#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_ ensembl_gene_id	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP	i_default_gene_name	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
SLCO3A1	28232	genome.wustl.edu	37	15	92647634	92647634	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr15:92647634C>A	ENST00000318445.6	+	4	1085	c.871C>A	c.(871-873)Ccg>Acg	p.P291T	SLCO3A1_ENST00000555549.1_3'UTR|SLCO3A1_ENST00000424469.2_Missense_Mutation_p.P291T	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	291					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	GTCCCTGCCCCCGCACTCAGA	0.617													ENSG00000176463																																					0													131.0	111.0	118.0					15																	92647634		2198	4298	6496	SO:0001583	missense	0			-	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"""Solute carriers"""	10952	protein-coding gene	gene with protein product		612435	"""solute carrier family 21 (organic anion transporter), member 11"""	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.871C>A	15.37:g.92647634C>A	ENSP00000320634:p.Pro291Thr		A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	pfam_OA_transporter,pfam_MFS,pfam_Kazal_dom,superfamily_MFS_dom_general_subst_transpt,tigrfam_OA_transporter	p.P291T	ENST00000318445.6	37	c.871	CCDS10371.1	15	.	.	.	.	.	.	.	.	.	.	C	14.30	2.492885	0.44352	.	.	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000556649;ENST00000555549	T;T	0.37915	1.17;1.17	5.12	5.12	0.69794	Major facilitator superfamily domain, general substrate transporter (1);	0.891618	0.09850	N	0.747740	T	0.34890	0.0913	L	0.36672	1.1	0.44061	D	0.996803	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.11329	0.003;0.001;0.006	T	0.08889	-1.0700	10	0.25106	T	0.35	.	18.5528	0.91072	0.0:1.0:0.0:0.0	.	233;291;291	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	T	291;291;84;10	ENSP00000320634:P291T;ENSP00000387846:P291T	ENSP00000320634:P291T	P	+	1	0	SLCO3A1	90448638	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	4.252000	0.58785	2.353000	0.79882	0.655000	0.94253	CCG	-	SLCO3A1	-	pfam_OA_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,tigrfam_OA_transporter		0.617	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLCO3A1	HGNC	protein_coding	OTTHUMT00000313529.1	0	0	0	90	90	64	0.00	0.00	C	NM_013272		92647634	+1	24	9	61	36	tier1	no_errors	ENST00000318445	ensembl	human	known	74_37	missense	27.91	20.00	SNP	0.995	A	24	61
HIST1H1B	3009	genome.wustl.edu	37	6	27834759	27834759	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr6:27834759C>T	ENST00000331442.3	-	1	600	c.549G>A	c.(547-549)ccG>ccA	p.P183P		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	183					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						TTGCCTTTTTCGGTTTGGCAG	0.572													ENSG00000184357																																					0													77.0	77.0	77.0					6																	27834759		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.549G>A	6.37:g.27834759C>T			Q14529|Q3MJ42	Silent	SNP	pfam_Histone_H1/H5_H15,smart_Histone_H1/H5_H15,prints_Histone_H5	p.P183	ENST00000331442.3	37	c.549	CCDS4635.1	6																																																																																			-	HIST1H1B	-	prints_Histone_H5		0.572	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST1H1B	HGNC	protein_coding	OTTHUMT00000043371.1	0	0	0	64	64	85	0.00	0.00	C	NM_005322		27834759	-1	18	19	21	50	tier1	no_errors	ENST00000331442	ensembl	human	known	74_37	silent	46.15	27.54	SNP	0.634	T	18	21
STAT2	6773	genome.wustl.edu	37	12	56743168	56743168	+	Intron	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr12:56743168C>T	ENST00000314128.4	-	15	1365				STAT2_ENST00000556539.1_Intron|STAT2_ENST00000418572.2_Nonsense_Mutation_p.W457*|STAT2_ENST00000557235.1_Intron			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa						cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						ATGCCTTCTTCCAAAGCTGCT	0.473													ENSG00000170581																																					0													130.0	134.0	133.0					12																	56743168		2203	4300	6503	SO:0001627	intron_variant	0			-	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1341+41G>A	12.37:g.56743168C>T			B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Nonsense_Mutation	SNP	pfam_STAT_TF_alpha,pfam_STAT_TF_D-bd,pfam_STAT_TF_prot_interaction,superfamily_STAT_TF_coiled-coil,superfamily_p53-like_TF_D-bd,superfamily_STAT_TF_prot_interaction,smart_STAT_TF_prot_interaction	p.W457*	ENST00000314128.4	37	c.1371	CCDS8917.1	12	.	.	.	.	.	.	.	.	.	.	C	15.13	2.742219	0.49151	.	.	ENSG00000170581	ENST00000418572	.	.	.	5.3	0.333	0.15943	.	.	.	.	.	.	.	.	.	.	.	0.25495	N	0.98761	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.0791	0.09917	0.1531:0.5088:0.0:0.3381	.	.	.	.	X	457	.	ENSP00000387354:W457X	W	-	3	0	STAT2	55029435	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.056000	0.11787	-0.135000	0.11495	-0.244000	0.11960	TGG	-	STAT2	-	NULL		0.473	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	STAT2	HGNC	protein_coding	OTTHUMT00000410277.1	0	0	0	97	97	153	0.00	0.00	C	NM_005419		56743168	-1	1257	2157	112	131	tier1	no_errors	ENST00000418572	ensembl	human	putative	74_37	nonsense	91.82	94.07	SNP	0.000	T	1257	112
RAVER2	55225	genome.wustl.edu	37	1	65247087	65247087	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:65247087G>A	ENST00000294428.3	+	4	889	c.811G>A	c.(811-813)Gtt>Att	p.V271I	RAVER2_ENST00000371072.4_Missense_Mutation_p.V271I|RAVER2_ENST00000430964.2_De_novo_Start_OutOfFrame			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	271	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						AGGTAGTTACGTTGGTGGCTT	0.418													ENSG00000162437																																					0													142.0	142.0	142.0					1																	65247087		2006	4174	6180	SO:0001583	missense	0			-	AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.811G>A	1.37:g.65247087G>A	ENSP00000294428:p.Val271Ile		Q6P141|Q9NPV7	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.V271I	ENST00000294428.3	37	c.811		1	.	.	.	.	.	.	.	.	.	.	G	4.508	0.094166	0.08632	.	.	ENSG00000162437	ENST00000371072;ENST00000294428	T;T	0.15603	2.41;2.41	5.43	5.43	0.79202	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.390908	0.25836	N	0.027987	T	0.04137	0.0115	N	0.22421	0.69	0.46113	D	0.998875	B;B	0.11235	0.004;0.003	B;B	0.10450	0.005;0.003	T	0.34527	-0.9825	10	0.17832	T	0.49	-16.6374	8.0904	0.30797	0.0853:0.0:0.7557:0.159	.	271;271	Q9HCJ3;Q9HCJ3-2	RAVR2_HUMAN;.	I	271	ENSP00000360112:V271I;ENSP00000294428:V271I	ENSP00000294428:V271I	V	+	1	0	RAVER2	65019675	0.190000	0.23276	0.039000	0.18376	0.010000	0.07245	1.237000	0.32695	2.562000	0.86427	0.591000	0.81541	GTT	-	RAVER2	-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom		0.418	RAVER2-201	KNOWN	basic	protein_coding	RAVER2	HGNC	protein_coding		0	0	0	68	68	83	0.00	0.00	G	NM_018211		65247087	+1	34	29	51	64	tier1	no_errors	ENST00000294428	ensembl	human	known	74_37	missense	40.00	31.18	SNP	0.016	A	34	51
STAT2	6773	genome.wustl.edu	37	12	56743279	56743279	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr12:56743279C>T	ENST00000314128.4	-	15	1295	c.1272G>A	c.(1270-1272)gtG>gtA	p.V424V	STAT2_ENST00000556539.1_5'UTR|RNU7-40P_ENST00000516397.1_RNA|STAT2_ENST00000418572.2_Silent_p.V420V|STAT2_ENST00000557235.1_Silent_p.V420V			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	424					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						GTTCCTCTGTCACACCTAGTG	0.517													ENSG00000170581																																					0													173.0	167.0	169.0					12																	56743279		2203	4300	6503	SO:0001819	synonymous_variant	0			-	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1272G>A	12.37:g.56743279C>T			B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Silent	SNP	pfam_STAT_TF_D-bd,pfam_STAT_TF_alpha,pfam_STAT_TF_prot_interaction,pfam_STAT2_C,pfam_SH2,superfamily_p53-like_TF_D-bd,superfamily_STAT_TF_coiled-coil,superfamily_STAT_TF_prot_interaction,smart_STAT_TF_prot_interaction,smart_SH2,pfscan_SH2	p.V424	ENST00000314128.4	37	c.1272	CCDS8917.1	12																																																																																			-	STAT2	-	pfam_STAT_TF_D-bd,superfamily_p53-like_TF_D-bd		0.517	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	STAT2	HGNC	protein_coding	OTTHUMT00000410277.1	0	0	1	79	79	106	0.00	0.93	C	NM_005419		56743279	-1	1135	1769	73	123	tier1	no_errors	ENST00000314128	ensembl	human	known	74_37	silent	93.88	93.45	SNP	0.990	T	1135	73
POLN	353497	genome.wustl.edu	37	4	2181178	2181178	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr4:2181178C>T	ENST00000511885.2	-	8	1389	c.1036G>A	c.(1036-1038)Ggg>Agg	p.G346R	POLN_ENST00000382865.1_Missense_Mutation_p.G346R|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	346					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			GGATCTAGCCCTATAAAATCA	0.363								DNA polymerases (catalytic subunits)					ENSG00000130997																																					0													67.0	65.0	66.0					4																	2181178		2203	4300	6503	SO:0001583	missense	0			-	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.1036G>A	4.37:g.2181178C>T	ENSP00000435506:p.Gly346Arg		A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	pfam_D-dir_D_pol_A_palm_dom,superfamily_RNaseH-like_dom,smart_D-dir_D_pol_A_palm_dom,prints_D_polymerase_A	p.G346R	ENST00000511885.2	37	c.1036	CCDS3360.1	4	.	.	.	.	.	.	.	.	.	.	C	18.03	3.531552	0.64972	.	.	ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313	T;T	0.04454	3.62;3.62	5.61	5.61	0.85477	.	0.187268	0.35124	N	0.003437	T	0.16981	0.0408	M	0.63428	1.95	0.27464	N	0.953058	D;D	0.71674	0.998;0.988	D;P	0.65010	0.931;0.629	T	0.01557	-1.1325	10	0.41790	T	0.15	-20.53	15.1521	0.72709	0.0:1.0:0.0:0.0	.	346;346	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	R	346;346;37	ENSP00000435506:G346R;ENSP00000372316:G346R	ENSP00000253313:G37R	G	-	1	0	POLN	2150976	0.886000	0.30341	0.876000	0.34364	0.800000	0.45204	2.890000	0.48609	2.656000	0.90262	0.561000	0.74099	GGG	-	POLN	-	superfamily_RNaseH-like_dom		0.363	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLN	HGNC	protein_coding	OTTHUMT00000205684.2	0	0	1	37	37	130	0.00	0.76	C	NM_181808		2181178	-1	9	34	26	68	tier1	no_errors	ENST00000382865	ensembl	human	known	74_37	missense	25.71	33.33	SNP	0.564	T	9	26
AP2A2	161	genome.wustl.edu	37	11	993375	993375	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr11:993375G>C	ENST00000448903.2	+	12	1685	c.1544G>C	c.(1543-1545)aGa>aCa	p.R515T	AP2A2_ENST00000332231.5_Missense_Mutation_p.R516T|AP2A2_ENST00000534328.1_Intron	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	515					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.R516K(1)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		GGAGACCCGAGATCCAGGTGA	0.657													ENSG00000183020																																					1	Substitution - Missense(1)	ovary(1)											37.0	41.0	40.0					11																	993375		1925	4129	6054	SO:0001583	missense	0			-	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1544G>C	11.37:g.993375G>C	ENSP00000413234:p.Arg515Thr		O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a-adaptin_app_sub_C,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/calthrin_app_sub_C,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP2_complex_asu	p.R516T	ENST00000448903.2	37	c.1547	CCDS44512.1	11	.	.	.	.	.	.	.	.	.	.	G	10.60	1.395537	0.25205	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310	T;T	0.28454	1.61;1.61	3.51	3.51	0.40186	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.49575	0.1565	L	0.61218	1.895	0.80722	D	1	D;P;P	0.64830	0.994;0.898;0.91	D;B;P	0.73708	0.981;0.43;0.566	T	0.44817	-0.9303	10	0.21014	T	0.42	-44.1555	15.903	0.79397	0.0:0.0:1.0:0.0	.	254;516;515	B7Z1Q4;O94973-2;O94973	.;.;AP2A2_HUMAN	T	515;516;516;252;255	ENSP00000413234:R515T;ENSP00000327694:R516T	ENSP00000327694:R516T	R	+	2	0	AP2A2	983375	1.000000	0.71417	0.218000	0.23776	0.076000	0.17211	9.709000	0.98729	1.896000	0.54893	0.462000	0.41574	AGA	-	AP2A2	-	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP2_complex_asu		0.657	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	AP2A2	HGNC	protein_coding	OTTHUMT00000385431.2	0	0	0	54	54	51	0.00	0.00	G	NM_012305		993375	+1	9	4	56	29	tier1	no_errors	ENST00000332231	ensembl	human	known	74_37	missense	13.85	11.76	SNP	0.970	C	9	56
DCLK3	85443	genome.wustl.edu	37	3	36759633	36759633	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr3:36759633C>T	ENST00000416516.2	-	4	2111	c.1621G>A	c.(1621-1623)Gtg>Atg	p.V541M	DCLK3_ENST00000498047.1_5'UTR	NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	541	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						TAGAGGATCACGCCAGCAGCC	0.547													ENSG00000163673																																					0													145.0	159.0	154.0					3																	36759633		2142	4280	6422	SO:0001583	missense	0			-	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.1621G>A	3.37:g.36759633C>T	ENSP00000394484:p.Val541Met			Missense_Mutation	SNP	pfam_Prot_kinase_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_dom	p.V541M	ENST00000416516.2	37	c.1621	CCDS43064.1	3	.	.	.	.	.	.	.	.	.	.	C	17.12	3.309393	0.60414	.	.	ENSG00000163673	ENST00000416516	T	0.51817	0.69	5.51	5.51	0.81932	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.30159	N	0.010275	T	0.77089	0.4079	M	0.92026	3.265	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.81722	-0.0803	10	0.87932	D	0	.	19.7913	0.96458	0.0:1.0:0.0:0.0	.	541	Q9C098	DCLK3_HUMAN	M	541	ENSP00000394484:V541M	ENSP00000394484:V541M	V	-	1	0	DCLK3	36734637	1.000000	0.71417	0.960000	0.40013	0.060000	0.15804	6.079000	0.71291	2.765000	0.95021	0.555000	0.69702	GTG	-	DCLK3	-	pfam_Prot_kinase_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_dom		0.547	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCLK3	HGNC	protein_coding	OTTHUMT00000341727.1	0	0	0	40	40	78	0.00	0.00	C	XM_047355		36759633	-1	16	28	32	59	tier1	no_errors	ENST00000416516	ensembl	human	known	74_37	missense	33.33	32.18	SNP	1.000	T	16	32
DGCR2	9993	genome.wustl.edu	37	22	19026588	19026588	+	Silent	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr22:19026588C>A	ENST00000263196.7	-	10	1690	c.1443G>T	c.(1441-1443)ggG>ggT	p.G481G	DGCR2_ENST00000537045.1_Silent_p.G440G|DGCR2_ENST00000545799.1_3'UTR	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	481					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					TCCCACCATCCCCAGGGGCTG	0.642													ENSG00000070413																																					0													38.0	39.0	39.0					22																	19026588		2202	4298	6500	SO:0001819	synonymous_variant	0			-	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1443G>T	22.37:g.19026588C>A			A6NIB5|A8K6K5|B5TY34|B7Z935	Silent	SNP	pfam_LDrepeatLR_classA_rpt,superfamily_C-type_lectin_fold,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_C-type_lectin,smart_VWF_C,pfscan_LDrepeatLR_classA_rpt,pfscan_C-type_lectin	p.G481	ENST00000263196.7	37	c.1443	CCDS33598.1	22																																																																																			-	DGCR2	-	NULL		0.642	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	DGCR2	HGNC	protein_coding	OTTHUMT00000316504.1	0	0	0	109	109	46	0.00	0.00	C	NM_005137		19026588	-1	36	24	64	48	tier1	no_errors	ENST00000263196	ensembl	human	known	74_37	silent	35.64	33.33	SNP	0.306	A	36	64
SENP2	59343	genome.wustl.edu	37	3	185316763	185316763	+	Silent	SNP	A	A	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr3:185316763A>T	ENST00000296257.5	+	4	549	c.309A>T	c.(307-309)tcA>tcT	p.S103S	SENP2_ENST00000465201.1_3'UTR|SENP2_ENST00000545472.1_Silent_p.S93S|SENP2_ENST00000427465.2_Intron	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	103					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CGAACTCTTCATCTTGTGAAC	0.363													ENSG00000163904																																					0													132.0	125.0	128.0					3																	185316763		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"""SUMO1/sentrin/SMT3 specific protease 2"""			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.309A>T	3.37:g.185316763A>T			B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Missense_Mutation	SNP	NULL	p.I59F	ENST00000296257.5	37	c.175	CCDS33902.1	3																																																																																			-	SENP2	-	NULL		0.363	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SENP2	HGNC	protein_coding	OTTHUMT00000345159.1	0	0	0	48	48	132	0.00	0.00	A	NM_021627		185316763	+1	38	38	20	27	tier1	no_errors	ENST00000439684	ensembl	human	known	74_37	missense	65.52	58.46	SNP	0.965	T	38	20
BAI3	577	genome.wustl.edu	37	6	70034783	70034783	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr6:70034783C>A	ENST00000370598.1	+	21	3655	c.2834C>A	c.(2833-2835)aCt>aAt	p.T945N	BAI3_ENST00000238918.8_Missense_Mutation_p.T151N	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	945	Poly-Thr.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				ACAACCACCACTGCATTTTTG	0.418													ENSG00000135298																																					0													142.0	130.0	134.0					6																	70034783		2203	4300	6503	SO:0001583	missense	0			-	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2834C>A	6.37:g.70034783C>A	ENSP00000359630:p.Thr945Asn		B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	pfam_GPCR_2_secretin-like,pfam_DUF3497,pfam_Thrombospondin_1_rpt,pfam_GPS_dom,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,smart_GPCR_2_extracellular_dom,smart_GPS_dom,pfscan_CUB_dom,pfscan_GPS_dom,pfscan_Thrombospondin_1_rpt,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_GPCR_2_brain-spec_angio_inhib,prints_GPCR_2_secretin-like	p.T945N	ENST00000370598.1	37	c.2834	CCDS4968.1	6	.	.	.	.	.	.	.	.	.	.	C	34	5.330994	0.95733	.	.	ENSG00000135298	ENST00000370598;ENST00000238918	T;T	0.44881	0.91;0.91	6.07	6.07	0.98685	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.66439	2.03	0.80722	D	1	D;P;D	0.63880	0.992;0.872;0.993	D;P;D	0.65233	0.933;0.659;0.909	T	0.58869	-0.7560	10	0.87932	D	0	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	151;945;945	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	N	945;151	ENSP00000359630:T945N;ENSP00000238918:T151N	ENSP00000238918:T151N	T	+	2	0	BAI3	70091504	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.792000	0.85828	2.885000	0.99019	0.655000	0.94253	ACT	-	BAI3	-	pfam_GPCR_2_secretin-like,pfscan_GPCR_2-like,prints_GPCR_2_secretin-like		0.418	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BAI3	HGNC	protein_coding	OTTHUMT00000041120.1	0	0	0	122	122	69	0.00	0.00	C			70034783	+1	40	29	106	53	tier1	no_errors	ENST00000370598	ensembl	human	known	74_37	missense	27.40	35.37	SNP	1.000	A	40	106
RYR1	6261	genome.wustl.edu	37	19	38951142	38951142	+	Missense_Mutation	SNP	C	C	T	rs142548565		TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr19:38951142C>T	ENST00000359596.3	+	20	2488	c.2488C>T	c.(2488-2490)Cgg>Tgg	p.R830W	RYR1_ENST00000360985.3_Missense_Mutation_p.R830W|RYR1_ENST00000355481.4_Missense_Mutation_p.R830W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	830					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R830W(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGAGTATCGACGGGAGGGGCC	0.632													ENSG00000196218																																					1	Substitution - Missense(1)	large_intestine(1)						C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	68.0	73.0	71.0		2488,2488	1.9	0.9	19	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	101,101	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	830/5039,830/5034	38951142	4,13002	2203	4300	6503	SO:0001583	missense	0			-	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2488C>T	19.37:g.38951142C>T	ENSP00000352608:p.Arg830Trp		Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	pfam_Ca-rel_channel,pfam_Ryanodine_rcpt,pfam_Ryanrecept_TM4-6,pfam_SPRY_rcpt,pfam_Ins145_P3_rcpt,pfam_MIR_motif,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR_motif,superfamily_ConA-like_lec_gl_sf,superfamily_MG_RAP_rcpt_1,smart_MIR_motif,smart_SPla/RYanodine_receptor_subgr,prints_Ryan_recept,pfscan_B30.2/SPRY,pfscan_MIR_motif	p.R830W	ENST00000359596.3	37	c.2488	CCDS33011.1	19	.	.	.	.	.	.	.	.	.	.	c	15.55	2.866632	0.51588	0.0	4.65E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96940	-4.17;-4.18;-4.17	4.13	1.89	0.25635	.	0.091594	0.43416	U	0.000573	D	0.96583	0.8885	L	0.57536	1.79	0.26910	N	0.966923	D;D	0.89917	1.0;0.999	D;D	0.70016	0.967;0.96	D	0.91398	0.5141	10	0.51188	T	0.08	.	8.8285	0.35069	0.3047:0.556:0.1393:0.0	.	830;830	P21817-2;P21817	.;RYR1_HUMAN	W	830	ENSP00000352608:R830W;ENSP00000347667:R830W;ENSP00000354254:R830W	ENSP00000347667:R830W	R	+	1	2	RYR1	43642982	0.468000	0.25839	0.892000	0.35008	0.972000	0.66771	1.165000	0.31822	0.447000	0.26695	0.299000	0.19835	CGG	rs142548565	RYR1	-	NULL		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RYR1	HGNC	protein_coding	OTTHUMT00000462137.1	0	0	0	65	65	20	0.00	0.00	C			38951142	+1	15	12	28	22	tier1	no_errors	ENST00000359596	ensembl	human	known	74_37	missense	34.88	35.29	SNP	0.739	T	15	28
AKAP6	9472	genome.wustl.edu	37	14	33147640	33147640	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr14:33147640A>G	ENST00000280979.4	+	8	3024	c.2854A>G	c.(2854-2856)Aaa>Gaa	p.K952E	AKAP6_ENST00000557272.1_Missense_Mutation_p.K952E|AKAP6_ENST00000557354.1_Missense_Mutation_p.K952E	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	952					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TGATATGTCAAAAGTTCATTC	0.413													ENSG00000151320																									Melanoma(49;821 1200 7288 13647 42351)												0													191.0	180.0	184.0					14																	33147640		2203	4300	6503	SO:0001583	missense	0			-	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.2854A>G	14.37:g.33147640A>G	ENSP00000280979:p.Lys952Glu		A7E242|A7E2D4|O15028	Missense_Mutation	SNP	smart_Spectrin/alpha-actinin	p.K952E	ENST00000280979.4	37	c.2854	CCDS9644.1	14	.	.	.	.	.	.	.	.	.	.	A	19.29	3.798775	0.70567	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.19806	3.39;2.12;2.14	5.0	5.0	0.66597	.	0.078146	0.56097	D	0.000032	T	0.25901	0.0631	N	0.08118	0	0.39895	D	0.973829	D;D	0.76494	0.999;0.997	D;D	0.75020	0.918;0.985	T	0.33369	-0.9871	10	0.62326	D	0.03	-17.2443	13.565	0.61813	1.0:0.0:0.0:0.0	.	952;952	A7E242;Q13023	.;AKAP6_HUMAN	E	952	ENSP00000280979:K952E;ENSP00000450531:K952E;ENSP00000451247:K952E	ENSP00000280979:K952E	K	+	1	0	AKAP6	32217391	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.358000	0.73055	2.007000	0.58848	0.477000	0.44152	AAA	-	AKAP6	-	NULL		0.413	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AKAP6	HGNC	protein_coding	OTTHUMT00000276617.2	0	0	0	58	58	152	0.00	0.00	A	NM_004274		33147640	+1	16	21	46	45	tier1	no_errors	ENST00000280979	ensembl	human	known	74_37	missense	25.81	30.88	SNP	1.000	G	16	46
SENP1	29843	genome.wustl.edu	37	12	48459425	48459425	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr12:48459425C>T	ENST00000004980.5	-	11	1551	c.1073G>A	c.(1072-1074)cGc>cAc	p.R358H	SENP1_ENST00000551330.1_Missense_Mutation_p.R358H|SENP1_ENST00000549595.1_Missense_Mutation_p.R358H|SENP1_ENST00000448372.1_Missense_Mutation_p.R358H|SENP1_ENST00000339976.6_3'UTR|SENP1_ENST00000549518.1_Missense_Mutation_p.R358H			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	358					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TTCAATCTGGCGCAATCTTTC	0.338													ENSG00000079387																																					0													63.0	56.0	58.0					12																	48459425		1848	4077	5925	SO:0001583	missense	0			-	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.1073G>A	12.37:g.48459425C>T	ENSP00000004980:p.Arg358His		A8K7P5|Q86XC8	Missense_Mutation	SNP	pfam_Peptidase_C48,pfscan_Peptidase_C48	p.R358H	ENST00000004980.5	37	c.1073	CCDS44868.2	12	.	.	.	.	.	.	.	.	.	.	C	34	5.327461	0.95733	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518	T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.44307	0.1287	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.25641	-1.0126	10	0.72032	D	0.01	-8.0321	20.017	0.97481	0.0:1.0:0.0:0.0	.	358;358	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	H	358	ENSP00000004980:R358H;ENSP00000394791:R358H;ENSP00000446681:R358H;ENSP00000450076:R358H;ENSP00000447328:R358H	ENSP00000004980:R358H	R	-	2	0	SENP1	46745692	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.202000	0.72131	2.832000	0.97577	0.655000	0.94253	CGC	-	SENP1	-	NULL		0.338	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SENP1	HGNC	protein_coding	OTTHUMT00000406471.1	0	0	1	42	42	111	0.00	0.89	C	NM_014554		48459425	-1	8	35	25	59	tier1	no_errors	ENST00000004980	ensembl	human	known	74_37	missense	23.53	37.23	SNP	1.000	T	8	25
PKLR	5313	genome.wustl.edu	37	1	155269901	155269901	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:155269901T>C	ENST00000342741.4	-	2	309	c.271A>G	c.(271-273)Att>Gtt	p.I91V	PKLR_ENST00000392414.3_Missense_Mutation_p.I60V	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	91					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	ATGGTGGCAATGATGCTGGTA	0.552													ENSG00000143627																																					0													70.0	69.0	69.0					1																	155269901		2203	4300	6503	SO:0001583	missense	0			-	BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.271A>G	1.37:g.155269901T>C	ENSP00000339933:p.Ile91Val		O75758|P11973	Missense_Mutation	SNP	pfam_Pyrv_Knase_brl,pfam_Pyrv_Knase_C,superfamily_Pyrv/PenolPyrv_Kinase-like_dom,superfamily_Pyrv_Knase_C,superfamily_Pyrv_Knase-like_insert_dom,prints_Pyr_Knase,tigrfam_Pyr_Knase	p.I91V	ENST00000342741.4	37	c.271	CCDS1109.1	1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.785272	0.31593	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99207	-5.56;-5.56	4.02	4.02	0.46733	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.055870	0.64402	D	0.000001	D	0.92273	0.7549	N	0.10645	0.015	0.47737	D	0.999504	B;B	0.19935	0.04;0.01	B;B	0.26864	0.074;0.074	D	0.89859	0.4015	10	0.14252	T	0.57	-11.6263	5.9764	0.19382	0.0:0.1172:0.0:0.8828	.	91;82	P30613;B1AVT1	KPYR_HUMAN;.	V	116;60;91;27	ENSP00000376214:I60V;ENSP00000339933:I91V	ENSP00000271946:I27V	I	-	1	0	PKLR	153536525	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.669000	0.37492	1.663000	0.50791	0.472000	0.43445	ATT	-	PKLR	-	pfam_Pyrv_Knase_brl,superfamily_Pyrv/PenolPyrv_Kinase-like_dom,tigrfam_Pyr_Knase		0.552	PKLR-001	KNOWN	basic|CCDS	protein_coding	PKLR	HGNC	protein_coding	OTTHUMT00000087407.2	0	0	0	70	70	111	0.00	0.00	T	NM_000298		155269901	-1	24	40	42	66	tier1	no_errors	ENST00000342741	ensembl	human	known	74_37	missense	36.36	37.74	SNP	1.000	C	24	42
LOC63930	63930	genome.wustl.edu	37	20	61665964	61665964	+	lincRNA	SNP	A	A	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr20:61665964A>T	ENST00000607802.1	+	0	91				LINC00029_ENST00000370341.3_lincRNA	NR_033370.1																						AGAAATCCGGAAACAAGGGAC	0.517													ENSG00000125514																																					0																																												0			-																													20.37:g.61665964A>T				R	SNP	-	NULL	ENST00000607802.1	37	NULL		20																																																																																			-	LINC00029	-	-		0.517	RP11-305P22.9-001	KNOWN	basic	lincRNA	LINC00029	HGNC	lincRNA	OTTHUMT00000470475.1	0	0	0	45	45	78	0.00	0.00	A			61665964	-1	12	21	27	34	tier1	no_errors	ENST00000370341	ensembl	human	known	74_37	rna	30.77	38.18	SNP	0.001	T	12	27
GAL3ST1	9514	genome.wustl.edu	37	22	30950947	30950947	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr22:30950947C>T	ENST00000402321.1	-	3	1582	c.1265G>A	c.(1264-1266)cGg>cAg	p.R422Q	GAL3ST1_ENST00000443111.2_Missense_Mutation_p.R422Q|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.R422Q|GAL3ST1_ENST00000338911.5_Missense_Mutation_p.R422Q|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.R422Q|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.R422Q|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.R422Q			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	422				R -> E (in Ref. 1; AA sequence). {ECO:0000305}.	galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						ACGTCACCACCGCAGGAAATC	0.682													ENSG00000128242																																					0													45.0	41.0	42.0					22																	30950947		2203	4300	6503	SO:0001583	missense	0			-	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"""Sulfotransferases, membrane-bound"""	24240	protein-coding gene	gene with protein product	"""cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"""	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.1265G>A	22.37:g.30950947C>T	ENSP00000385735:p.Arg422Gln		Q96C63	Missense_Mutation	SNP	pfam_Gal-3-0_sulfotransfrase,superfamily_P-loop_NTPase	p.R422Q	ENST00000402321.1	37	c.1265	CCDS13879.1	22	.	.	.	.	.	.	.	.	.	.	c	10.12	1.263311	0.23051	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111	T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.73	-1.77	0.07982	.	0.424732	0.26146	N	0.026068	T	0.07324	0.0185	N	0.13043	0.29	0.45452	D	0.998428	B	0.06786	0.001	B	0.01281	0.0	T	0.36237	-0.9756	10	0.20519	T	0.43	-10.2743	7.1798	0.25765	0.1094:0.4456:0.0:0.445	.	422	Q99999	G3ST1_HUMAN	Q	422	ENSP00000385825:R422Q;ENSP00000385735:R422Q;ENSP00000384122:R422Q;ENSP00000384388:R422Q;ENSP00000343234:R422Q;ENSP00000385207:R422Q;ENSP00000402587:R422Q	ENSP00000343234:R422Q	R	-	2	0	GAL3ST1	29280947	0.999000	0.42202	0.098000	0.21074	0.792000	0.44763	1.935000	0.40173	-0.553000	0.06158	-0.291000	0.09656	CGG	-	GAL3ST1	-	NULL		0.682	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GAL3ST1	HGNC	protein_coding	OTTHUMT00000321745.1	0	0	0	49	49	49	0.00	0.00	C	NM_004861		30950947	-1	23	22	30	20	tier1	no_errors	ENST00000338911	ensembl	human	known	74_37	missense	43.40	52.38	SNP	0.346	T	23	30
EPHB1	2047	genome.wustl.edu	37	3	134644703	134644703	+	Missense_Mutation	SNP	C	C	T	rs536029159		TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr3:134644703C>T	ENST00000398015.3	+	2	474	c.104C>T	c.(103-105)aCg>aTg	p.T35M	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	35	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CTGGGCTGGACGGCCAATCCT	0.458													ENSG00000154928	C|||	1	0.000199681	0.0	0.0	5008	,	,		20439	0.001		0.0	False		,,,				2504	0.0																0																																										SO:0001583	missense	0			-	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.104C>T	3.37:g.134644703C>T	ENSP00000381097:p.Thr35Met		A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ephrin_rcpt_lig-bd_dom,pfam_Prot_kinase_dom,pfam_Fibronectin_type3,pfam_SAM_type1,pfam_SAM_2,superfamily_Galactose-bd-like,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_SAM/pointed,superfamily_Growth_fac_rcpt_N_dom,smart_Ephrin_rcpt_lig-bd_dom,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_SAM,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_SAM,pfscan_Prot_kinase_dom	p.T35M	ENST00000398015.3	37	c.104	CCDS46921.1	3	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735981	0.49045	.	.	ENSG00000154928	ENST00000460895;ENST00000398015;ENST00000497173;ENST00000473867;ENST00000474732	T;T;T;T;T	0.03831	3.79;3.79;3.79;3.79;3.79	4.33	4.33	0.51752	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.067175	0.56097	D	0.000023	T	0.14442	0.0349	L	0.48642	1.525	0.80722	D	1	D;D	0.64830	0.994;0.988	D;P	0.63793	0.918;0.797	T	0.02391	-1.1166	10	0.40728	T	0.16	.	17.0176	0.86423	0.0:1.0:0.0:0.0	.	35;35	B5A969;P54762	.;EPHB1_HUMAN	M	13;35;13;13;13	ENSP00000417435:T13M;ENSP00000381097:T35M;ENSP00000419688:T13M;ENSP00000417216:T13M;ENSP00000418352:T13M	ENSP00000381097:T35M	T	+	2	0	EPHB1	136127393	0.999000	0.42202	1.000000	0.80357	0.975000	0.68041	5.278000	0.65592	2.253000	0.74438	0.555000	0.69702	ACG	-	EPHB1	-	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ephrin_rcpt_lig-bd_dom,superfamily_Galactose-bd-like,smart_Ephrin_rcpt_lig-bd_dom		0.458	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	EPHB1	HGNC	protein_coding	OTTHUMT00000357671.1	0	0	0	35	35	104	0.00	0.00	C	NM_004441		134644703	+1	30	51	19	38	tier1	no_errors	ENST00000398015	ensembl	human	known	74_37	missense	61.22	57.30	SNP	1.000	T	30	19
ASTN1	460	genome.wustl.edu	37	1	176903441	176903441	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:176903441T>C	ENST00000367654.3	-	16	2753	c.2542A>G	c.(2542-2544)Aca>Gca	p.T848A	ASTN1_ENST00000367657.3_Missense_Mutation_p.T840A|ASTN1_ENST00000361833.2_Missense_Mutation_p.T840A|ASTN1_ENST00000424564.2_Missense_Mutation_p.T840A|ASTN1_ENST00000281881.3_5'Flank	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	848					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.T840A(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GCACGAGATGTAGCCCCATCC	0.527													ENSG00000152092																																					1	Substitution - Missense(1)	lung(1)											93.0	80.0	84.0					1																	176903441		2203	4300	6503	SO:0001583	missense	0			-	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2542A>G	1.37:g.176903441T>C	ENSP00000356626:p.Thr848Ala		A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	superfamily_Fibronectin_type3,smart_EG-like_dom,smart_MACPF,pfscan_Fibronectin_type3	p.T848A	ENST00000367654.3	37	c.2542		1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.809980	0.90707	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.61173	0.2326	L	0.40543	1.245	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.72982	0.979;0.979	T	0.63440	-0.6637	10	0.72032	D	0.01	-17.3327	16.0098	0.80391	0.0:0.0:0.0:1.0	.	840;840	O14525-2;B1AJS1	.;.	A	840;840;848;840;840	ENSP00000356629:T840A;ENSP00000354536:T840A;ENSP00000356626:T848A;ENSP00000395041:T840A	ENSP00000354536:T840A	T	-	1	0	ASTN1	175170064	1.000000	0.71417	0.989000	0.46669	0.950000	0.60333	7.517000	0.81783	2.254000	0.74563	0.533000	0.62120	ACA	-	ASTN1	-	smart_MACPF		0.527	ASTN1-201	KNOWN	basic	protein_coding	ASTN1	HGNC	protein_coding		0	0	0	28	28	113	0.00	0.00	T	NM_004319		176903441	-1	15	30	33	53	tier1	no_errors	ENST00000367654	ensembl	human	known	74_37	missense	31.25	36.14	SNP	0.998	C	15	33
SLC4A4	8671	genome.wustl.edu	37	4	72412086	72412086	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr4:72412086T>A	ENST00000264485.5	+	19	2579	c.2462T>A	c.(2461-2463)tTg>tAg	p.L821*	SLC4A4_ENST00000425175.1_Nonsense_Mutation_p.L821*|SLC4A4_ENST00000340595.3_Nonsense_Mutation_p.L777*|SLC4A4_ENST00000351898.6_Intron	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	821					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)	GGGTATCACTTGGATCTCTTT	0.438													ENSG00000080493																																					0													259.0	213.0	228.0					4																	72412086		2203	4300	6503	SO:0001587	stop_gained	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.2462T>A	4.37:g.72412086T>A	ENSP00000264485:p.Leu821*		C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Nonsense_Mutation	SNP	pfam_HCO3_transpt_C,pfam_Band3_cytoplasmic_dom,superfamily_PTrfase/Anion_transptr,prints_HCO3_transpt_euk,prints_Na/HCO3_transpt,tigrfam_HCO3_transpt_euk	p.L821*	ENST00000264485.5	37	c.2462	CCDS43236.1	4	.	.	.	.	.	.	.	.	.	.	T	42	9.480197	0.99183	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000340595	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7067	0.77588	0.0:0.0:0.0:1.0	.	.	.	.	X	821;821;777	.	ENSP00000264485:L821X	L	+	2	0	SLC4A4	72630950	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.040000	0.89188	2.104000	0.64026	0.528000	0.53228	TTG	-	SLC4A4	-	pfam_HCO3_transpt_C,tigrfam_HCO3_transpt_euk		0.438	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC4A4	HGNC	protein_coding	OTTHUMT00000362090.1	0	0	0	117	117	81	0.00	0.00	T	NM_003759		72412086	+1	23	20	62	61	tier1	no_errors	ENST00000425175	ensembl	human	known	74_37	nonsense	27.06	24.69	SNP	1.000	A	23	62
TNPO3	23534	genome.wustl.edu	37	7	128640525	128640525	+	Silent	SNP	A	A	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr7:128640525A>C	ENST00000265388.5	-	7	1112	c.969T>G	c.(967-969)acT>acG	p.T323T	TNPO3_ENST00000471166.1_Silent_p.T323T|TNPO3_ENST00000393245.1_Silent_p.T323T|TNPO3_ENST00000471234.1_Silent_p.T323T|TNPO3_ENST00000482320.1_Silent_p.T257T			Q9Y5L0	TNPO3_HUMAN	transportin 3	323					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						GCAGCTCCAGAGTTCGAAGGT	0.413													ENSG00000064419																									Pancreas(147;583 2585 39696 52331)												0													83.0	89.0	87.0					7																	128640525		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.969T>G	7.37:g.128640525A>C			A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	pfam_Exportin-1/Importin-b-like,superfamily_ARM-type_fold	p.T323	ENST00000265388.5	37	c.969	CCDS5809.1	7																																																																																			-	TNPO3	-	superfamily_ARM-type_fold		0.413	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNPO3	HGNC	protein_coding	OTTHUMT00000350929.1	0	0	0	22	22	92	0.00	0.00	A	NM_012470		128640525	-1	8	34	26	64	tier1	no_errors	ENST00000393245	ensembl	human	known	74_37	silent	23.53	34.69	SNP	0.999	C	8	26
EPHB2	2048	genome.wustl.edu	37	1	23233390	23233390	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:23233390C>T	ENST00000400191.3	+	11	2094	c.2076C>T	c.(2074-2076)agC>agT	p.S692S	EPHB2_ENST00000374630.3_Silent_p.S692S|EPHB2_ENST00000374632.3_Silent_p.S693S|EPHB2_ENST00000374627.1_Silent_p.S687S	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	692	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		TGACCAAGAGCACACCTGTGA	0.602													ENSG00000133216																																					0													97.0	69.0	78.0					1																	23233390		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.2076C>T	1.37:g.23233390C>T			O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ephrin_rcpt_lig-bd_dom,pfam_Prot_kinase_dom,pfam_Fibronectin_type3,pfam_SAM_type1,pfam_SAM_2,pfam_Tyr-kin_ephrin_A/B_rcpt-like,superfamily_Galactose-bd-like,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_SAM/pointed,superfamily_Growth_fac_rcpt_N_dom,smart_Ephrin_rcpt_lig-bd_dom,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_SAM,pfscan_Fibronectin_type3,pfscan_SAM,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.S692	ENST00000400191.3	37	c.2076		1																																																																																			-	EPHB2	-	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.602	EPHB2-001	KNOWN	basic	protein_coding	EPHB2	HGNC	protein_coding	OTTHUMT00000008060.2	0	0	0	35	35	74	0.00	0.00	C	NM_017449		23233390	+1	22	27	28	45	tier1	no_errors	ENST00000400191	ensembl	human	known	74_37	silent	44.00	37.50	SNP	1.000	T	22	28
AP2A2	161	genome.wustl.edu	37	11	993284	993284	+	Splice_Site	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr11:993284G>A	ENST00000448903.2	+	12	1594	c.1453G>A	c.(1453-1455)Gct>Act	p.A485T	AP2A2_ENST00000332231.5_Splice_Site_p.A486T|AP2A2_ENST00000534328.1_Intron	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	485					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGCTTCGCAGGCTCTTCAGGC	0.632													ENSG00000183020																																					0													31.0	36.0	35.0					11																	993284		1989	4157	6146	SO:0001630	splice_region_variant	0			-	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1453-1G>A	11.37:g.993284G>A			O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a-adaptin_app_sub_C,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/calthrin_app_sub_C,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP2_complex_asu	p.A486T	ENST00000448903.2	37	c.1456	CCDS44512.1	11	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439772	0.43326	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310	T;T	0.26373	1.74;1.74	3.66	3.66	0.41972	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.52805	0.1757	M	0.80746	2.51	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.997	D;D;P	0.85130	0.981;0.997;0.884	T	0.60286	-0.7293	9	.	.	.	-11.868	16.226	0.82293	0.0:0.0:1.0:0.0	.	224;486;485	B7Z1Q4;O94973-2;O94973	.;.;AP2A2_HUMAN	T	485;486;486;222;225	ENSP00000413234:A485T;ENSP00000327694:A486T	.	A	+	1	0	AP2A2	983284	1.000000	0.71417	0.807000	0.32361	0.265000	0.26407	7.837000	0.86796	1.979000	0.57680	0.462000	0.41574	GCT	-	AP2A2	-	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP2_complex_asu		0.632	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	AP2A2	HGNC	protein_coding	OTTHUMT00000385431.2	0	0	0	61	61	52	0.00	0.00	G	NM_012305	Missense_Mutation	993284	+1	10	6	54	36	tier1	no_errors	ENST00000332231	ensembl	human	known	74_37	missense	15.62	14.29	SNP	1.000	A	10	54
RP11-826N14.1	0	genome.wustl.edu	37	5	175467785	175467785	+	RNA	SNP	G	G	A	rs187668175	byFrequency	TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr5:175467785G>A	ENST00000509643.1	+	0	39																											CATCGTGGACGGGAGTAAAGT	0.527													ENSG00000250992	g|||	2	0.000399361	0.0	0.0014	5008	,	,		34306	0.0		0.0	False		,,,				2504	0.001																0																																												0			GMAF=0.0005																													5.37:g.175467785G>A				R	SNP	-	NULL	ENST00000509643.1	37	NULL		5																																																																																			rs187668175	RP11-826N14.1	-	-		0.527	RP11-826N14.1-001	KNOWN	basic	antisense	ENSG00000250992	Clone_based_vega_gene	antisense	OTTHUMT00000371916.1	0	0	0	134	134	129	0.00	0.00	G			175467785	+1	20	16	138	116	tier1	no_errors	ENST00000509643	ensembl	human	known	74_37	rna	12.66	12.12	SNP	0.037	A	20	138
CXorf22	170063	genome.wustl.edu	37	X	35969300	35969300	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chrX:35969300G>T	ENST00000297866.5	+	5	775	c.709G>T	c.(709-711)Gtt>Ttt	p.V237F		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	237										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AGCTCATGTGGTTGAGCAGAT	0.348													ENSG00000165164																																					0													116.0	102.0	107.0					X																	35969300		2202	4300	6502	SO:0001583	missense	0			-	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.709G>T	X.37:g.35969300G>T	ENSP00000297866:p.Val237Phe		Q5JRM8|Q8N6X8	Missense_Mutation	SNP	superfamily_PapD-like	p.V237F	ENST00000297866.5	37	c.709	CCDS14237.2	X	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295943	0.81025	.	.	ENSG00000165164	ENST00000297866	T	0.21361	2.01	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.49864	0.1582	M	0.78049	2.395	0.38991	D	0.959153	D	0.89917	1.0	D	0.97110	1.0	T	0.53085	-0.8488	10	0.51188	T	0.08	-25.866	17.7567	0.88451	0.0:0.0:1.0:0.0	.	237	Q6ZTR5	CX022_HUMAN	F	237	ENSP00000297866:V237F	ENSP00000297866:V237F	V	+	1	0	CXorf22	35879221	1.000000	0.71417	0.888000	0.34837	0.960000	0.62799	6.957000	0.76019	2.412000	0.81896	0.506000	0.49869	GTT	-	CXorf22	-	NULL		0.348	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CXorf22	HGNC	protein_coding	OTTHUMT00000056216.2	0	0	0	18	18	38	0.00	0.00	G	NM_152632		35969300	+1	12	20	5	13	tier1	no_errors	ENST00000297866	ensembl	human	known	74_37	missense	70.59	60.61	SNP	0.923	T	12	5
NKX2-2	4821	genome.wustl.edu	37	20	21492811	21492811	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr20:21492811C>A	ENST00000377142.4	-	2	928	c.572G>T	c.(571-573)gGt>gTt	p.G191V	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	191					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						CACCTCCATACCTTTCTCGGC	0.667													ENSG00000125820																																					0													39.0	41.0	40.0					20																	21492811		2202	4300	6502	SO:0001583	missense	0			-	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"""Homeoboxes / ANTP class : NKL subclass"""	7835	protein-coding gene	gene with protein product		604612	"""NK-2 (Drosophila) homolog B"", ""NK2 transcription factor related, locus 2 (Drosophila)"""	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.572G>T	20.37:g.21492811C>A	ENSP00000366347:p.Gly191Val			Missense_Mutation	SNP	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom,prints_Homeobox_metazoa	p.G191V	ENST00000377142.4	37	c.572	CCDS13145.1	20	.	.	.	.	.	.	.	.	.	.	C	17.51	3.407232	0.62399	.	.	ENSG00000125820	ENST00000377142	D	0.91996	-2.95	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.91140	0.7210	M	0.62723	1.935	0.80722	D	1	B	0.23490	0.086	B	0.24269	0.052	D	0.87890	0.2683	10	0.35671	T	0.21	.	19.0448	0.93015	0.0:1.0:0.0:0.0	.	191	O95096	NKX22_HUMAN	V	191	ENSP00000366347:G191V	ENSP00000366347:G191V	G	-	2	0	NKX2-2	21440811	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.078000	0.57606	2.489000	0.83994	0.462000	0.41574	GGT	-	NKX2-2	-	NULL		0.667	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NKX2-2	HGNC	protein_coding	OTTHUMT00000078278.9	0	0	0	120	120	36	0.00	0.00	C			21492811	-1	36	7	54	19	tier1	no_errors	ENST00000377142	ensembl	human	known	74_37	missense	40.00	26.92	SNP	1.000	A	36	54
RNF43	54894	genome.wustl.edu	37	17	56435245	56435245	+	Missense_Mutation	SNP	C	C	A	rs35946293		TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr17:56435245C>A	ENST00000584437.1	-	8	3847	c.1892G>T	c.(1891-1893)aGc>aTc	p.S631I	RNF43_ENST00000581868.1_Missense_Mutation_p.S504I|RNF43_ENST00000577716.1_Missense_Mutation_p.S631I|RNF43_ENST00000500597.2_Missense_Mutation_p.S590I|RNF43_ENST00000577625.1_Missense_Mutation_p.S504I|RNF43_ENST00000583753.1_Missense_Mutation_p.S590I|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Missense_Mutation_p.S631I			Q68DV7	RNF43_HUMAN	ring finger protein 43	631	Pro-rich.				negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGGGCAGATGCTGGAGGCGTC	0.647													ENSG00000108375																																					0													64.0	74.0	70.0					17																	56435245		2201	4296	6497	SO:0001583	missense	0			-		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1892G>T	17.37:g.56435245C>A	ENSP00000463069:p.Ser631Ile		A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	pfam_Znf_C3HC4_RING-type,superfamily_PAS,smart_Znf_RING,pfscan_Znf_RING	p.S631I	ENST00000584437.1	37	c.1892	CCDS11607.1	17	.	.	.	.	.	.	.	.	.	.	C	6.476	0.455964	0.12283	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09163	3.15;3.01	5.18	0.772	0.18510	.	0.707659	0.14067	N	0.343638	T	0.07234	0.0183	L	0.27053	0.805	0.09310	N	1	P;P;B	0.47677	0.571;0.899;0.435	B;B;B	0.41988	0.206;0.372;0.102	T	0.27297	-1.0078	10	0.56958	D	0.05	-11.4638	5.0337	0.14423	0.0:0.583:0.1513:0.2657	.	590;631;631	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	I	631;590	ENSP00000385328:S631I;ENSP00000441969:S590I	ENSP00000385328:S631I	S	-	2	0	RNF43	53790244	0.000000	0.05858	0.019000	0.16419	0.137000	0.21094	-0.814000	0.04486	0.188000	0.20168	0.205000	0.17691	AGC	-	RNF43	-	NULL		0.647	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	RNF43	HGNC	protein_coding	OTTHUMT00000444713.1	0	0	0	68	68	49	0.00	0.00	C	NM_017763		56435245	-1	29	14	32	13	tier1	no_errors	ENST00000407977	ensembl	human	known	74_37	missense	47.54	51.85	SNP	0.002	A	29	32
GLT8D2	83468	genome.wustl.edu	37	12	104397053	104397053	+	Missense_Mutation	SNP	T	T	G			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr12:104397053T>G	ENST00000360814.4	-	5	549	c.144A>C	c.(142-144)gaA>gaC	p.E48D	GLT8D2_ENST00000546436.1_Missense_Mutation_p.E48D|GLT8D2_ENST00000548660.1_Missense_Mutation_p.E48D	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	48						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						GAATCTCTTCTTCCAGTTCTT	0.448													ENSG00000120820																																					0													185.0	157.0	166.0					12																	104397053		2203	4300	6503	SO:0001583	missense	0			-	BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"""Glycosyltransferase family 8 domain containing"""	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.144A>C	12.37:g.104397053T>G	ENSP00000354053:p.Glu48Asp		Q96KA2	Missense_Mutation	SNP	pfam_Glyco_trans_8	p.E48D	ENST00000360814.4	37	c.144	CCDS9096.1	12	.	.	.	.	.	.	.	.	.	.	t	12.59	1.984196	0.35036	.	.	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660	T;T;T	0.32272	1.46;1.46;1.46	5.73	-9.86	0.00473	.	0.318283	0.36703	N	0.002457	T	0.13200	0.0320	N	0.24115	0.695	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.27571	-1.0070	10	0.20519	T	0.43	.	11.3669	0.49677	0.0:0.4436:0.3741:0.1822	.	48	Q9H1C3	GL8D2_HUMAN	D	48	ENSP00000354053:E48D;ENSP00000449750:E48D;ENSP00000447450:E48D	ENSP00000354053:E48D	E	-	3	2	GLT8D2	102921183	0.001000	0.12720	0.083000	0.20561	0.887000	0.51463	-1.684000	0.01932	-2.286000	0.00670	-0.363000	0.07495	GAA	-	GLT8D2	-	NULL		0.448	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	GLT8D2	HGNC	protein_coding	OTTHUMT00000407371.1	0	0	0	47	47	142	0.00	0.00	T	NM_031302		104397053	-1	27	36	39	54	tier1	no_errors	ENST00000360814	ensembl	human	known	74_37	missense	40.30	40.00	SNP	0.171	G	27	39
XYLB	9942	genome.wustl.edu	37	3	38411731	38411732	+	Intron	INS	-	-	CACACACACA	rs196387|rs71085317|rs150130857	byFrequency	TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	-	-	-	CACACACACA	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr3:38411731_38411732insCACACACACA	ENST00000207870.3	+	9	855				XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)						carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		GCACTGTAGCGcacacacacac	0.5													ENSG00000093217		304	0.0607029	0.0484	0.0548	5008	,	,		17817	0.0655		0.0825	False		,,,				2504	0.0542																0																																										SO:0001627	intron_variant	0				AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.765+66->CACACACACA	3.37:g.38411732_38411741dupCACACACACA			B2RAW4|B4DDT2|B9EH64	R	INS	-	NULL	ENST00000207870.3	37	NULL	CCDS2678.1	3																																																																																				XYLB	-	-		0.500	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XYLB	HGNC	protein_coding	OTTHUMT00000254062.2	0	0	0	15	15	15	0.00	0.00	-	NM_005108		38411732	+1	2	2	12	12	tier1	no_errors	ENST00000487569	ensembl	human	putative	74_37	rna	14.29	14.29	INS	0.000:0.000	CACACACACA	2	12
DCX	1641	genome.wustl.edu	37	X	110644349	110644349	+	Missense_Mutation	SNP	G	G	A	rs104894780		TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chrX:110644349G>A	ENST00000338081.3	-	3	988	c.817C>T	c.(817-819)Cgg>Tgg	p.R273W	DCX_ENST00000356915.2_Missense_Mutation_p.R192W|DCX_ENST00000488120.1_Missense_Mutation_p.R192W|DCX_ENST00000356220.3_Missense_Mutation_p.R192W|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000371993.2_Missense_Mutation_p.R192W	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	273	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		R -> W (in LISX1 and SBHX). {ECO:0000269|PubMed:11175293, ECO:0000269|PubMed:9489699}.		axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						ACAGCCTTCCGAGGCTTCACC	0.557													ENSG00000077279																																					0			GRCh37	CM980529	DCX	M	rs104894780						118.0	100.0	106.0					X																	110644349		2203	4300	6503	SO:0001583	missense	0			-	AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"""doublecortex"""	300121	"""doublecortex; lissencephaly, X-linked (doublecortin)"""			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.817C>T	X.37:g.110644349G>A	ENSP00000337697:p.Arg273Trp		A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	pfam_Doublecortin_dom,smart_Doublecortin_dom,pirsf_Doublecortin_chordata,pfscan_Doublecortin_dom	p.R273W	ENST00000338081.3	37	c.817	CCDS14556.1	X	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043537	0.75732	.	.	ENSG00000077279	ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120	D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27	4.74	2.85	0.33270	Doublecortin domain (4);	0.128241	0.52532	D	0.000064	D	0.96463	0.8846	M	0.86178	2.8	0.80722	A	1	D;P	0.89917	1.0;0.454	D;B	0.78314	0.991;0.161	D	0.97370	0.9975	9	0.72032	D	0.01	.	13.0367	0.58877	0.0:0.0:0.7066:0.2934	.	261;273	B4DM53;O43602	.;DCX_HUMAN	W	192;192;273;192;192	ENSP00000349385:R192W;ENSP00000361061:R192W;ENSP00000337697:R273W;ENSP00000348553:R192W;ENSP00000419861:R192W	ENSP00000337697:R273W	R	-	1	2	DCX	110531005	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	5.691000	0.68249	0.438000	0.26450	0.600000	0.82982	CGG	rs104894780	DCX	-	smart_Doublecortin_dom,pirsf_Doublecortin_chordata,pfscan_Doublecortin_dom		0.557	DCX-006	KNOWN	basic|CCDS	protein_coding	DCX	HGNC	protein_coding	OTTHUMT00000357058.1	0	0	0	27	27	34	0.00	0.00	G	NM_178153		110644349	-1	31	22	17	4	tier1	no_errors	ENST00000338081	ensembl	human	known	74_37	missense	63.27	84.62	SNP	1.000	A	31	17
HFM1	164045	genome.wustl.edu	37	1	91818856	91818856	+	Splice_Site	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:91818856C>T	ENST00000370425.3	-	14	1784	c.1686G>A	c.(1684-1686)agG>agA	p.R562R	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000462405.1_5'Flank|HFM1_ENST00000370424.3_Splice_Site_p.R241R	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	562	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		ACTTCTGTAACCTATTTAAAA	0.274													ENSG00000162669																																					0													68.0	65.0	66.0					1																	91818856		1782	4038	5820	SO:0001630	splice_region_variant	0			-	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1686-1G>A	1.37:g.91818856C>T			B1B0B6|Q8N9Q0	Silent	SNP	pfam_Sec63-dom,pfam_D/R_helicase_DEAD/DEAH_N,pfam_Helicase_C,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Sec63-dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.R562	ENST00000370425.3	37	c.1686	CCDS30769.2	1																																																																																			-	HFM1	-	superfamily_P-loop_NTPase,pfscan_Helicase_C		0.274	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	HFM1	HGNC	protein_coding	OTTHUMT00000316716.2	0	0	0	34	34	114	0.00	0.00	C	NM_001017975	Silent	91818856	-1	8	6	37	78	tier1	no_errors	ENST00000370425	ensembl	human	known	74_37	silent	17.78	7.14	SNP	1.000	T	8	37
AP2A2	161	genome.wustl.edu	37	11	993358	993358	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr11:993358G>C	ENST00000448903.2	+	12	1668	c.1527G>C	c.(1525-1527)ttG>ttC	p.L509F	AP2A2_ENST00000332231.5_Missense_Mutation_p.L510F|AP2A2_ENST00000534328.1_Intron	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	509					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TTGGAAACTTGATAGCTGGAG	0.637													ENSG00000183020																																					0													40.0	46.0	44.0					11																	993358		1930	4140	6070	SO:0001583	missense	0			-	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1527G>C	11.37:g.993358G>C	ENSP00000413234:p.Leu509Phe		O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a-adaptin_app_sub_C,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/calthrin_app_sub_C,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP2_complex_asu	p.L510F	ENST00000448903.2	37	c.1530	CCDS44512.1	11	.	.	.	.	.	.	.	.	.	.	G	9.611	1.131336	0.21041	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310	T;T	0.39406	1.08;1.08	3.51	3.51	0.40186	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000006	T	0.65903	0.2736	M	0.87038	2.855	0.58432	D	0.999996	D;B;B	0.69078	0.997;0.304;0.238	D;B;B	0.77557	0.99;0.15;0.233	T	0.71368	-0.4614	10	0.54805	T	0.06	-40.4217	11.9147	0.52759	0.0:0.1768:0.8231:0.0	.	248;510;509	B7Z1Q4;O94973-2;O94973	.;.;AP2A2_HUMAN	F	509;510;510;246;249	ENSP00000413234:L509F;ENSP00000327694:L510F	ENSP00000327694:L510F	L	+	3	2	AP2A2	983358	1.000000	0.71417	0.996000	0.52242	0.308000	0.27856	0.668000	0.25127	1.896000	0.54893	0.462000	0.41574	TTG	-	AP2A2	-	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP2_complex_asu		0.637	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	AP2A2	HGNC	protein_coding	OTTHUMT00000385431.2	0	0	0	62	62	54	0.00	0.00	G	NM_012305		993358	+1	11	4	65	41	tier1	no_errors	ENST00000332231	ensembl	human	known	74_37	missense	14.29	8.89	SNP	1.000	C	11	65
FAM182B	728882	genome.wustl.edu	37	20	25840516	25840516	+	Intron	SNP	T	T	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr20:25840516T>C	ENST00000376403.1	-	1	142				FAM182B_ENST00000478164.1_Intron|FAM182B_ENST00000376404.2_Intron			Q5T319	F182B_HUMAN	family with sequence similarity 182, member B											lung(1)	1						tgtggagaggtcaggccggag	0.627													ENSG00000175170																																					0																																										SO:0001627	intron_variant	0			-			20p11.1	2010-07-14			ENSG00000175170	ENSG00000175170			34503	pseudogene	pseudogene							Standard	NR_027061		Approved			Q5T319	OTTHUMG00000032136	ENST00000376403.1:c.236+3179A>G	20.37:g.25840516T>C			Q4G0Q1	R	SNP	-	NULL	ENST00000376403.1	37	NULL		20																																																																																			-	FAM182B	-	-		0.627	FAM182B-003	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	FAM182B	HGNC	protein_coding	OTTHUMT00000078463.2	0	0	0	63	63	9	0.00	0.00	T	NR_026714		25840516	-1	5	0	37	7	tier1	no_errors	ENST00000584356	ensembl	human	known	74_37	rna	11.90	0.00	SNP	0.024	C	5	37
LOR	4014	genome.wustl.edu	37	1	153233991	153233992	+	In_Frame_Ins	INS	-	-	CTCTGGCGGCGG	rs11272549|rs547333583|rs561634896	byFrequency	TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:153233991_153233992insCTCTGGCGGCGG	ENST00000368742.3	+	2	623_624	c.566_567insCTCTGGCGGCGG	c.(565-570)tactct>taCTCTGGCGGCGGctct	p.194_195insGGGS		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	194					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gtctgcggctactctggcggcg	0.743													ENSG00000203782		3247	0.648363	0.6664	0.7954	5008	,	,		5032	0.4563		0.7147	False		,,,				2504	0.6493																0										178,190		86,6,92						-7.1	0.0		dbSNP_120	1	749,435		350,49,193	no	coding	LOR	NM_000427.2		436,55,285	A1A1,A1R,RR		36.7399,48.3696,40.2706				927,625				SO:0001652	inframe_insertion	0				M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.567_578dupCTCTGGCGGCGG	1.37:g.153233991_153233992insCTCTGGCGGCGG	ENSP00000357731:p.Gly191_Ser194dup		Q5T869|Q5XKF8	In_Frame_Ins	INS	NULL	p.193in_frame_insGSGG	ENST00000368742.3	37	c.566_567	CCDS30870.1	1																																																																																				LOR	-	NULL		0.743	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOR	HGNC	protein_coding	OTTHUMT00000039107.1	0	0	0	0	0	0	0.00	0.00	-	NM_000427		153233992	+1	0	0	3	3	tier1	no_errors	ENST00000368742	ensembl	human	known	74_37	in_frame_ins	0.00	0.00	INS	0.014:0.200	CTCTGGCGGCGG	0	3
SPPL2B	56928	genome.wustl.edu	37	19	2341094	2341101	+	RNA	DEL	CTCCCTGG	CTCCCTGG	-	rs77642174|rs76166147|rs386805838|rs547300749	byFrequency	TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	CTCCCTGG	CTCCCTGG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr19:2341094_2341101delCTCCCTGG	ENST00000452401.2	+	0	1033							Q8TCT7	SPP2B_HUMAN	signal peptide peptidase like 2B						membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	endosome membrane (GO:0010008)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACTCCCTGCCCTCCCTGGAGGCCGCCCC	0.702													ENSG00000005206		1248	0.249201	0.0469	0.3718	5008	,	,		14617	0.25		0.4294	False		,,,				2504	0.2495																0																																												0					CCDS74252.1, CCDS74253.1	19p13.3	2012-02-21			ENSG00000005206	ENSG00000005206			30627	protein-coding gene	gene with protein product	"""intramembrane protease 4"""	608239				10819331	Standard	NM_001077238		Approved	IMP4, PSL1, KIAA1532	uc002lvs.3	Q8TCT7			19.37:g.2341094_2341101delCTCCCTGG			D6W609|O60365|Q567S3|Q8IUH9|Q9BUY6|Q9H3M4|Q9NPN2|Q9P1Z6	R	DEL	-	NULL	ENST00000452401.2	37	NULL		19																																																																																				SPPL2B	-	-		0.702	SPPL2B-202	KNOWN	basic	processed_transcript	SPPL2B	HGNC	processed_transcript		0	0	0	0	0	0	0.00	0.00	CTCCCTGG	NM_020172		2341101	+1	0	0	0	0	tier1	no_errors	ENST00000592738	ensembl	human	known	74_37	rna	0.00	0.00	DEL	0.000:0.000:0.010:0.001:0.000:0.000:0.001:0.000	-	0	0
WASH4P	374677	genome.wustl.edu	37	16	64458	64458	+	Missense_Mutation	SNP	G	G	A	rs12444477	byFrequency	TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr16:64458G>A	ENST00000326592.9	-	10	2015	c.1357C>T	c.(1357-1359)Cgc>Tgc	p.R453C	DDX11L10_ENST00000513886.1_RNA			A8MWX3	WASH4_HUMAN	WAS protein family homolog 4 pseudogene	453					Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										TCTGACACGCGGGCAAAGGCT	0.647													ENSG00000234769	G|||	1540	0.307508	0.2057	0.438	5008	,	,		8528	0.0298		0.5865	False		,,,				2504	0.3517																0																																										SO:0001583	missense	0			-			16p13.3	2014-08-28	2008-01-16	2008-01-16	ENSG00000234769	ENSG00000234769		"""WAS protein homologs"""	14126	other	unknown			"""family with sequence similarity 39, member C pseudogene"""	FAM39CP		9054936, 11701968, 18159949	Standard	NG_003159		Approved	FLJ31670		A8MWX3	OTTHUMG00000059914	ENST00000326592.9:c.1357C>T	16.37:g.64458G>A	ENSP00000317542:p.Arg453Cys			Missense_Mutation	SNP	pfam_WASH1_WAHD	p.R453C	ENST00000326592.9	37	c.1357		16	.	.	.	.	.	.	.	.	.	.	g	14.62	2.590989	0.46214	.	.	ENSG00000234769	ENST00000326592	.	.	.	0.379	0.379	0.16213	.	0.059594	0.64402	N	0.000005	T	0.56217	0.1970	.	.	.	0.09310	P	0.99999140115	.	.	.	.	.	.	T	0.67848	-0.5564	4	0.87932	D	0	-0.2976	.	.	.	.	.	.	.	C	453	.	ENSP00000317542:R453C	R	-	1	0	WASH4P	4458	1.000000	0.71417	0.794000	0.32065	0.583000	0.36354	2.115000	0.41921	0.437000	0.26423	0.184000	0.17185	CGC	rs12444477	WASH4P	-	NULL		0.647	WASH4P-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal	protein_coding	WASH4P	HGNC	protein_coding	OTTHUMT00000133175.2	0	0	0	58	58	0	0.00	0.00	G	NG_003159		64458	-1	5	0	47	0	tier1	no_errors	ENST00000326592	ensembl	human	novel	74_37	missense	9.62	0.00	SNP	1.000	A	5	47
GPR78	27201	genome.wustl.edu	37	4	8583114	8583114	+	Silent	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr4:8583114G>A	ENST00000382487.4	+	1	822	c.405G>A	c.(403-405)ctG>ctA	p.L135L	GPR78_ENST00000509216.1_Intron	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	135					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						GACAGTCGCTGGCCTTCTCAG	0.706													ENSG00000155269																																					0													11.0	13.0	12.0					4																	8583114		2175	4261	6436	SO:0001819	synonymous_variant	0			-	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"""GPCR / Class A : Orphans"""	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.405G>A	4.37:g.8583114G>A			Q8NGV3	Silent	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn	p.L135	ENST00000382487.4	37	c.405	CCDS3403.1	4																																																																																			-	GPR78	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM		0.706	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR78	HGNC	protein_coding	OTTHUMT00000359201.1	0	0	0	29	29	4	0.00	0.00	G			8583114	+1	3	2	10	1	tier1	no_errors	ENST00000382487	ensembl	human	known	74_37	silent	23.08	66.67	SNP	1.000	A	3	10
PGBD2	267002	genome.wustl.edu	37	1	249212342	249212348	+	Frame_Shift_Del	DEL	TTGCCTG	TTGCCTG	-	rs374563843		TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	TTGCCTG	TTGCCTG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	g.chr1:249212342_249212348delTTGCCTG	ENST00000329291.5	+	3	1706_1712	c.1559_1565delTTGCCTG	c.(1558-1566)attgcctgtfs	p.IAC520fs	PGBD2_ENST00000355360.4_Frame_Shift_Del_p.IAC269fs|PGBD2_ENST00000539153.1_Frame_Shift_Del_p.IAC517fs	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	520										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CGGAGATACATTGCCTGTGTGTATCTG	0.522													ENSG00000185220																																					0																																										SO:0001589	frameshift_variant	0				AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.1559_1565delTTGCCTG	1.37:g.249212342_249212348delTTGCCTG	ENSP00000331643:p.Ile520fs		B3KVR8|Q6MZF8	Frame_Shift_Del	DEL	NULL	p.I520fs	ENST00000329291.5	37	c.1559_1565	CCDS31128.1	1																																																																																				PGBD2	-	NULL		0.522	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PGBD2	HGNC	protein_coding	OTTHUMT00000097318.1	0	0	0	59	59	59	0.00	0.00	TTGCCTG			249212348	+1	3	3	48	48	tier1	no_errors	ENST00000329291	ensembl	human	known	74_37	frame_shift_del	5.88	5.88	DEL	0.060:0.048:0.922:0.964:0.963:0.966:0.961	-	3	48
