#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
ARL6IP6	151188	genome.wustl.edu	37	2	153575506	153575508	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	TCC	TCC					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr2:153575506_153575508delTCC	ENST00000326446.5	+	1	1079_1081	c.368_370delTCC	c.(367-372)ttcctc>ttc	p.L125del	PRPF40A_ENST00000486100.1_5'Flank|PRPF40A_ENST00000410080.1_5'Flank	NM_152522.5	NP_689735.1	Q8N6S5	AR6P6_HUMAN	ADP-ribosylation factor-like 6 interacting protein 6	125						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	5						CTTCTCGCCTTCCTCCTCGCCAT	0.596																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AK023109	CCDS2197.1	2q23	2014-05-12	2014-05-12		ENSG00000177917	ENSG00000177917			24048	protein-coding gene	gene with protein product							Standard	NM_152522		Approved	MGC33864	uc002tyn.3	Q8N6S5	OTTHUMG00000131901	ENST00000326446.5:c.368_370delTCC	2.37:g.153575509_153575511delTCC	ENSP00000315357:p.Leu125del		B2RDS6|Q7Z4G7	In_Frame_Del	DEL	NULL	p.L125in_frame_del	ENST00000326446.5	37	c.368_370	CCDS2197.1	2																																																																																			ARL6IP6	-	NULL	ENSG00000177917		0.596	ARL6IP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARL6IP6	HGNC	protein_coding	OTTHUMT00000254852.3	100	0.00	0	TCC	NM_152522		153575506	153575508	+1	no_errors	ENST00000326446	ensembl	human	known	69_37n	in_frame_del	79	31.62	37	DEL	0.946:0.969:0.994	-
CASS4	57091	genome.wustl.edu	37	20	55021046	55021046	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr20:55021046G>A	ENST00000360314.3	+	4	775	c.550G>A	c.(550-552)Gtg>Atg	p.V184M	CASS4_ENST00000371336.3_Missense_Mutation_p.V184M|CASS4_ENST00000434344.1_Missense_Mutation_p.V184M	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	184					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						CCGGGGCCCCGTGGTCCTGAA	0.622																																						dbGAP											0													53.0	49.0	50.0					20																	55021046		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.550G>A	20.37:g.55021046G>A	ENSP00000353462:p.Val184Met		E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	pfam_Serine_rich,pfam_CAS_DUF3513,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain	p.V184M	ENST00000360314.3	37	c.550	CCDS33492.1	20	.	.	.	.	.	.	.	.	.	.	G	8.168	0.790994	0.16258	.	.	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.20463	2.58;2.58;2.07	5.16	-5.83	0.02325	.	1.342070	0.04408	N	0.365542	T	0.08626	0.0214	N	0.08118	0	0.09310	N	1	B;B;B;B	0.13594	0.001;0.008;0.007;0.001	B;B;B;B	0.09377	0.001;0.002;0.004;0.001	T	0.24657	-1.0154	10	0.33940	T	0.23	1.5217	3.5467	0.07831	0.0925:0.276:0.1084:0.5232	.	130;184;184;184	B4DII4;Q9NQ75-3;Q9NQ75-2;Q9NQ75	.;.;.;CASS4_HUMAN	M	184	ENSP00000353462:V184M;ENSP00000360387:V184M;ENSP00000410027:V184M	ENSP00000353462:V184M	V	+	1	0	CASS4	54454453	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.311000	0.01128	-1.116000	0.02969	-1.136000	0.01936	GTG	CASS4	-	NULL	ENSG00000087589		0.622	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CASS4	HGNC	protein_coding	OTTHUMT00000079789.2	54	0.00	0	G	NM_020356		55021046	55021046	+1	no_errors	ENST00000360314	ensembl	human	known	69_37n	missense	42	66.13	82	SNP	0.000	A
CCP110	9738	genome.wustl.edu	37	16	19556523	19556523	+	Silent	SNP	C	C	G			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr16:19556523C>G	ENST00000381396.5	+	10	2941	c.2694C>G	c.(2692-2694)ctC>ctG	p.L898L	CCP110_ENST00000396212.2_Silent_p.L898L|CCP110_ENST00000396208.2_Silent_p.L898L	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	898					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						AGAAAATGCTCAGGCAAATGG	0.368																																						dbGAP											0													89.0	83.0	85.0					16																	19556523		2196	4300	6496	-	-	-	SO:0001819	synonymous_variant	0			AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.2694C>G	16.37:g.19556523C>G			B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	NULL	p.L898	ENST00000381396.5	37	c.2694	CCDS55992.1	16																																																																																			CCP110	-	NULL	ENSG00000103540		0.368	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CCP110	HGNC	protein_coding	OTTHUMT00000254284.2	120	0.00	0	C	NM_014711		19556523	19556523	+1	no_errors	ENST00000381396	ensembl	human	known	69_37n	silent	63	22.22	18	SNP	1.000	G
CHD1	1105	genome.wustl.edu	37	5	98240749	98240749	+	Missense_Mutation	SNP	G	G	C			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr5:98240749G>C	ENST00000284049.3	-	2	256	c.107C>G	c.(106-108)tCt>tGt	p.S36C		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	36	Ser-rich.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	ACTGCTTCCAGAACTCGAACC	0.443																																						dbGAP											0													119.0	123.0	122.0					5																	98240749		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.107C>G	5.37:g.98240749G>C	ENSP00000284049:p.Ser36Cys		Q17RZ3	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Chromo_domain,pfam_Helicase_C,superfamily_Chromodomain-like,superfamily_Homeodomain-like,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.S36C	ENST00000284049.3	37	c.107	CCDS34204.1	5	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650866	0.87958	.	.	ENSG00000153922	ENST00000284049;ENST00000540681	D	0.90900	-2.75	4.85	4.85	0.62838	.	0.000000	0.33691	U	0.004645	D	0.94915	0.8356	M	0.74881	2.28	0.80722	D	1	D	0.69078	0.997	D	0.70935	0.971	D	0.94505	0.7713	10	0.48119	T	0.1	.	18.851	0.92230	0.0:0.0:1.0:0.0	.	36	O14646	CHD1_HUMAN	C	36	ENSP00000284049:S36C	ENSP00000284049:S36C	S	-	2	0	CHD1	98268649	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.044000	0.89434	2.624000	0.88883	0.563000	0.77884	TCT	CHD1	-	NULL	ENSG00000153922		0.443	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD1	HGNC	protein_coding	OTTHUMT00000370295.1	74	0.00	0	G	NM_001270		98240749	98240749	-1	no_errors	ENST00000284049	ensembl	human	known	69_37n	missense	52	35.00	28	SNP	1.000	C
CYB561A3	220002	genome.wustl.edu	37	11	61120579	61120579	+	Silent	SNP	G	G	C			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr11:61120579G>C	ENST00000294072.4	-	5	1103	c.426C>G	c.(424-426)ccC>ccG	p.P142P	CYB561A3_ENST00000426130.2_Silent_p.P159P|CYB561A3_ENST00000546151.1_Missense_Mutation_p.P86R|CYB561A3_ENST00000540317.1_5'UTR|CYB561A3_ENST00000447532.2_Silent_p.P142P|CYB561A3_ENST00000539890.1_Intron|CYB561A3_ENST00000544118.1_Intron|CYB561A3_ENST00000536915.1_Silent_p.P142P	NM_001161452.1|NM_153611.4	NP_001154924.1|NP_705839.3	Q8NBI2	CYAC3_HUMAN	cytochrome b561 family, member A3	142	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)										TGGACGCCCAGGGCAGGAGGA	0.557																																						dbGAP											0													78.0	59.0	65.0					11																	61120579		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AK024953	CCDS8004.1, CCDS53639.1, CCDS73296.1	11q12.2	2013-03-14	2013-03-14	2013-03-14		ENSG00000162144		"""Cytochrome b genes"""	23014	protein-coding gene	gene with protein product			"""cytochrome b, ascorbate dependent 3"""	CYBASC3		23249217	Standard	NM_153611		Approved		uc001nrf.4	Q8NBI2		ENST00000294072.4:c.426C>G	11.37:g.61120579G>C			B3KPU2|B4DLN9|J3KQH4|Q6PK96	Missense_Mutation	SNP	NULL	p.L73V	ENST00000294072.4	37	c.217	CCDS8004.1	11	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014002	0.35511	.	.	ENSG00000162144	ENST00000546151	.	.	.	6.02	4.14	0.48551	.	0.000000	0.85682	D	0.000000	T	0.62368	0.2422	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64093	-0.6488	6	0.56958	D	0.05	-43.3022	7.5256	0.27653	0.1348:0.1436:0.7216:0.0	.	.	.	.	R	86	.	ENSP00000441834:P86R	P	-	2	0	CYBASC3	60877155	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.957000	0.40392	1.546000	0.49388	0.655000	0.94253	CCT	CYBASC3	-	NULL	ENSG00000162144		0.557	CYB561A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYBASC3	HGNC	protein_coding	OTTHUMT00000398714.2	33	0.00	0	G	NM_153611		61120579	61120579	-1	no_errors	ENST00000540755	ensembl	human	known	69_37n	missense	23	30.30	10	SNP	1.000	C
FAM157B	100132403	genome.wustl.edu	37	9	141107536	141107537	+	lincRNA	INS	-	-	GCA	rs367832601|rs554298933|rs370981092		TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr9:141107536_141107537insGCA	ENST00000446912.2	+	0	19_20							P0CG42	F157B_HUMAN	family with sequence similarity 157, member B																		CGgcagcggcggcagcagcagc	0.545																																						dbGAP											0																																										-	-	-			0					9q34	2013-01-24			ENSG00000233013	ENSG00000233013			34080	other	unknown							Standard	NM_001145249		Approved		uc011mfe.1	P0CG42	OTTHUMG00000021000		9.37:g.141107543_141107545dupGCA				RNA	INS	-	NULL	ENST00000446912.2	37	NULL		9																																																																																			FAM157B	-	-	ENSG00000233013		0.545	FAM157B-001	KNOWN	mRNA_end_NF|basic	lincRNA	FAM157B	HGNC	lincRNA	OTTHUMT00000055378.2	47	0.00	0	-	NM_001145249		141107536	141107537	+1	no_errors	ENST00000446912	ensembl	human	known	69_37n	rna	52	24.64	17	INS	0.033:0.036	GCA
FOXA3	3171	genome.wustl.edu	37	19	46376175	46376175	+	Silent	SNP	C	C	T			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr19:46376175C>T	ENST00000302177.2	+	2	1109	c.912C>T	c.(910-912)ttC>ttT	p.F304F		NM_004497.2	NP_004488.2	P55318	FOXA3_HUMAN	forkhead box A3	304					cell differentiation (GO:0030154)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|chromatin modification (GO:0016568)|endocrine pancreas development (GO:0031018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	13		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)		ACCACCCTTTCTCCATCAACA	0.587																																						dbGAP											0													67.0	59.0	62.0					19																	46376175		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L12141	CCDS12677.1	19q13.32	2014-09-11		2002-09-20	ENSG00000170608	ENSG00000170608		"""Forkhead boxes"""	5023	protein-coding gene	gene with protein product		602295	"""hepatocyte nuclear factor 3, gamma"""	HNF3G		9119385	Standard	NM_004497		Approved		uc002pdr.3	P55318	OTTHUMG00000182484	ENST00000302177.2:c.912C>T	19.37:g.46376175C>T			A9LYI5|Q53F16|Q9UMW9	Silent	SNP	pfam_TF_fork_head,pfam_Fork-head_N,pfam_Forkhead_box_C,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.F304	ENST00000302177.2	37	c.912	CCDS12677.1	19																																																																																			FOXA3	-	pfam_Forkhead_box_C	ENSG00000170608		0.587	FOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXA3	HGNC	protein_coding	OTTHUMT00000461682.1	44	0.00	0	C			46376175	46376175	+1	no_errors	ENST00000302177	ensembl	human	known	69_37n	silent	13	27.78	5	SNP	1.000	T
FXR2	9513	genome.wustl.edu	37	17	7496417	7496417	+	Silent	SNP	C	C	T			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr17:7496417C>T	ENST00000250113.7	-	13	1747	c.1413G>A	c.(1411-1413)agG>agA	p.R471R	SOX15_ENST00000250055.2_5'Flank|FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	471						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		TTGGGGGATCCCTGTCGCCAG	0.632																																						dbGAP											0													20.0	20.0	20.0					17																	7496417		1857	4098	5955	-	-	-	SO:0001819	synonymous_variant	0			U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1413G>A	17.37:g.7496417C>T			B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Silent	SNP	pfam_Frag_X_MRP_fam,pfam_KH_dom_type_1,pfam_Agenet,smart_KH_dom,pfscan_KH_dom_type_1	p.R471	ENST00000250113.7	37	c.1413	CCDS45604.1	17																																																																																			FXR2	-	pfam_Frag_X_MRP_fam	ENSG00000129245		0.632	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FXR2	HGNC	protein_coding	OTTHUMT00000441084.1	25	0.00	0	C			7496417	7496417	-1	no_errors	ENST00000250113	ensembl	human	known	69_37n	silent	22	31.25	10	SNP	0.981	T
GEMIN2	8487	genome.wustl.edu	37	14	39584053	39584053	+	Missense_Mutation	SNP	C	C	T			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr14:39584053C>T	ENST00000308317.6	+	2	274	c.191C>T	c.(190-192)cCa>cTa	p.P64L	GEMIN2_ENST00000396249.2_Missense_Mutation_p.P64L|GEMIN2_ENST00000250379.8_Missense_Mutation_p.P64L	NM_003616.2	NP_003607.1	O14893	GEMI2_HUMAN	gem (nuclear organelle) associated protein 2	64					gene expression (GO:0010467)|mRNA processing (GO:0006397)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)											GCTCAATGTCCAGATGTTGTG	0.388																																						dbGAP											0													143.0	132.0	136.0					14																	39584053		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF027150	CCDS9669.1, CCDS32068.1, CCDS41946.1	14q21.1	2011-08-04	2011-08-04	2011-08-04	ENSG00000092208	ENSG00000092208			10884	protein-coding gene	gene with protein product		602595	"""survival of motor neuron protein interacting protein 1"""	SIP1		9323130, 9323129, 11121410	Standard	NM_003616		Approved		uc001wuq.3	O14893	OTTHUMG00000028816	ENST00000308317.6:c.191C>T	14.37:g.39584053C>T	ENSP00000308533:p.Pro64Leu		B2R9W8|Q2M3B3|Q9H4F5|Q9NS77|Q9NS78|Q9NS79	Nonsense_Mutation	SNP	NULL	p.Q53*	ENST00000308317.6	37	c.157	CCDS9669.1	14	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.187155|5.187155	0.94923|0.94923	.|.	.|.	ENSG00000092208|ENSG00000092208	ENST00000308317;ENST00000396249;ENST00000250379|ENST00000527381	.|.	.|.	.|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.85440|.	0.5697|.	M|M	0.89715|0.89715	3.055|3.055	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;0.995;0.999|.	D|.	0.87118|.	0.2189|.	9|.	0.72032|.	D|.	0.01|.	-12.2279|-12.2279	19.0276|19.0276	0.92939|0.92939	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	64;64;64|.	O14893-2;O14893-3;O14893|.	.;.;GEMI2_HUMAN|.	L|X	64|53	.|.	ENSP00000250379:P64L|.	P|Q	+|+	2|1	0|0	GEMIN2|GEMIN2	38653804|38653804	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.123000|6.123000	0.71614|0.71614	2.797000|2.797000	0.96272|0.96272	0.563000|0.563000	0.77884|0.77884	CCA|CAG	GEMIN2	-	NULL	ENSG00000092208		0.388	GEMIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GEMIN2	HGNC	protein_coding	OTTHUMT00000276730.2	160	0.00	0	C			39584053	39584053	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000527381	ensembl	human	novel	69_37n	nonsense	114	31.33	52	SNP	1.000	T
HEATR5B	54497	genome.wustl.edu	37	2	37306265	37306265	+	Silent	SNP	T	T	C			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr2:37306265T>C	ENST00000233099.5	-	3	431	c.336A>G	c.(334-336)aaA>aaG	p.K112K	HEATR5B_ENST00000354531.2_Silent_p.K112K	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	112						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				GTACTTACAATTTTGTTGGTA	0.368																																						dbGAP											0													37.0	35.0	35.0					2																	37306265		2203	4298	6501	-	-	-	SO:0001819	synonymous_variant	0			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.336A>G	2.37:g.37306265T>C			B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	superfamily_ARM-type_fold	p.K112	ENST00000233099.5	37	c.336	CCDS33181.1	2																																																																																			HEATR5B	-	superfamily_ARM-type_fold	ENSG00000008869		0.368	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HEATR5B	HGNC	protein_coding	OTTHUMT00000325492.1	66	0.00	0	T	NM_019024		37306265	37306265	-1	no_errors	ENST00000233099	ensembl	human	known	69_37n	silent	54	27.03	20	SNP	1.000	C
HEPACAM	220296	genome.wustl.edu	37	11	124794753	124794753	+	Nonsense_Mutation	SNP	G	G	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr11:124794753G>A	ENST00000298251.4	-	2	703	c.298C>T	c.(298-300)Cga>Tga	p.R100*		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule									p.R100*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		TCAAAGAGTCGGATACGGTCT	0.587																																						dbGAP											1	Substitution - Nonsense(1)	prostate(1)											146.0	131.0	136.0					11																	124794753		2201	4299	6500	-	-	-	SO:0001587	stop_gained	0			AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.298C>T	11.37:g.124794753G>A	ENSP00000298251:p.Arg100*			Nonsense_Mutation	SNP	pfam_Ig_V-set,pfam_Ig_I-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	p.R100*	ENST00000298251.4	37	c.298	CCDS8456.1	11	.	.	.	.	.	.	.	.	.	.	G	40	8.111036	0.98659	.	.	ENSG00000165478	ENST00000298251;ENST00000374961	.	.	.	5.84	3.9	0.45041	.	0.232564	0.45867	D	0.000325	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-22.7351	14.7064	0.69194	0.0:0.0:0.6256:0.3744	.	.	.	.	X	100	.	ENSP00000298251:R100X	R	-	1	2	HEPACAM	124299963	0.998000	0.40836	0.999000	0.59377	0.862000	0.49288	1.743000	0.38258	1.462000	0.47948	-0.309000	0.09137	CGA	HEPACAM	-	pfam_Ig_V-set,smart_Ig_sub	ENSG00000165478		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HEPACAM	HGNC	protein_coding	OTTHUMT00000387125.1	64	0.00	0	G	NM_152722		124794753	124794753	-1	no_errors	ENST00000298251	ensembl	human	known	69_37n	nonsense	21	33.33	11	SNP	0.950	A
MMACHC	25974	genome.wustl.edu	37	1	45974548	45974548	+	Silent	SNP	G	G	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr1:45974548G>A	ENST00000401061.4	+	4	790	c.510G>A	c.(508-510)gaG>gaA	p.E170E		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	170					cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGGGATAGAGGTGCCAGATC	0.552																																						dbGAP											0													91.0	99.0	97.0					1																	45974548		2044	4200	6244	-	-	-	SO:0001819	synonymous_variant	0				CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.510G>A	1.37:g.45974548G>A			Q5T157|Q9BRQ7	Silent	SNP	NULL	p.E170	ENST00000401061.4	37	c.510	CCDS41324.1	1																																																																																			MMACHC	-	NULL	ENSG00000132763		0.552	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MMACHC	HGNC	protein_coding	OTTHUMT00000020864.2	86	0.00	0	G	NM_015506		45974548	45974548	+1	no_errors	ENST00000401061	ensembl	human	known	69_37n	silent	60	25.00	20	SNP	0.999	A
NUP98	4928	genome.wustl.edu	37	11	3803284	3803284	+	Missense_Mutation	SNP	T	T	C			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr11:3803284T>C	ENST00000324932.7	-	2	484	c.64A>G	c.(64-66)Aca>Gca	p.T22A	NUP98_ENST00000359171.4_Missense_Mutation_p.T22A|RNU7-50P_ENST00000459175.1_RNA|NUP98_ENST00000397007.4_Missense_Mutation_p.T22A|NUP98_ENST00000397004.4_Missense_Mutation_p.T22A|NUP98_ENST00000355260.3_Missense_Mutation_p.T22A	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	22	FG repeats 1.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TGTCCAAATGTTGAAGTTGTG	0.388			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																	dbGAP		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	0													91.0	87.0	88.0					11																	3803284		2201	4298	6499	-	-	-	SO:0001583	missense	0			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.64A>G	11.37:g.3803284T>C	ENSP00000316032:p.Thr22Ala		Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	pfam_Nup96,pfam_Peptidase_S59,superfamily_Peptidase_S59	p.T22A	ENST00000324932.7	37	c.64	CCDS7746.1	11	.	.	.	.	.	.	.	.	.	.	T	14.02	2.410267	0.42715	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007;ENST00000532475	.	.	.	5.54	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.26846	0.0657	N	0.20685	0.6	0.41643	D	0.989088	B;B;B;P;P	0.39576	0.055;0.105;0.105;0.679;0.679	B;B;B;B;B	0.34138	0.023;0.056;0.056;0.176;0.176	T	0.05022	-1.0911	9	0.10636	T	0.68	.	10.7233	0.46052	0.1429:0.0:0.0:0.8571	.	22;22;22;22;22	P52948;P52948-3;P52948-4;P52948-2;P52948-5	NUP98_HUMAN;.;.;.;.	A	22	.	ENSP00000316032:T22A	T	-	1	0	NUP98	3759860	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.736000	0.55052	0.898000	0.36418	0.533000	0.62120	ACA	NUP98	-	NULL	ENSG00000110713		0.388	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NUP98	HGNC	protein_coding	OTTHUMT00000032766.3	109	0.00	0	T	NM_016320		3803284	3803284	-1	no_errors	ENST00000324932	ensembl	human	known	69_37n	missense	57	29.63	24	SNP	1.000	C
OSBPL6	114880	genome.wustl.edu	37	2	179213982	179213982	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr2:179213982G>A	ENST00000190611.4	+	12	1395	c.1019G>A	c.(1018-1020)cGc>cAc	p.R340H	OSBPL6_ENST00000357080.4_Missense_Mutation_p.R309H|OSBPL6_ENST00000409045.3_Missense_Mutation_p.R309H|OSBPL6_ENST00000409631.1_Missense_Mutation_p.R340H|OSBPL6_ENST00000392505.2_Missense_Mutation_p.R365H|OSBPL6_ENST00000359685.3_Missense_Mutation_p.R340H|OSBPL6_ENST00000315022.2_Missense_Mutation_p.R344H	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	340					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCACCAGTTCGCTTGCATTCC	0.428																																						dbGAP											0													255.0	243.0	247.0					2																	179213982		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1019G>A	2.37:g.179213982G>A	ENSP00000190611:p.Arg340His		B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	pfam_Oxysterol-bd,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.R344H	ENST00000190611.4	37	c.1031	CCDS2277.1	2	.	.	.	.	.	.	.	.	.	.	G	29.6	5.019880	0.93462	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000361154;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.32023	2.42;2.5;1.47;2.26;2.65;2.5;2.42	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.57198	0.2037	M	0.72894	2.215	0.80722	D	1	P;D;D;D;D;D	0.89917	0.924;1.0;0.999;1.0;1.0;1.0	P;D;D;D;D;D	0.87578	0.629;0.998;0.984;0.998;0.991;0.996	T	0.54316	-0.8312	10	0.42905	T	0.14	-12.135	19.3979	0.94614	0.0:0.0:1.0:0.0	.	309;344;340;365;340;309	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	H	365;340;125;309;309;340;340;344	ENSP00000376293:R365H;ENSP00000352713:R340H;ENSP00000349591:R309H;ENSP00000387248:R309H;ENSP00000190611:R340H;ENSP00000386885:R340H;ENSP00000318723:R344H	ENSP00000190611:R340H	R	+	2	0	OSBPL6	178922228	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.390000	0.79816	2.595000	0.87683	0.655000	0.94253	CGC	OSBPL6	-	NULL	ENSG00000079156		0.428	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	OSBPL6	HGNC	protein_coding	OTTHUMT00000334393.2	145	0.00	0	G	NM_032523		179213982	179213982	+1	no_errors	ENST00000315022	ensembl	human	known	69_37n	missense	108	22.86	32	SNP	1.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	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	73	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	46	16.36	9	SNP	1.000	G
PLK4	10733	genome.wustl.edu	37	4	128804491	128804491	+	Silent	SNP	G	G	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr4:128804491G>A	ENST00000270861.5	+	3	475	c.201G>A	c.(199-201)ttG>ttA	p.L67L	PLK4_ENST00000513090.1_Intron|PLK4_ENST00000507249.1_Silent_p.L67L|PLK4_ENST00000515069.1_Silent_p.L67L|PLK4_ENST00000511942.1_3'UTR|PLK4_ENST00000514379.1_Silent_p.L26L	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	67	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						ATTGCCAATTGAAACATCCTT	0.313																																					Colon(135;508 1718 19061 31832 42879)	dbGAP											0													70.0	70.0	70.0					4																	128804491		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.201G>A	4.37:g.128804491G>A			B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_POLO_box_duplicated_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_POLO_box_duplicated_dom,pfscan_Prot_kinase_cat_dom	p.L67	ENST00000270861.5	37	c.201	CCDS3735.1	4																																																																																			PLK4	-	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	ENSG00000142731		0.313	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLK4	HGNC	protein_coding	OTTHUMT00000257095.3	82	0.00	0	G			128804491	128804491	+1	no_errors	ENST00000270861	ensembl	human	known	69_37n	silent	41	34.92	22	SNP	1.000	A
PSTPIP2	9050	genome.wustl.edu	37	18	43579418	43579418	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr18:43579418G>A	ENST00000409746.5	-	7	571	c.500C>T	c.(499-501)cCg>cTg	p.P167L	PSTPIP2_ENST00000588801.1_5'UTR|PSTPIP2_ENST00000589328.1_Missense_Mutation_p.P167L	NM_024430.3	NP_077748.3	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting protein 2	167						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)		p.P167Q(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	17						TTGTTGCTTCGGGTTCACCAG	0.458																																						dbGAP											2	Substitution - Missense(2)	lung(2)											176.0	173.0	174.0					18																	43579418		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS32820.2	18q12	2008-07-28			ENSG00000152229	ENSG00000152229			9581	protein-coding gene	gene with protein product						9804817	Standard	NM_024430		Approved		uc002lbp.4	Q9H939	OTTHUMG00000152674	ENST00000409746.5:c.500C>T	18.37:g.43579418G>A	ENSP00000387261:p.Pro167Leu			Missense_Mutation	SNP	pfam_FCH,smart_FCH,pfscan_FCH	p.P167L	ENST00000409746.5	37	c.500	CCDS32820.2	18	.	.	.	.	.	.	.	.	.	.	G	8.266	0.812301	0.16537	.	.	ENSG00000152229	ENST00000409746;ENST00000360076	T	0.46063	0.88	5.23	-2.99	0.05497	.	0.639586	0.17393	N	0.175856	T	0.31295	0.0792	L	0.57536	1.79	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.001	T	0.15578	-1.0432	10	0.39692	T	0.17	-10.4489	6.2544	0.20865	0.196:0.0:0.2713:0.5327	.	167;167	Q9H939-2;Q9H939	.;PPIP2_HUMAN	L	167	ENSP00000387261:P167L	ENSP00000353189:P167L	P	-	2	0	PSTPIP2	41833416	0.062000	0.20869	0.069000	0.20011	0.793000	0.44817	0.195000	0.17155	-0.925000	0.03775	-0.448000	0.05591	CCG	PSTPIP2	-	NULL	ENSG00000152229		0.458	PSTPIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PSTPIP2	HGNC	protein_coding	OTTHUMT00000327522.1	161	0.00	0	G			43579418	43579418	-1	no_errors	ENST00000409746	ensembl	human	known	69_37n	missense	111	23.81	35	SNP	0.078	A
RTN3	10313	genome.wustl.edu	37	11	63525654	63525654	+	Missense_Mutation	SNP	C	C	T			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr11:63525654C>T	ENST00000377819.5	+	9	3234	c.3080C>T	c.(3079-3081)gCc>gTc	p.A1027V	RTN3_ENST00000341307.2_Silent_p.R211R|RTN3_ENST00000537981.1_Missense_Mutation_p.A231V|C11orf95_ENST00000433688.1_lincRNA|RTN3_ENST00000354497.4_Missense_Mutation_p.P146S|RTN3_ENST00000339997.4_Missense_Mutation_p.A1008V|RTN3_ENST00000356000.3_Missense_Mutation_p.A250V|RTN3_ENST00000540798.1_Missense_Mutation_p.A915V	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	1027	Interaction with FADD.|Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						CCTGGAATCGCCAAAAAAAAG	0.338																																						dbGAP											0													73.0	69.0	70.0					11																	63525654		2201	4298	6499	-	-	-	SO:0001583	missense	0			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.3080C>T	11.37:g.63525654C>T	ENSP00000367050:p.Ala1027Val		B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	pfam_Reticulon,pfscan_Reticulon	p.A1027V	ENST00000377819.5	37	c.3080	CCDS58141.1	11	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.73|16.73	3.204411|3.204411	0.58234|0.58234	.|.	.|.	ENSG00000133318|ENSG00000133318	ENST00000356000;ENST00000377819;ENST00000339997;ENST00000540798;ENST00000537981|ENST00000354497	T;T;T;T;T|T	0.33865|0.55588	1.42;1.61;1.62;1.64;1.39|0.51	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.265266|.	0.38217|.	N|.	0.001764|.	T|T	0.48978|0.48978	0.1530|0.1530	.|.	.|.	.|.	0.38733|0.38733	D|D	0.953716|0.953716	P;B;B;P;B|B	0.35174|0.20052	0.488;0.356;0.003;0.488;0.013|0.041	P;B;B;P;B|B	0.49085|0.19391	0.496;0.396;0.018;0.6;0.006|0.025	T|T	0.48031|0.48031	-0.9070|-0.9070	9|8	0.52906|0.52906	T|T	0.07|0.07	-9.5056|-9.5056	17.1412|17.1412	0.86754|0.86754	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	915;1027;231;1008;250|146	F5H774;O95197;O95197-3;O95197-2;O95197-4|B7Z4M0	.;RTN3_HUMAN;.;.;.|.	V|S	250;1027;1008;915;231|146	ENSP00000348279:A250V;ENSP00000367050:A1027V;ENSP00000344106:A1008V;ENSP00000442733:A915V;ENSP00000440874:A231V|ENSP00000346492:P146S	ENSP00000344106:A1008V|ENSP00000346492:P146S	A|P	+|+	2|1	0|0	RTN3|RTN3	63282230|63282230	0.979000|0.979000	0.34478|0.34478	0.984000|0.984000	0.44739|0.44739	0.987000|0.987000	0.75469|0.75469	2.460000|2.460000	0.45031|0.45031	2.650000|2.650000	0.89964|0.89964	0.591000|0.591000	0.81541|0.81541	GCC|CCA	RTN3	-	pfscan_Reticulon	ENSG00000133318		0.338	RTN3-002	KNOWN	basic|CCDS	protein_coding	RTN3	HGNC	protein_coding	OTTHUMT00000397846.1	70	0.00	0	C	NM_006054		63525654	63525654	+1	no_errors	ENST00000377819	ensembl	human	known	69_37n	missense	51	17.74	11	SNP	1.000	T
SARDH	1757	genome.wustl.edu	37	9	136531950	136531950	+	Silent	SNP	G	G	T			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr9:136531950G>T	ENST00000371872.4	-	20	2795	c.2538C>A	c.(2536-2538)ggC>ggA	p.G846G	SARDH_ENST00000469828.1_5'UTR|SARDH_ENST00000422262.2_Silent_p.G678G|SARDH_ENST00000439388.1_Silent_p.G846G|SARDH_ENST00000371868.1_Silent_p.G296G	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	846					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CCACCACTTGGCCGTTCCTCC	0.617																																						dbGAP											0													64.0	53.0	57.0					9																	136531950		2202	4296	6498	-	-	-	SO:0001819	synonymous_variant	0				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2538C>A	9.37:g.136531950G>T			B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	pfam_FAD-dep_OxRdtase,pfam_GCV_T_N,pfam_GCV_T_C	p.G846	ENST00000371872.4	37	c.2538	CCDS6978.1	9																																																																																			SARDH	-	pfam_GCV_T_C	ENSG00000123453		0.617	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SARDH	HGNC	protein_coding	OTTHUMT00000054931.1	46	0.00	0	G			136531950	136531950	-1	no_errors	ENST00000371872	ensembl	human	known	69_37n	silent	29	27.50	11	SNP	0.876	T
SPTA1	6708	genome.wustl.edu	37	1	158583566	158583566	+	Nonsense_Mutation	SNP	C	C	A			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr1:158583566C>A	ENST00000368147.4	-	50	7114	c.6934G>T	c.(6934-6936)Gag>Tag	p.E2312*	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2312					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGTTCATCCTCCTCCACCATG	0.512																																						dbGAP											0													72.0	70.0	71.0					1																	158583566		1925	4138	6063	-	-	-	SO:0001587	stop_gained	0			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6934G>T	1.37:g.158583566C>A	ENSP00000357129:p.Glu2312*		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Nonsense_Mutation	SNP	pfam_Spectrin_repeat,pfam_EF-hand_Ca_insen,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_Spectrin/alpha-actinin,smart_SH3_domain,pfscan_EF_HAND_2,pfscan_SH3_domain,prints_Spectrin_alpha_SH3	p.E2312*	ENST00000368147.4	37	c.6934	CCDS41423.1	1	.	.	.	.	.	.	.	.	.	.	C	48	14.191730	0.99784	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	.	.	.	5.1	5.1	0.69264	.	0.000000	0.32488	N	0.006035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.2641	0.87081	0.0:1.0:0.0:0.0	.	.	.	.	X	2312;2309	.	ENSP00000357129:E2309X	E	-	1	0	SPTA1	156850190	1.000000	0.71417	0.998000	0.56505	0.487000	0.33371	6.900000	0.75687	2.661000	0.90470	0.650000	0.86243	GAG	SPTA1	-	NULL	ENSG00000163554		0.512	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPTA1	HGNC	protein_coding	OTTHUMT00000051851.3	44	0.00	0	C	NM_003126		158583566	158583566	-1	no_errors	ENST00000368148	ensembl	human	known	69_37n	nonsense	45	28.57	18	SNP	1.000	A
TNP2	7142	genome.wustl.edu	37	16	11362818	11362818	+	Missense_Mutation	SNP	C	C	T			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr16:11362818C>T	ENST00000312693.3	-	1	371	c.302G>A	c.(301-303)cGc>cAc	p.R101H	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	101					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						CTTGGGGCAGCGGCAGTGCAG	0.532																																						dbGAP											1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)											72.0	76.0	75.0					16																	11362818		1984	4164	6148	-	-	-	SO:0001583	missense	0				CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.302G>A	16.37:g.11362818C>T	ENSP00000325738:p.Arg101His		Q9NZB0	Missense_Mutation	SNP	pfam_TP2	p.R101H	ENST00000312693.3	37	c.302	CCDS45410.1	16	.	.	.	.	.	.	.	.	.	.	C	5.657	0.305788	0.10733	.	.	ENSG00000178279	ENST00000312693	T	0.47177	0.85	3.54	2.59	0.31030	.	0.000000	0.41712	D	0.000836	T	0.26846	0.0657	N	0.14661	0.345	0.09310	N	1	B	0.20459	0.045	B	0.08055	0.003	T	0.20739	-1.0266	10	0.87932	D	0	-6.1303	6.7717	0.23596	0.0:0.8724:0.0:0.1276	.	101	Q05952	STP2_HUMAN	H	101	ENSP00000325738:R101H	ENSP00000325738:R101H	R	-	2	0	TNP2	11270319	0.002000	0.14202	0.026000	0.17262	0.024000	0.10985	0.004000	0.13106	1.064000	0.40671	0.650000	0.86243	CGC	TNP2	-	pfam_TP2	ENSG00000178279		0.532	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNP2	HGNC	protein_coding	OTTHUMT00000417806.1	208	0.00	0	C	NM_005425		11362818	11362818	-1	no_errors	ENST00000312693	ensembl	human	known	69_37n	missense	149	30.05	64	SNP	0.036	T
TRPV2	51393	genome.wustl.edu	37	17	16335490	16335492	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-E9-A229-01A-31D-A17G-09	TCGA-E9-A229-10B-01D-A159-09	TGC	TGC					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a27fa57d-d1ad-4534-a933-0fdcc5f06a8c	32df7bac-7bb4-4538-800f-893a1ab3d28c	g.chr17:16335490_16335492delTGC	ENST00000338560.7	+	12	2264_2266	c.1865_1867delTGC	c.(1864-1869)gtgctg>gtg	p.L627del	TRPV2_ENST00000583241.1_3'UTR|TRPV2_ENST00000577397.1_In_Frame_Del_p.L197del	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	627					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		CGCGGCATGGTGCTGCTGCTGCT	0.596																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1865_1867delTGC	17.37:g.16335499_16335501delTGC	ENSP00000342222:p.Leu627del		A6NML2|A8K0Z0|Q9Y670	In_Frame_Del	DEL	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_TRPV1-4_channel,tigrfam_TRP_channel	p.L626in_frame_del	ENST00000338560.7	37	c.1865_1867	CCDS32576.1	17																																																																																			TRPV2	-	tigrfam_TRP_channel	ENSG00000187688		0.596	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRPV2	HGNC	protein_coding	OTTHUMT00000130464.2	45	0.00	0	TGC	NM_016113		16335490	16335492	+1	no_errors	ENST00000338560	ensembl	human	known	69_37n	in_frame_del	23	11.54	3	DEL	1.000:1.000:1.000	-
