ggC>ggT	p.G211G	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GCCCCTTTGGCCTCATCCTGG	0.592																																						dbGAP											0													195.0	206.0	202.0					6																	29408425		1511	2709	4220	-	-	-	SO:0001819	synonymous_variant	0				CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.633C>T	6.37:g.29408425C>T			Q5SUN7|Q96R18	Silent	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.G211	ENST00000444197.2	37	c.633	CCDS34364.1	6																																																																																			OR10C1	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000206474		0.592	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR10C1	HGNC	protein_coding	OTTHUMT00000076415.2	492	0.00	0	C			29408425	29408425	+1	no_errors	ENST00000444197	ensembl	human	known	69_37n	silent	142	72.50	377	SNP	0.002	T
PCDHB16	57717	genome.wustl.edu	37	5	140564268	140564268	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr5:140564268C>T	ENST00000361016.2	+	1	3289	c.2134C>T	c.(2134-2136)Cgg>Tgg	p.R712W		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	712					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R712W(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTGGCGGTGCGGCTGTGCAG	0.682																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)											68.0	78.0	74.0					5																	140564268		2196	4287	6483	-	-	-	SO:0001583	missense	0			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.2134C>T	5.37:g.140564268C>T	ENSP00000354293:p.Arg712Trp		B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R712W	ENST00000361016.2	37	c.2134	CCDS4251.1	5	.	.	.	.	.	.	.	.	.	.	c	12.63	1.996809	0.35226	.	.	ENSG00000196963	ENST00000361016	T	0.17054	2.3	3.91	-1.09	0.09904	.	0.249082	0.20865	N	0.084278	T	0.30448	0.0765	H	0.98048	4.135	0.09310	N	1	P	0.36412	0.552	B	0.33690	0.168	T	0.33471	-0.9867	10	0.87932	D	0	.	7.4933	0.27475	0.697:0.1547:0.0:0.1482	.	712	Q9NRJ7	PCDBG_HUMAN	W	712	ENSP00000354293:R712W	ENSP00000354293:R712W	R	+	1	2	PCDHB16	140544452	0.000000	0.05858	0.353000	0.25747	0.127000	0.20565	0.647000	0.24812	-0.246000	0.09611	-2.031000	0.00424	CGG	PCDHB16	-	NULL	ENSG00000196963		0.682	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB16	HGNC	protein_coding	OTTHUMT00000251800.1	60	0.00	0	C	NM_020957		140564268	140564268	+1	no_errors	ENST00000361016	ensembl	human	known	69_37n	missense	20	59.18	29	SNP	0.000	T
PDE1A	5136	genome.wustl.edu	37	2	183099185	183099185	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr2:183099185G>A	ENST00000410103.1	-	5	522	c.439C>T	c.(439-441)Cca>Tca	p.P147S	PDE1A_ENST00000482538.1_5'UTR|PDE1A_ENST00000358139.2_Missense_Mutation_p.P147S|PDE1A_ENST00000435564.1_Missense_Mutation_p.P147S|PDE1A_ENST00000351439.5_Missense_Mutation_p.P131S|PDE1A_ENST00000346717.4_Missense_Mutation_p.P113S|PDE1A_ENST00000409365.1_Missense_Mutation_p.P131S|PDE1A_ENST00000456212.1_Missense_Mutation_p.P147S|PDE1A_ENST00000331935.6_Missense_Mutation_p.P147S|PDE1A_ENST00000536095.1_Missense_Mutation_p.P43S	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	147					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	ACAGCTGCTGGATATGCCAAA	0.259																																						dbGAP											0													79.0	79.0	79.0					2																	183099185		2203	4298	6501	-	-	-	SO:0001583	missense	0				CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"""Phosphodiesterases"""	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.439C>T	2.37:g.183099185G>A	ENSP00000387037:p.Pro147Ser		D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	pfam_PDEase_catalytic_dom,pfam_PDEase_N,superfamily_GRIP,smart_HD/PDEase_dom,prints_PDEase	p.P147S	ENST00000410103.1	37	c.439	CCDS33344.1	2	.	.	.	.	.	.	.	.	.	.	G	16.73	3.205311	0.58234	.	.	ENSG00000115252	ENST00000435564;ENST00000346717;ENST00000536095;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	T;T;T;T;T;T;T;T;T	0.71934	-0.61;-0.61;-0.56;-0.6;-0.61;-0.59;-0.59;-0.59;-0.58	5.15	5.15	0.70609	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.126681	0.56097	D	0.000031	T	0.74726	0.3754	L	0.58510	1.815	0.58432	D	0.999999	P;P;P;D;P	0.53312	0.795;0.739;0.899;0.959;0.939	B;B;P;P;P	0.54346	0.408;0.343;0.53;0.749;0.721	T	0.74699	-0.3577	10	0.42905	T	0.14	.	11.1404	0.48400	0.0844:0.0:0.9156:0.0	.	43;113;147;131;147	B7Z3A7;P54750-3;P54750;P54750-2;P54750-4	.;.;PDE1A_HUMAN;.;.	S	147;113;43;131;147;131;147;147;147	ENSP00000410309:P147S;ENSP00000329112:P113S;ENSP00000439938:P43S;ENSP00000386767:P131S;ENSP00000331574:P147S;ENSP00000309269:P131S;ENSP00000387037:P147S;ENSP00000350858:P147S;ENSP00000408874:P147S	ENSP00000331574:P147S	P	-	1	0	PDE1A	182807430	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.379000	0.66196	2.387000	0.81309	0.650000	0.86243	CCA	PDE1A	-	NULL	ENSG00000115252		0.259	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	PDE1A	HGNC	protein_coding	OTTHUMT00000334356.1	154	0.00	0	G			183099185	183099185	-1	no_errors	ENST00000456212	ensembl	human	known	69_37n	missense	148	12.87	22	SNP	1.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		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.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		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)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	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"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	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.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		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.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	145	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	76	69.35	172	SNP	1.000	G
RSPH10B	222967	genome.wustl.edu	37	7	5992828	5992828	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr7:5992828C>T	ENST00000405415.1	-	9	1366	c.980G>A	c.(979-981)gGg>gAg	p.G327E	RSPH10B_ENST00000539903.1_Missense_Mutation_p.G93E|RSPH10B_ENST00000441023.2_Missense_Mutation_p.G327E|RSPH10B_ENST00000337579.3_Missense_Mutation_p.G327E|RSPH10B_ENST00000535104.1_5'UTR|RSPH10B_ENST00000404406.1_Missense_Mutation_p.G327E			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	327										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		GTACACACGCCCGTTCTTGAA	0.473																																						dbGAP											0													1.0	1.0	1.0					7																	5992828		50	198	248	-	-	-	SO:0001583	missense	0				CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.980G>A	7.37:g.5992828C>T	ENSP00000385443:p.Gly327Glu		A6NMW7|Q86ST9|Q8NE68	Missense_Mutation	SNP	pfam_MORN,smart_MORN	p.G327E	ENST00000405415.1	37	c.980	CCDS34598.1	7	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859321	0.71834	.	.	ENSG00000155026	ENST00000539903;ENST00000405415;ENST00000404406;ENST00000337579;ENST00000354951;ENST00000441023	T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3	4.17	4.17	0.49024	.	0.235442	0.34777	U	0.003681	D	0.91566	0.7336	M	0.93241	3.395	0.50467	D	0.999876	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.93500	0.6843	10	0.87932	D	0	.	13.2334	0.59957	0.0:1.0:0.0:0.0	.	93;327;186	B7Z298;P0C881;F5GXE3	.;R10B1_HUMAN;.	E	93;327;327;327;186;327	ENSP00000445203:G93E;ENSP00000385443:G327E;ENSP00000384097:G327E;ENSP00000338556:G327E;ENSP00000400988:G327E	ENSP00000338556:G327E	G	-	2	0	RSPH10B	5959354	1.000000	0.71417	0.996000	0.52242	0.775000	0.43874	6.452000	0.73485	1.877000	0.54381	0.555000	0.69702	GGG	RSPH10B	-	pfam_MORN	ENSG00000155026		0.473	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RSPH10B	HGNC	protein_coding	OTTHUMT00000325465.2	10	0.00	0	C	NM_173565		5992828	5992828	-1	no_errors	ENST00000337579	ensembl	human	known	69_37n	missense	1	85.71	6	SNP	1.000	T
SDHAP1	255812	genome.wustl.edu	37	3	195701310	195701311	+	RNA	INS	-	-	AA	rs369138533		TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr3:195701310_195701311insAA	ENST00000427841.1	-	0	1513_1514					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		CATGCCTGACCAGACAACCAGG	0.574																																					Ovarian(67;1158 1227 12109 20189 43170)	dbGAP											0																																										-	-	-			0			BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195701310_195701311insAA				Splice_Site	INS	-	NULL	ENST00000427841.1	37	c.NULL		3																																																																																			SDHAP1	-	-	ENSG00000185485		0.574	SDHAP1-002	KNOWN	basic	processed_transcript	SDHAP1	HGNC	pseudogene	OTTHUMT00000341367.1	31	0.00	0	-			195701310	195701311	-1	no_coding_region:pseudogene	ENST00000354937	ensembl	human	known	69_37n	splice_site_ins	25	24.24	8	INS	1.000:0.999	AA
SH3PXD2A	9644	genome.wustl.edu	37	10	105484097	105484098	+	Frame_Shift_Ins	INS	-	-	G	rs149867987		TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr10:105484097_105484098insG	ENST00000369774.4	-	5	604_605	c.328_329insC	c.(328-330)cacfs	p.H110fs	SH3PXD2A_ENST00000355946.2_Frame_Shift_Ins_p.H110fs			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	110	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CTGTGAGATGTGGGGGGGCAGC	0.535																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.329dupC	10.37:g.105484104_105484104dupG	ENSP00000358789:p.His110fs		D3DR98|O43302|Q5TCZ2|Q5TDQ8	Frame_Shift_Ins	INS	pfam_SH3_domain,pfam_SH3_2,pfam_Phox,superfamily_Phox,superfamily_SH3_domain,smart_Phox,smart_SH3_domain,pfscan_Phox,pfscan_SH3_domain	p.H110fs	ENST00000369774.4	37	c.329_328		10																																																																																			SH3PXD2A	-	pfam_Phox,superfamily_Phox,smart_Phox,pfscan_Phox	ENSG00000107957		0.535	SH3PXD2A-001	KNOWN	basic	protein_coding	SH3PXD2A	HGNC	protein_coding	OTTHUMT00000050178.1	16	0.00	0	-	NM_014631		105484097	105484098	-1	no_errors	ENST00000369774	ensembl	human	known	69_37n	frame_shift_ins	18	18.18	4	INS	1.000:0.989	G
SLC22A2	6582	genome.wustl.edu	37	6	160671727	160671727	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr6:160671727delG	ENST00000366953.3	-	3	784	c.526delC	c.(526-528)cgtfs	p.R176fs	SLC22A2_ENST00000491092.1_5'UTR|SLC22A2_ENST00000366952.1_Frame_Shift_Del_p.R155fs	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	176					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	CAGAGCTTACGGCCAAACCTG	0.393																																						dbGAP											0													64.0	64.0	64.0					6																	160671727		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.526delC	6.37:g.160671727delG	ENSP00000355920:p.Arg176fs		Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Frame_Shift_Del	DEL	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom,tigrfam_Orgcat_transp	p.R176fs	ENST00000366953.3	37	c.526	CCDS5276.1	6																																																																																			SLC22A2	-	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom,tigrfam_Orgcat_transp	ENSG00000112499		0.393	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC22A2	HGNC	protein_coding	OTTHUMT00000042943.1	157	0.00	0	G	NM_003058		160671727	160671727	-1	no_errors	ENST00000366953	ensembl	human	known	69_37n	frame_shift_del	64	65.67	132	DEL	1.000	-
SLC4A4	8671	genome.wustl.edu	37	4	72121014	72121014	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr4:72121014C>A	ENST00000264485.5	+	3	268	c.151C>A	c.(151-153)Cac>Aac	p.H51N	SLC4A4_ENST00000425175.1_Missense_Mutation_p.H51N|SLC4A4_ENST00000351898.6_Missense_Mutation_p.H51N|SLC4A4_ENST00000514331.1_3'UTR	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	51					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	AAAGACAGGGCACAAAGAAAA	0.438																																						dbGAP											0													161.0	164.0	163.0					4																	72121014		1936	4129	6065	-	-	-	SO:0001583	missense	0			AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.151C>A	4.37:g.72121014C>A	ENSP00000264485:p.His51Asn		C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	pfam_HCO3_transpt_C,pfam_HCO3_transpt_cyt,superfamily_PTrfase/Anion_transptr,prints_HCO3_transpt_euk,prints_Na/HCO3_transpt,tigrfam_HCO3_transpt_euk	p.H51N	ENST00000264485.5	37	c.151	CCDS43236.1	4	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179045	0.57692	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898	T;T;T	0.79141	-1.24;-1.24;-0.88	5.7	5.7	0.88788	.	0.161446	0.56097	D	0.000031	T	0.78329	0.4266	M	0.75085	2.285	0.80722	D	1	B;B;B	0.31817	0.227;0.341;0.224	B;B;B	0.31946	0.138;0.116;0.076	T	0.74717	-0.3571	10	0.21540	T	0.41	.	18.8365	0.92165	0.0:1.0:0.0:0.0	.	51;51;51	A5JJ20;Q9Y6R1-4;Q9Y6R1	.;.;S4A4_HUMAN	N	51	ENSP00000264485:H51N;ENSP00000393557:H51N;ENSP00000307349:H51N	ENSP00000264485:H51N	H	+	1	0	SLC4A4	72339878	1.000000	0.71417	0.989000	0.46669	0.699000	0.40488	7.252000	0.78309	2.690000	0.91761	0.650000	0.86243	CAC	SLC4A4	-	NULL	ENSG00000080493		0.438	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC4A4	HGNC	protein_coding	OTTHUMT00000362090.1	288	0.35	1	C	NM_003759		72121014	72121014	+1	no_errors	ENST00000425175	ensembl	human	known	69_37n	missense	85	73.54	239	SNP	1.000	A
ZFYVE26	23503	genome.wustl.edu	37	14	68236344	68236344	+	Missense_Mutation	SNP	A	A	C			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr14:68236344A>C	ENST00000347230.4	-	29	5726	c.5588T>G	c.(5587-5589)gTg>gGg	p.V1863G	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.V1863G	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1863					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CTGATCACACACACGAGCAGG	0.537																																						dbGAP											0													133.0	109.0	117.0					14																	68236344		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.5588T>G	14.37:g.68236344A>C	ENSP00000251119:p.Val1863Gly		B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	pfam_Znf_FYVE,superfamily_Znf_FYVE_PHD,smart_Znf_FYVE,pfscan_Znf_FYVE-rel	p.V1863G	ENST00000347230.4	37	c.5588	CCDS9788.1	14	.	.	.	.	.	.	.	.	.	.	A	26.4	4.730823	0.89390	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.78003	-1.14;-1.14	5.69	5.69	0.88448	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.91915	0.7440	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.94358	0.7585	10	0.87932	D	0	-8.6214	15.9361	0.79707	1.0:0.0:0.0:0.0	.	1863;1863	G3V2D8;Q68DK2	.;ZFY26_HUMAN	G	1863;1842;1863	ENSP00000251119:V1863G;ENSP00000450603:V1863G	ENSP00000251119:V1863G	V	-	2	0	ZFYVE26	67306097	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	7.523000	0.81856	2.168000	0.68352	0.454000	0.30748	GTG	ZFYVE26	-	pfam_Znf_FYVE,superfamily_Znf_FYVE_PHD,smart_Znf_FYVE,pfscan_Znf_FYVE-rel	ENSG00000072121		0.537	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZFYVE26	HGNC	protein_coding	OTTHUMT00000412736.2	79	0.00	0	A	NM_015346		68236344	68236344	-1	no_errors	ENST00000347230	ensembl	human	known	69_37n	missense	29	71.00	71	SNP	1.000	C
ZNF362	149076	genome.wustl.edu	37	1	33745932	33745933	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A8-A07Z-01A-11W-A019-09	TCGA-A8-A07Z-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e4af33f9-f5fe-4e52-8ca0-991bbce2270d	a9ac6ea6-e114-4fac-8372-86cb23c835ec	g.chr1:33745932_33745933insC	ENST00000539719.1	+	5	727_728	c.557_558insC	c.(556-561)ggccccfs	p.GP186fs	ZNF362_ENST00000373428.5_Frame_Shift_Ins_p.GP186fs	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GGCCTGCTTGGCCCCCCCAAGT	0.658																																					Pancreas(162;1431 2676 35353 38425)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"""Zinc fingers, C2H2-type"""	18079	protein-coding gene	gene with protein product	"""rotund homolog (Drosophila)"""						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.564dupC	1.37:g.33745939_33745939dupC	ENSP00000446335:p.Gly186fs		Q8WYU4	Frame_Shift_Ins	INS	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.K189fs	ENST00000539719.1	37	c.557_558	CCDS377.1	1																																																																																			ZNF362	-	NULL	ENSG00000160094		0.658	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF362	HGNC	protein_coding	OTTHUMT00000011857.2	28	0.00	0	-	NM_152493		33745932	33745933	+1	no_errors	ENST00000373428	ensembl	human	known	69_37n	frame_shift_ins	29	12.12	4	INS	1.000:1.000	C
