#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ARL4A	10124	genome.wustl.edu	37	7	12728294	12728294	+	Missense_Mutation	SNP	A	A	G			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr7:12728294A>G	ENST00000396663.1	+	2	897	c.415A>G	c.(415-417)Agg>Ggg	p.R139G	ARL4A_ENST00000356797.3_Missense_Mutation_p.R139G|ARL4A_ENST00000396664.2_Missense_Mutation_p.R139G|ARL4A_ENST00000404894.1_Missense_Mutation_p.R139G|ARL4A_ENST00000396662.1_Missense_Mutation_p.R139G	NM_001037164.2|NM_001195396.1|NM_005738.4|NM_212460.3	NP_001032241.1|NP_001182325.1|NP_005729.1|NP_997625.1	P40617	ARL4A_HUMAN	ADP-ribosylation factor-like 4A	139			R -> K (in dbSNP:rs2953325).		brown fat cell differentiation (GO:0050873)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			NS(2)|lung(3)|ovary(1)	6				UCEC - Uterine corpus endometrioid carcinoma (126;0.176)		ACAAGATTTGAGGAACTCATT	0.398																																						dbGAP											0													83.0	78.0	80.0					7																	12728294		2203	4300	6503	-	-	-	SO:0001583	missense	0			U73960	CCDS5359.1	7p21.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000122644	ENSG00000122644		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	695	protein-coding gene	gene with protein product		604786	"""ADP-ribosylation factor-like 4"""	ARL4			Standard	NM_212460		Approved		uc003ssq.3	P40617	OTTHUMG00000023374	ENST00000396663.1:c.415A>G	7.37:g.12728294A>G	ENSP00000379898:p.Arg139Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D119|P80418|Q49AF5	Missense_Mutation	SNP	pfam_Small_GTPase_ARF/SAR,pfam_Small_GTPase,pfam_MIRO-like,pfam_SRP_receptor_beta_su,pfam_ProtSyn_GTP-bd,pfam_Gtr1_RagA,smart_Small_GTPase_ARF,smart_Small_GTPase_SAR1,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,prints_Small_GTPase,prints_Small_GTPase_ARF/SAR,tigrfam_Small_GTP-bd_dom	p.R139G	ENST00000396663.1	37	c.415	CCDS5359.1	7	.	.	.	.	.	.	.	.	.	.	A	10.72	1.429572	0.25726	.	.	ENSG00000122644	ENST00000396662;ENST00000356797;ENST00000396664;ENST00000396663;ENST00000404894	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	4.67	2.13	0.27403	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.76800	0.4038	L	0.46741	1.465	0.44918	D	0.997931	P	0.42161	0.772	B	0.42319	0.383	T	0.76016	-0.3113	10	0.87932	D	0	.	7.816	0.29260	0.7856:0.1382:0.0762:0.0	.	139	P40617	ARL4A_HUMAN	G	139	ENSP00000379897:R139G;ENSP00000349250:R139G;ENSP00000379899:R139G;ENSP00000379898:R139G;ENSP00000385236:R139G	ENSP00000349250:R139G	R	+	1	2	ARL4A	12694819	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	1.710000	0.37920	0.923000	0.37045	0.454000	0.30748	AGG	ARL4A	-	pfam_Small_GTPase_ARF/SAR,pfam_Small_GTPase,pfam_SRP_receptor_beta_su,pfam_ProtSyn_GTP-bd,smart_Small_GTPase_ARF,smart_Small_GTPase_SAR1,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,prints_Small_GTPase_ARF/SAR,tigrfam_Small_GTP-bd_dom	ENSG00000122644		0.398	ARL4A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	ARL4A	HGNC	protein_coding	OTTHUMT00000326036.1	67	0.00	0	A	NM_005738		12728294	12728294	+1	no_errors	ENST00000356797	ensembl	human	known	69_37n	missense	119	17.36	25	SNP	1.000	G
ARMC5	79798	genome.wustl.edu	37	16	31474092	31474093	+	Missense_Mutation	DNP	GG	GG	AT			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr16:31474092_31474093GG>AT	ENST00000563544.1	+	4	1770_1771	c.1224_1225GG>AT	c.(1222-1227)caGGct>caATct	p.A409S	ARMC5_ENST00000457010.2_Missense_Mutation_p.A409S|ARMC5_ENST00000538189.1_Missense_Mutation_p.A441S|ARMC5_ENST00000412665.2_Splice_Site_p.A53S|ARMC5_ENST00000268314.4_Missense_Mutation_p.A409S|ARMC5_ENST00000408912.3_Missense_Mutation_p.A504S			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	409										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GCCGGCTGCAGGCTCTGGGACT	0.629																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	Exception_encountered	16.37:g.31474092_31474093delinsAT	ENSP00000456877:p.Ala409Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q86WM9|Q9H7P8|Q9H925	Splice_Site|Missense_Mutation	SNP	-|superfamily_ARM-type_fold,superfamily_BTB/POZ_fold,smart_Armadillo,pfscan_Armadillo,pfscan_BTB/POZ-like	e3-1|p.A504S	ENST00000563544.1	37	c.157-1|c.1510	CCDS45472.1	16																																																																																			ARMC5	-	-|superfamily_ARM-type_fold	ENSG00000140691		0.629	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ARMC5	HGNC	protein_coding	OTTHUMT00000432847.1	49|47	0.00	0	G	NM_024742		31474092|31474093	31474092|31474093	+1	no_errors	ENST00000412665|ENST00000408912	ensembl	human	known	69_37n	splice_site|missense	63|62	22.22|22.50	18	SNP	1.000	A|T
BOD1L1	259282	genome.wustl.edu	37	4	13601548	13601548	+	Missense_Mutation	SNP	C	C	T	rs541123232		TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr4:13601548C>T	ENST00000040738.5	-	10	7111	c.6976G>A	c.(6976-6978)Gat>Aat	p.D2326N		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2326						nucleus (GO:0005634)	DNA binding (GO:0003677)										ATGGCAGCATCGCTCAAGTCT	0.502																																						dbGAP											0													114.0	85.0	95.0					4																	13601548		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.6976G>A	4.37:g.13601548C>T	ENSP00000040738:p.Asp2326Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	NULL	p.D2326N	ENST00000040738.5	37	c.6976	CCDS3411.2	4	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915701	0.92178	.	.	ENSG00000038219	ENST00000040738	T	0.18174	2.23	5.37	5.37	0.77165	.	0.000000	0.51477	D	0.000096	T	0.37320	0.0999	M	0.73962	2.25	0.22779	N	0.998745	D	0.71674	0.998	P	0.57152	0.814	T	0.23868	-1.0176	10	0.66056	D	0.02	-8.957	15.8307	0.78749	0.0:1.0:0.0:0.0	.	2326	Q8NFC6	BOD1L_HUMAN	N	2326	ENSP00000040738:D2326N	ENSP00000040738:D2326N	D	-	1	0	BOD1L	13210646	0.959000	0.32827	0.105000	0.21289	0.333000	0.28666	4.576000	0.60915	2.525000	0.85131	0.650000	0.86243	GAT	BOD1L1	-	NULL	ENSG00000038219		0.502	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BOD1L1	HGNC	protein_coding	OTTHUMT00000207321.1	42	0.00	0	C	NM_148894		13601548	13601548	-1	no_errors	ENST00000040738	ensembl	human	known	69_37n	missense	107	43.68	83	SNP	0.378	T
C2orf16	84226	genome.wustl.edu	37	2	27802528	27802528	+	Nonsense_Mutation	SNP	C	C	A			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr2:27802528C>A	ENST00000408964.2	+	1	3140	c.3089C>A	c.(3088-3090)tCa>tAa	p.S1030*	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1030						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTGGTAAAGTCAGAGTCTTCC	0.438																																						dbGAP											0													98.0	102.0	101.0					2																	27802528		2105	4249	6354	-	-	-	SO:0001587	stop_gained	0			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3089C>A	2.37:g.27802528C>A	ENSP00000386190:p.Ser1030*	Somatic		WXS	Illumina GAIIx	Phase_IV	B9EIQ4|Q53S01|Q8ND64|Q9H088	Nonsense_Mutation	SNP	NULL	p.S1030*	ENST00000408964.2	37	c.3089	CCDS42666.1	2	.	.	.	.	.	.	.	.	.	.	C	22.5	4.300388	0.81136	.	.	ENSG00000221843	ENST00000408964	.	.	.	4.39	2.35	0.29111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.9531	0.14025	0.0:0.6619:0.2139:0.1241	.	.	.	.	X	1030	.	ENSP00000386190:S1030X	S	+	2	0	C2orf16	27656032	0.170000	0.23016	0.236000	0.24074	0.036000	0.12997	0.394000	0.20834	1.130000	0.42092	0.467000	0.42956	TCA	C2orf16	-	NULL	ENSG00000221843		0.438	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C2orf16	HGNC	protein_coding	OTTHUMT00000353292.1	40	0.00	0	C	NM_032266		27802528	27802528	+1	no_errors	ENST00000408964	ensembl	human	known	69_37n	nonsense	52	20.00	13	SNP	0.128	A
CDH1	999	genome.wustl.edu	37	16	68867353	68867353	+	Missense_Mutation	SNP	A	A	G	rs587782623		TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr16:68867353A>G	ENST00000261769.5	+	16	2791	c.2600A>G	c.(2599-2601)aAt>aGt	p.N867S	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.N806S	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	867	Required for binding alpha, beta and gamma catenins.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GAATGGGGCAATCGCTTCAAG	0.552			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	0													90.0	84.0	86.0					16																	68867353		2198	4300	6498	-	-	-	SO:0001583	missense	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2600A>G	16.37:g.68867353A>G	ENSP00000261769:p.Asn867Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.N867S	ENST00000261769.5	37	c.2600	CCDS10869.1	16	.	.	.	.	.	.	.	.	.	.	A	15.10	2.734094	0.48939	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	T;T	0.74947	-0.89;-0.89	6.17	3.94	0.45596	Cadherin, cytoplasmic domain (1);	0.111733	0.39475	N	0.001349	T	0.57213	0.2038	N	0.11560	0.145	0.35326	D	0.785194	B;B	0.29766	0.169;0.256	B;B	0.38056	0.193;0.264	T	0.59857	-0.7375	10	0.45353	T	0.12	.	6.6449	0.22929	0.7386:0.1286:0.1327:0.0	.	806;867	Q9UII8;P12830	.;CADH1_HUMAN	S	867;885;806	ENSP00000261769:N867S;ENSP00000414946:N806S	ENSP00000261769:N867S	N	+	2	0	CDH1	67424854	0.029000	0.19370	0.998000	0.56505	0.981000	0.71138	0.980000	0.29513	0.555000	0.29079	-0.290000	0.09829	AAT	CDH1	-	pfam_Cadherin_cytoplasmic-dom	ENSG00000039068		0.552	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	39	0.00	0	A	NM_004360		68867353	68867353	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	missense	35	38.60	22	SNP	1.000	G
DNAH14	127602	genome.wustl.edu	37	1	225306960	225306960	+	Intron	SNP	T	T	G	rs199634734		TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr1:225306960T>G	ENST00000445597.2	+	17	3051				DNAH14_ENST00000430092.1_Missense_Mutation_p.V1377G|DNAH14_ENST00000439375.2_Missense_Mutation_p.V1377G			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CAGTGGCTGGTAAATGTAGAA	0.244																																						dbGAP											0													30.0	31.0	31.0					1																	225306960		692	1578	2270	-	-	-	SO:0001627	intron_variant	0			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3052-21510T>G	1.37:g.225306960T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	pfam_Dynein_heavy,pfam_Dynein_heavy_dom-2,superfamily_Tautomerase,smart_AAA+_ATPase	p.V1377G	ENST00000445597.2	37	c.4130		1	.	.	.	.	.	.	.	.	.	.	T	3.380	-0.126606	0.06795	.	.	ENSG00000185842	ENST00000430092;ENST00000439375;ENST00000328556	T;T;T	0.60424	0.19;0.19;0.19	5.17	4.04	0.47022	.	.	.	.	.	T	0.33059	0.0850	N	0.13003	0.285	0.80722	D	1	B	0.22909	0.077	B	0.19391	0.025	T	0.06463	-1.0825	9	0.13853	T	0.58	.	5.3197	0.15874	0.0:0.0928:0.1784:0.7288	.	1377	Q0VDD8-4	.	G	1377;1377;455	ENSP00000414402:V1377G;ENSP00000392061:V1377G;ENSP00000332424:V455G	ENSP00000332424:V455G	V	+	2	0	DNAH14	223373583	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	1.224000	0.32539	0.809000	0.34255	0.438000	0.28831	GTA	DNAH14	-	pfam_Dynein_heavy_dom-2	ENSG00000185842		0.244	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	DNAH14	HGNC	protein_coding	OTTHUMT00000331217.3	40	0.00	0	T	XM_059166		225306960	225306960	+1	no_errors	ENST00000430092	ensembl	human	known	69_37n	missense	35	38.60	22	SNP	1.000	G
EXOSC9	5393	genome.wustl.edu	37	4	122737961	122737961	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr4:122737961C>T	ENST00000243498.5	+	12	1378	c.1270C>T	c.(1270-1272)Cca>Tca	p.P424S	EXOSC9_ENST00000379663.3_Missense_Mutation_p.P441S|EXOSC9_ENST00000512454.1_Missense_Mutation_p.P408S|CCNA2_ENST00000274026.5_3'UTR	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	424					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						AGAAAAAGCACCAAGTAAAAA	0.303																																						dbGAP											0													35.0	35.0	35.0					4																	122737961		2200	4297	6497	-	-	-	SO:0001583	missense	0			M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 1 (75kD)"""	606180	"""polymyositis/scleroderma autoantigen 1, 75kDa"""	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.1270C>T	4.37:g.122737961C>T	ENSP00000243498:p.Pro424Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q12883|Q4W5P5|Q86Y41|Q86Y48	Missense_Mutation	SNP	pfam_ExoRNase_PH_dom1,pfam_ExoRNase_PH_dom2,superfamily_Ribosomal_S5_D2-typ_fold,superfamily_ExoRNase_PH_dom2	p.P441S	ENST00000243498.5	37	c.1321	CCDS3722.2	4	.	.	.	.	.	.	.	.	.	.	C	12.83	2.056718	0.36277	.	.	ENSG00000123737	ENST00000243498;ENST00000379663;ENST00000512454	T;T;T	0.21031	2.05;2.03;2.05	4.96	3.19	0.36642	.	0.752409	0.12797	N	0.438344	T	0.05960	0.0155	N	0.00707	-1.245	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.001;0.002	T	0.20338	-1.0278	10	0.30854	T	0.27	-24.0396	6.5082	0.22206	0.0:0.6966:0.2046:0.0988	.	408;424;441	D6RIY6;Q06265;Q06265-2	.;EXOS9_HUMAN;.	S	424;441;408	ENSP00000243498:P424S;ENSP00000368984:P441S;ENSP00000425782:P408S	ENSP00000243498:P424S	P	+	1	0	EXOSC9	122957411	0.993000	0.37304	1.000000	0.80357	0.978000	0.69477	0.271000	0.18626	1.403000	0.46800	0.557000	0.71058	CCA	EXOSC9	-	NULL	ENSG00000123737		0.303	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EXOSC9	HGNC	protein_coding	OTTHUMT00000250708.2	63	0.00	0	C	NM_005033		122737961	122737961	+1	no_errors	ENST00000379663	ensembl	human	known	69_37n	missense	84	23.64	26	SNP	1.000	T
FAM153B	202134	genome.wustl.edu	37	5	175540973	175540973	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr5:175540973C>T	ENST00000253490.4	+	21	1142	c.1085C>T	c.(1084-1086)cCc>cTc	p.P362L	FAM153B_ENST00000512862.1_Missense_Mutation_p.P119L|FAM153B_ENST00000510151.1_Missense_Mutation_p.P285L|FAM153B_ENST00000515817.1_Missense_Mutation_p.P285L			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	362										endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		ACCAGAAAGCCCAAGAAGAAA	0.463																																						dbGAP											0													2.0	2.0	2.0					5																	175540973		1005	2396	3401	-	-	-	SO:0001583	missense	0			AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.1085C>T	5.37:g.175540973C>T	ENSP00000253490:p.Pro362Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MTI1	Missense_Mutation	SNP	prints_FAM153	p.P362L	ENST00000253490.4	37	c.1085		5	.	.	.	.	.	.	.	.	.	.	C	9.299	1.052514	0.19907	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	0.765	-0.422	0.12329	.	.	.	.	.	T	0.16599	0.0399	N	0.08118	0	0.09310	N	1	P	0.50710	0.938	P	0.46479	0.518	T	0.11867	-1.0570	8	0.87932	D	0	.	3.666	0.08255	0.4321:0.5679:0.0:0.0	.	362	P0C7A2	F153B_HUMAN	L	285;362	.	ENSP00000253490:P362L	P	+	2	0	FAM153B	175473579	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.805000	0.27112	-0.164000	0.10927	0.405000	0.27470	CCC	FAM153B	-	NULL	ENSG00000182230		0.463	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	FAM153B	HGNC	protein_coding		26	0.00	0	C	NM_001079529		175540973	175540973	+1	no_errors	ENST00000253490	ensembl	human	known	69_37n	missense	40	24.07	13	SNP	0.000	T
GRIN2B	2904	genome.wustl.edu	37	12	13715969	13715969	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr12:13715969G>T	ENST00000609686.1	-	13	4412	c.4203C>A	c.(4201-4203)agC>agA	p.S1401R		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1401					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGTAGGATTTGCTGCCATGGA	0.627																																						dbGAP											0													42.0	41.0	41.0					12																	13715969		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.4203C>A	12.37:g.13715969G>T	ENSP00000477455:p.Ser1401Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	pfam_NMDAR2_C,pfam_Iontro_glu_rcpt,pfam_SBP_bac_3,pfam_Glu_rcpt_Glu/Gly-bd,pfam_ANF_lig-bd_rcpt,smart_Iontro_glu_rcpt,smart_Glu_rcpt_Glu/Gly-bd,prints_NMDA_rcpt	p.S1401R	ENST00000609686.1	37	c.4203	CCDS8662.1	12	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440912	0.43326	.	.	ENSG00000150086	ENST00000279593	T	0.09817	2.94	5.09	3.28	0.37604	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.143817	0.64402	D	0.000004	T	0.08582	0.0213	L	0.34521	1.04	0.48135	D	0.999598	B	0.12013	0.005	B	0.15052	0.012	T	0.20075	-1.0286	10	0.22706	T	0.39	.	11.3593	0.49633	0.1461:0.0:0.8539:0.0	.	1401	Q13224	NMDE2_HUMAN	R	1401	ENSP00000279593:S1401R	ENSP00000279593:S1401R	S	-	3	2	GRIN2B	13607236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.283000	0.58977	0.741000	0.32674	0.561000	0.74099	AGC	GRIN2B	-	pfam_NMDAR2_C	ENSG00000150086		0.627	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIN2B	HGNC	protein_coding	OTTHUMT00000268014.2	42	0.00	0	G			13715969	13715969	-1	no_errors	ENST00000279593	ensembl	human	known	69_37n	missense	36	26.53	13	SNP	1.000	T
HDX	139324	genome.wustl.edu	37	X	83730290	83730290	+	Missense_Mutation	SNP	T	T	G			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chrX:83730290T>G	ENST00000297977.5	-	2	227	c.116A>C	c.(115-117)cAg>cCg	p.Q39P	HDX_ENST00000373177.2_Missense_Mutation_p.Q39P|HDX_ENST00000506585.2_Intron	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	39						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CTTAGTCTCCTGTGCACACTG	0.328																																					Pancreas(53;231 1169 36156 43751 51139)	dbGAP											0													106.0	90.0	95.0					X																	83730290		2203	4297	6500	-	-	-	SO:0001583	missense	0			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.116A>C	X.37:g.83730290T>G	ENSP00000297977:p.Gln39Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain	p.Q39P	ENST00000297977.5	37	c.116	CCDS35342.1	X	.	.	.	.	.	.	.	.	.	.	T	21.0	4.076129	0.76415	.	.	ENSG00000165259	ENST00000297977;ENST00000506585	T;T	0.35048	1.33;1.33	6.16	6.16	0.99307	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.56543	0.1992	L	0.54323	1.7	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.58370	-0.7648	10	0.72032	D	0.01	-11.9585	15.6684	0.77252	0.0:0.0:0.0:1.0	.	39	Q7Z353	HDX_HUMAN	P	39	ENSP00000297977:Q39P;ENSP00000423670:Q39P	ENSP00000297977:Q39P	Q	-	2	0	HDX	83616946	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.468000	0.80943	2.085000	0.62840	0.481000	0.45027	CAG	HDX	-	superfamily_Homeodomain-like,smart_Homeodomain	ENSG00000165259		0.328	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	HDX	HGNC	protein_coding	OTTHUMT00000057379.2	65	0.00	0	T	NM_144657		83730290	83730290	-1	no_errors	ENST00000297977	ensembl	human	known	69_37n	missense	90	26.83	33	SNP	1.000	G
LRRC4C	57689	genome.wustl.edu	37	11	40137268	40137268	+	Missense_Mutation	SNP	G	G	C			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr11:40137268G>C	ENST00000278198.2	-	2	2538	c.575C>G	c.(574-576)gCc>gGc	p.A192G	LRRC4C_ENST00000528697.1_Missense_Mutation_p.A192G|LRRC4C_ENST00000527150.1_Missense_Mutation_p.A192G|LRRC4C_ENST00000530763.1_Missense_Mutation_p.A192G			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	192					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ACCTTCAAAGGCACCTTCTGA	0.438																																						dbGAP											0													93.0	91.0	92.0					11																	40137268		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.575C>G	11.37:g.40137268G>C	ENSP00000278198:p.Ala192Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0T1|Q7L0N3	Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_Ig_I-set,pfam_Ig_V-set,pfam_Immunoglobulin,smart_LRR-contain_N,smart_Leu-rich_rpt_typical-subtyp,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,pfscan_Ig-like	p.A192G	ENST00000278198.2	37	c.575	CCDS31464.1	11	.	.	.	.	.	.	.	.	.	.	G	18.59	3.656731	0.67586	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.96256	0.8779	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96227	0.9165	10	0.72032	D	0.01	.	19.0894	0.93221	0.0:0.0:1.0:0.0	.	192	Q9HCJ2	LRC4C_HUMAN	G	192	ENSP00000278198:A192G;ENSP00000436976:A192G;ENSP00000437132:A192G;ENSP00000434761:A192G	ENSP00000278198:A192G	A	-	2	0	LRRC4C	40093844	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.754000	0.94517	0.650000	0.86243	GCC	LRRC4C	-	NULL	ENSG00000148948		0.438	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	LRRC4C	HGNC	protein_coding	OTTHUMT00000389499.1	44	0.00	0	G	NM_020929		40137268	40137268	-1	no_errors	ENST00000527150	ensembl	human	known	69_37n	missense	54	34.15	28	SNP	1.000	C
MAP2K4	6416	genome.wustl.edu	37	17	12032516	12032517	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	AC	AC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr17:12032516_12032517delAC	ENST00000353533.5	+	9	1015_1016	c.952_953delAC	c.(952-954)acafs	p.T318fs	MAP2K4_ENST00000415385.3_Frame_Shift_Del_p.T329fs	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TGATCAACTAACACAAGTCGTG	0.431			"""D, Mis, N"""		"""pancreatic, breast, colorectal"""																																	dbGAP		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|lung(1)|pancreas(1)																																								-	-	-	SO:0001589	frameshift_variant	0			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.952_953delAC	17.37:g.12032518_12032519delAC	ENSP00000262445:p.Thr318fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.Q330fs	ENST00000353533.5	37	c.985_986	CCDS11162.1	17																																																																																			MAP2K4	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000065559		0.431	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP2K4	HGNC	protein_coding	OTTHUMT00000441226.1	53	0.00	0	AC			12032516	12032517	+1	no_errors	ENST00000415385	ensembl	human	known	69_37n	frame_shift_del	39	36.51	23	DEL	1.000:1.000	-
MAP3K12	7786	genome.wustl.edu	37	12	53876974	53876974	+	Splice_Site	SNP	C	C	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr12:53876974C>T	ENST00000267079.2	-	12	1740		c.e12-1		MAP3K12_ENST00000547035.1_Splice_Site|MAP3K12_ENST00000547488.1_Splice_Site	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12						histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GATATCTGGCCTGGAAGAAGA	0.498																																						dbGAP											0													56.0	59.0	58.0					12																	53876974		2119	4253	6372	-	-	-	SO:0001630	splice_region_variant	0			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6851	protein-coding gene	gene with protein product	"""dual leucine zipper kinase DLK"""	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.1515-1G>A	12.37:g.53876974C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Splice_Site	SNP	-	e11-1	ENST00000267079.2	37	c.1515-1	CCDS8860.1	12	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424130	0.62733	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0539	0.86527	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAP3K12	52163241	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	5.278000	0.65592	2.640000	0.89533	0.655000	0.94253	.	MAP3K12	-	-	ENSG00000139625		0.498	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP3K12	HGNC	protein_coding	OTTHUMT00000406267.1	32	0.00	0	C	NM_006301	Intron	53876974	53876974	-1	no_errors	ENST00000267079	ensembl	human	known	69_37n	splice_site	35	30.00	15	SNP	1.000	T
MEFV	4210	genome.wustl.edu	37	16	3293864	3293864	+	Silent	SNP	A	A	G			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr16:3293864A>G	ENST00000219596.1	-	9	1827	c.1788T>C	c.(1786-1788)caT>caC	p.H596H	MEFV_ENST00000339854.4_Silent_p.H416H|MEFV_ENST00000536379.1_Silent_p.H385H|MEFV_ENST00000541159.1_Missense_Mutation_p.C444R	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	596	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						ACTTACCAGCATGTGCCTGAG	0.517																																						dbGAP											0													50.0	52.0	51.0					16																	3293864		2197	4300	6497	-	-	-	SO:0001819	synonymous_variant	0			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1788T>C	16.37:g.3293864A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	pfam_DAPIN,pfam_Znf_B-box,superfamily_DEATH-like,smart_Znf_B-box,pfscan_DAPIN,pfscan_Znf_B-box	p.C444R	ENST00000219596.1	37	c.1330	CCDS10498.1	16	.	.	.	.	.	.	.	.	.	.	A	6.478	0.456308	0.12283	.	.	ENSG00000103313	ENST00000541159	T	0.62364	0.03	4.46	3.32	0.38043	.	.	.	.	.	T	0.67183	0.2866	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67264	-0.5714	6	0.87932	D	0	-42.7183	7.1622	0.25671	0.8012:0.0:0.0:0.1988	.	.	.	.	R	444	ENSP00000438711:C444R	ENSP00000438711:C444R	C	-	1	0	MEFV	3233865	0.911000	0.30947	0.992000	0.48379	0.431000	0.31685	1.464000	0.35288	0.803000	0.34113	0.533000	0.62120	TGC	MEFV	-	NULL	ENSG00000103313		0.517	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MEFV	HGNC	protein_coding	OTTHUMT00000251464.1	34	0.00	0	A	NM_000243		3293864	3293864	-1	no_errors	ENST00000541159	ensembl	human	putative	69_37n	missense	44	26.67	16	SNP	0.911	G
MYT1L	23040	genome.wustl.edu	37	2	1842924	1842924	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr2:1842924C>T	ENST00000399161.2	-	21	3824	c.3077G>A	c.(3076-3078)cGc>cAc	p.R1026H	MYT1L_ENST00000471668.1_5'UTR|MYT1L_ENST00000428368.2_Missense_Mutation_p.R1024H|MYT1L_ENST00000407844.1_Missense_Mutation_p.R22H	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1026					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CACTCACCTGCGGTGTGTGAG	0.672																																						dbGAP											0													12.0	15.0	14.0					2																	1842924		1971	4127	6098	-	-	-	SO:0001583	missense	0			AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3077G>A	2.37:g.1842924C>T	ENSP00000382114:p.Arg1026His	Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	pfam_Myelin_TF,pfam_Znf_C2HC	p.R1026H	ENST00000399161.2	37	c.3077		2	.	.	.	.	.	.	.	.	.	.	C	36	5.600459	0.96614	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000407844;ENST00000399157;ENST00000428368	T;T	0.58506	0.34;0.33	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.72112	0.3420	L	0.46670	1.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.991	T	0.71504	-0.4573	10	0.51188	T	0.08	.	19.5365	0.95255	0.0:1.0:0.0:0.0	.	22;1026;1024	Q9UL68-3;Q9UL68;Q9UL68-4	.;MYT1L_HUMAN;.	H	1026;972;22;80;1024	ENSP00000382114:R1026H;ENSP00000396103:R1024H	ENSP00000295067:R972H	R	-	2	0	MYT1L	1821931	1.000000	0.71417	0.966000	0.40874	0.871000	0.50021	7.750000	0.85110	2.618000	0.88619	0.563000	0.77884	CGC	MYT1L	-	pfam_Znf_C2HC	ENSG00000186487		0.672	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	MYT1L	HGNC	protein_coding	OTTHUMT00000322493.1	9	0.00	0	C	NM_015025		1842924	1842924	-1	no_errors	ENST00000399161	ensembl	human	known	69_37n	missense	6	40.00	4	SNP	1.000	T
PIK3CA	5290	genome.wustl.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)											56.0	56.0	56.0					3																	178936082		1809	4069	5878	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E542K	ENST00000263967.3	37	c.1624	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	55	0.00	0	G			178936082	178936082	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	89	27.64	34	SNP	1.000	A
POLR2B	5431	genome.wustl.edu	37	4	57876368	57876368	+	Intron	SNP	T	T	G			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr4:57876368T>G	ENST00000381227.1	+	12	1817				POLR2B_ENST00000314595.5_Intron|POLR2B_ENST00000510355.1_Splice_Site|POLR2B_ENST00000441246.2_Intron|POLR2B_ENST00000431623.2_Intron			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa						7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					AAGTGGCAGGTAAGTTAAAGT	0.353																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1405-159T>G	4.37:g.57876368T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1A8|Q8IZ61	Splice_Site	SNP	-	NULL	ENST00000381227.1	37	c.NULL	CCDS3511.1	4																																																																																			POLR2B	-	-	ENSG00000047315		0.353	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLR2B	HGNC	protein_coding	OTTHUMT00000250692.1	8	0.00	0	T	NM_000938		57876368	57876368	+1	no_errors	ENST00000510355	ensembl	human	known	69_37n	splice_site	5	62.50	10	SNP	0.001	G
SHANK3	85358	genome.wustl.edu	37	22	51121781	51121781	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr22:51121781G>A	ENST00000414786.2	+	8	1126	c.899G>A	c.(898-900)cGt>cAt	p.R300H	SHANK3_ENST00000445220.2_Missense_Mutation_p.R300H|SHANK3_ENST00000262795.3_Missense_Mutation_p.R300H			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	300			R -> C (found in patients with neuropsychiatric disorders; unknown pathological significance; disrupts synaptic localization; may disrupt transsynaptic signaling and spine maturation). {ECO:0000269|PubMed:17173049}.		adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		AGCTGTGCTCGTGTCCTGCTC	0.582																																						dbGAP											0													61.0	71.0	67.0					22																	51121781		2123	4215	6338	-	-	-	SO:0001583	missense	0			AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.899G>A	22.37:g.51121781G>A	ENSP00000464552:p.Arg300His	Somatic		WXS	Illumina GAIIx	Phase_IV	D7UT47|Q8TET3	Missense_Mutation	SNP	pfam_SAM_type1,pfam_Ankyrin_rpt,pfam_SAM_2,pfam_SH3_2,pfam_PDZ,superfamily_Ankyrin_rpt-contain_dom,superfamily_PDZ,superfamily_SAM/pointed,superfamily_SH3_domain,smart_Ankyrin_rpt,smart_SH3_domain,smart_PDZ,smart_SAM,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_PDZ,pfscan_SAM,pfscan_SH3_domain	p.R300H	ENST00000414786.2	37	c.899		22	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902818	0.92035	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.65549	-0.16;-0.16	4.8	4.8	0.61643	.	.	.	.	.	T	0.73063	0.3539	L	0.44542	1.39	0.31043	N	0.716113	D	0.89917	1.0	D	0.91635	0.999	T	0.72893	-0.4154	9	0.56958	D	0.05	.	15.4269	0.75059	0.0:0.0:1.0:0.0	.	300	F2Z3L0	.	H	300	ENSP00000442518:R300H;ENSP00000446078:R300H	ENSP00000442518:R300H	R	+	2	0	SHANK3	49468647	1.000000	0.71417	0.875000	0.34327	0.996000	0.88848	8.666000	0.91149	2.495000	0.84180	0.645000	0.84053	CGT	SHANK3	-	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	ENSG00000251322		0.582	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	SHANK3	HGNC	protein_coding	OTTHUMT00000316674.2	46	0.00	0	G	NM_001080420		51121781	51121781	+1	no_errors	ENST00000262795	ensembl	human	known	69_37n	missense	86	39.58	57	SNP	0.951	A
SVIL	6840	genome.wustl.edu	37	10	29779847	29779847	+	Missense_Mutation	SNP	A	A	C	rs199726033	byFrequency	TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr10:29779847A>C	ENST00000355867.4	-	22	4873	c.4121T>G	c.(4120-4122)cTc>cGc	p.L1374R	SVIL_ENST00000538146.1_Missense_Mutation_p.L166R|SVIL_ENST00000535393.1_Missense_Mutation_p.L288R|SVIL_ENST00000375400.3_Missense_Mutation_p.L948R|SVIL_ENST00000375398.2_Missense_Mutation_p.L1374R	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1374					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.L1374R(2)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TTCCTGAAGGAGATCTTCTCT	0.522																																						dbGAP											2	Substitution - Missense(2)	stomach(1)|central_nervous_system(1)											61.0	64.0	63.0					10																	29779847		2203	4297	6500	-	-	-	SO:0001583	missense	0			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.4121T>G	10.37:g.29779847A>C	ENSP00000348128:p.Leu1374Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	pfam_Gelsolin_dom,pfam_Villin_headpiece,superfamily_Villin_headpiece,smart_Gelsolin,smart_Villin_headpiece,pfscan_Villin_headpiece,prints_Gelsolin	p.L1374R	ENST00000355867.4	37	c.4121	CCDS7164.1	10	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079593	0.55753	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;D	0.86164	2.23;2.3;2.3;2.07;-2.08	4.08	4.08	0.47627	.	0.052248	0.85682	D	0.000000	D	0.91402	0.7287	M	0.68952	2.095	0.43583	D	0.995928	P;D;D;P	0.62365	0.947;0.986;0.991;0.884	P;D;D;P	0.64506	0.789;0.921;0.926;0.507	D	0.92348	0.5887	10	0.87932	D	0	-17.1694	13.2793	0.60205	1.0:0.0:0.0:0.0	.	288;166;948;1374	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	R	948;1374;1374;288;328;166	ENSP00000364549:L948R;ENSP00000364547:L1374R;ENSP00000348128:L1374R;ENSP00000445472:L288R;ENSP00000440343:L166R	ENSP00000348128:L1374R	L	-	2	0	SVIL	29819853	1.000000	0.71417	0.983000	0.44433	0.278000	0.26855	8.642000	0.91036	1.714000	0.51371	0.397000	0.26171	CTC	SVIL	-	NULL	ENSG00000197321		0.522	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SVIL	HGNC	protein_coding	OTTHUMT00000047395.1	52	0.00	0	A			29779847	29779847	-1	no_errors	ENST00000355867	ensembl	human	known	69_37n	missense	125	11.27	16	SNP	1.000	C
TLR8	51311	genome.wustl.edu	37	X	12937900	12937900	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chrX:12937900delT	ENST00000218032.6	+	2	828	c.741delT	c.(739-741)aatfs	p.N247fs	TLR8_ENST00000311912.5_Frame_Shift_Del_p.N265fs	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	247					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	GATTGATAAATTTAACATTAC	0.428																																						dbGAP											0													74.0	68.0	70.0					X																	12937900		2203	4299	6502	-	-	-	SO:0001589	frameshift_variant	0			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.741delT	X.37:g.12937900delT	ENSP00000218032:p.Asn247fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Frame_Shift_Del	DEL	pfam_Leu-rich_rpt,pfam_TIR_dom,superfamily_TIR_dom,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_TIR_dom,pfscan_TIR_dom	p.L248fs	ENST00000218032.6	37	c.741	CCDS14152.1	X																																																																																			TLR8	-	NULL	ENSG00000101916		0.428	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TLR8	HGNC	protein_coding	OTTHUMT00000055784.2	49	0.00	0	T	NM_016610		12937900	12937900	+1	no_errors	ENST00000218032	ensembl	human	known	69_37n	frame_shift_del	36	26.42	14	DEL	0.827	-
TNXB	7148	genome.wustl.edu	37	6	32041597	32041597	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr6:32041597G>T	ENST00000375244.3	-	12	4709	c.4508C>A	c.(4507-4509)tCc>tAc	p.S1503Y	TNXB_ENST00000375247.2_Missense_Mutation_p.S1503Y			P22105	TENX_HUMAN	tenascin XB	1590	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GACTATGAAGGAGTCAAACTG	0.622																																						dbGAP											0													28.0	31.0	30.0					6																	32041597		1289	2576	3865	-	-	-	SO:0001583	missense	0			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4508C>A	6.37:g.32041597G>T	ENSP00000364393:p.Ser1503Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	pfam_Fibronectin_type3,pfam_Fibrinogen_a/b/g_C,pfam_EGF_extracell,superfamily_Fibrinogen_a/b/g_C,superfamily_Fibronectin_type3,smart_EGF-like,smart_Fibronectin_type3,smart_Fibrinogen_a/b/g_C,pfscan_EG-like_dom,pfscan_Fibronectin_type3	p.S1503Y	ENST00000375244.3	37	c.4508		6	.	.	.	.	.	.	.	.	.	.	G	17.65	3.442310	0.63067	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.58210	0.35;0.35	5.46	5.46	0.80206	.	0.000000	0.42294	D	0.000724	T	0.67163	0.2864	M	0.93062	3.375	0.38928	D	0.957881	D	0.62365	0.991	D	0.68192	0.956	T	0.74097	-0.3775	10	0.06757	T	0.87	.	16.2254	0.82286	0.0:0.0:1.0:0.0	.	1503	P22105-3	.	Y	1503	ENSP00000364393:S1503Y;ENSP00000364396:S1503Y	ENSP00000364393:S1503Y	S	-	2	0	TNXB	32149575	1.000000	0.71417	1.000000	0.80357	0.409000	0.31022	5.596000	0.67570	2.552000	0.86080	0.543000	0.68304	TCC	TNXB	-	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3	ENSG00000168477		0.622	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	TNXB	HGNC	protein_coding	OTTHUMT00000268927.2	10	0.00	0	G	NM_019105		32041597	32041597	-1	no_errors	ENST00000375247	ensembl	human	known	69_37n	missense	4	55.56	5	SNP	1.000	T
WHAMMP2	440253	genome.wustl.edu	37	15	28989968	28989968	+	RNA	SNP	G	G	T	rs200083792	byFrequency	TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr15:28989968G>T	ENST00000512149.2	+	0	0					NR_026589.1				WAS protein homolog associated with actin, golgi membranes and microtubules pseudogene 2																		GAATGGACCAGACGGGCTGGA	0.408																																						dbGAP											0																																										-	-	-			0			BC035099		15q13.1	2014-03-20	2011-06-24	2011-06-24	ENSG00000248334	ENSG00000248334			32360	pseudogene	pseudogene			"""WAS protein homology region 2 domain containing 1-like 2 (pseudogene)"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 2 (pseudogene)"""	WHDC1L2, WHAMML2			Standard	NR_026589		Approved		uc010uap.2		OTTHUMG00000176340		15.37:g.28989968G>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000512149.2	37	NULL		15																																																																																			WHAMMP2	-	-	ENSG00000248334		0.408	WHAMMP2-003	PUTATIVE	basic	processed_transcript	WHAMMP2	HGNC	pseudogene	OTTHUMT00000431783.1	37	0.00	0	G	NR_026589		28989968	28989968	+1	no_errors	ENST00000508764	ensembl	human	putative	69_37n	rna	38	17.39	8	SNP	0.204	T
WSCD2	9671	genome.wustl.edu	37	12	108618544	108618544	+	Silent	SNP	C	C	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr12:108618544C>T	ENST00000332082.4	+	6	1529	c.711C>T	c.(709-711)ttC>ttT	p.F237F	WSCD2_ENST00000549903.1_Silent_p.F237F|WSCD2_ENST00000261400.3_Silent_p.F237F|WSCD2_ENST00000547525.1_Silent_p.F237F			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	237	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						GGGGCTGCTTCCGCAGGCCCG	0.532																																						dbGAP											0													69.0	73.0	72.0					12																	108618544		1921	4136	6057	-	-	-	SO:0001819	synonymous_variant	0				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.711C>T	12.37:g.108618544C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	pfam_WSC_carb-bd,smart_WSC_carb-bd_subgr,pfscan_WSC_carb-bd	p.F237	ENST00000332082.4	37	c.711	CCDS41828.1	12																																																																																			WSCD2	-	pfam_WSC_carb-bd,smart_WSC_carb-bd_subgr,pfscan_WSC_carb-bd	ENSG00000075035		0.532	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	WSCD2	HGNC	protein_coding	OTTHUMT00000405554.1	27	0.00	0	C	NM_014653		108618544	108618544	+1	no_errors	ENST00000261400	ensembl	human	known	69_37n	silent	25	32.43	12	SNP	1.000	T
XIRP2	129446	genome.wustl.edu	37	2	168104843	168104843	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A1G0-01A-11D-A13L-09	TCGA-A2-A1G0-10A-01D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f7eacf95-478d-4d81-a5e3-f5a8938c83ec	eb1176bf-f7d8-4fdf-ae03-a998c8bdc047	g.chr2:168104843C>T	ENST00000409195.1	+	9	7030	c.6941C>T	c.(6940-6942)cCt>cTt	p.P2314L	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.P2092L|XIRP2_ENST00000295237.9_Missense_Mutation_p.P2314L|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2139					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CCTCCTCCACCTCCTTTGATG	0.448																																						dbGAP											0													109.0	105.0	106.0					2																	168104843		1894	4124	6018	-	-	-	SO:0001583	missense	0			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6941C>T	2.37:g.168104843C>T	ENSP00000386840:p.Pro2314Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	pfam_Actin-binding_Xin_repeat,superfamily_FH2_actin-bd	p.P2314L	ENST00000409195.1	37	c.6941	CCDS42769.1	2	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837937	0.91117	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.46819	0.86;0.86;0.86	6.17	6.17	0.99709	.	0.060598	0.64402	D	0.000003	T	0.70439	0.3224	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.70040	-0.4981	10	0.72032	D	0.01	-15.5081	19.6509	0.95805	0.0:1.0:0.0:0.0	.	2139;2139;2092	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	L	2314;2314;2092	ENSP00000386840:P2314L;ENSP00000295237:P2314L;ENSP00000387255:P2092L	ENSP00000295237:P2314L	P	+	2	0	XIRP2	167813089	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.007000	0.63984	2.941000	0.99782	0.655000	0.94253	CCT	XIRP2	-	NULL	ENSG00000163092		0.448	XIRP2-001	KNOWN	basic|CCDS	protein_coding	XIRP2	HGNC	protein_coding	OTTHUMT00000333547.1	40	0.00	0	C	NM_152381		168104843	168104843	+1	no_errors	ENST00000295237	ensembl	human	known	69_37n	missense	50	25.37	17	SNP	1.000	T
