#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_dbSNPPopFreq	i_dbSNP_AF	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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
AMY2A	279	hgsc.bcm.edu	37	1	104160634	104160634	+	Missense_Mutation	SNP	G	G	T	rs371720173		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr1:104160634G>T	ENST00000414303.2	+	2	291	c.227G>T	c.(226-228)aGa>aTa	p.R76I		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	76					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)			endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	TGGTGGGAAAGATACCAACCA	0.353																																					p.R76I		Atlas-SNP	.											.	AMY2A	36	.	0			c.G227T						.						170.0	155.0	160.0					1																	104160634		2201	4279	6480	SO:0001583	missense	279	exon2			GGGAAAGATACCA	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"""amylase, alpha 2A; pancreatic"""	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.227G>T	chr1.hg19:g.104160634G>T	ENSP00000397582:p.Arg76Ile	414.0	0.0		307.0	107.0	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	hg19	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	22.0|22.0	4.230811|4.230811	0.79688|0.79688	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000423678|ENST00000414303;ENST00000393932	.|D	.|0.98437	.|-4.93	3.47|3.47	3.47|3.47	0.39725|0.39725	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99080|0.99080	0.9684|0.9684	M|M	0.92738|0.92738	3.34|3.34	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	D|D	0.99285|0.99285	1.0897|1.0897	5|10	.|0.87932	.|D	.|0	.|.	15.0729|15.0729	0.72053|0.72053	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|76;76	.|B9EJG1;P04746	.|.;AMYP_HUMAN	N|I	74|76	.|ENSP00000397582:R76I	.|ENSP00000377509:R76I	K|R	+|+	3|2	2|0	AMY2A|AMY2A	103962157|103962157	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	9.276000|9.276000	0.95745|0.95745	1.927000|1.927000	0.55829|0.55829	0.455000|0.455000	0.32223|0.32223	AAG|AGA	.	.		0.353	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699	
NEB	4703	hgsc.bcm.edu	37	2	152499357	152499357	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:152499357T>C	ENST00000172853.10	-	59	8334	c.8187A>G	c.(8185-8187)aaA>aaG	p.K2729K	NEB_ENST00000604864.1_Silent_p.K2729K|NEB_ENST00000397345.3_Silent_p.K2729K|NEB_ENST00000409198.1_Silent_p.K2729K|NEB_ENST00000603639.1_Silent_p.K2729K|NEB_ENST00000427231.2_Silent_p.K2729K			P20929	NEBU_HUMAN	nebulin	2729					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGTTTTATCTTTATCCCAAG	0.348																																					p.K2729K		Atlas-SNP	.											.	NEB	1697	.	0			c.A8187G						.						48.0	47.0	47.0					2																	152499357		1829	4080	5909	SO:0001819	synonymous_variant	4703	exon59			TTTATCTTTATCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.8187A>G	chr2.hg19:g.152499357T>C		88.0	0.0		73.0	22.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.		0.348	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
TBR1	10716	hgsc.bcm.edu	37	2	162273413	162273413	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:162273413C>T	ENST00000389554.3	+	1	809	c.492C>T	c.(490-492)tcC>tcT	p.S164S	TBR1_ENST00000410035.1_5'Flank	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	164					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						TGTCCAACTCCTCGCCGCAGG	0.662																																					p.S164S		Atlas-SNP	.											.	TBR1	59	.	0			c.C492T						.						71.0	74.0	73.0					2																	162273413		2203	4300	6503	SO:0001819	synonymous_variant	10716	exon1			CAACTCCTCGCCG	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"""T-boxes"""	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.492C>T	chr2.hg19:g.162273413C>T		80.0	0.0		50.0	19.0	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Silent	SNP	ENST00000389554.3	hg19	CCDS33310.1																																																																																			.	.		0.662	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593	
HIBCH	26275	hgsc.bcm.edu	37	2	191110920	191110920	+	Nonsense_Mutation	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:191110920T>A	ENST00000359678.5	-	10	1063	c.769A>T	c.(769-771)Aag>Tag	p.K257*	HIBCH_ENST00000392332.3_Nonsense_Mutation_p.K257*|HIBCH_ENST00000410045.1_Nonsense_Mutation_p.K34*	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	257					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			ATAAAAGACTTGTCTCGATCA	0.249																																					p.K257X		Atlas-SNP	.											.	HIBCH	28	.	0			c.A769T						.						80.0	78.0	79.0					2																	191110920		2198	4294	6492	SO:0001587	stop_gained	26275	exon10			AAGACTTGTCTCG	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.769A>T	chr2.hg19:g.191110920T>A	ENSP00000352706:p.Lys257*	97.0	0.0		95.0	40.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Nonsense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	T	39	7.798293	0.98495	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000410045;ENST00000416732;ENST00000409820	.	.	.	4.73	4.73	0.59995	.	0.418322	0.27715	N	0.018156	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.0883	12.3549	0.55169	0.0:0.0:0.0:1.0	.	.	.	.	X	257;257;34;8;37	.	ENSP00000352706:K257X	K	-	1	0	HIBCH	190819165	1.000000	0.71417	0.987000	0.45799	0.800000	0.45204	5.426000	0.66476	2.108000	0.64289	0.533000	0.62120	AAG	.	.		0.249	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1		
SETD5	55209	hgsc.bcm.edu	37	3	9517712	9517712	+	Silent	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:9517712G>A	ENST00000406341.1	+	22	4456	c.4266G>A	c.(4264-4266)gtG>gtA	p.V1422V	SETD5_ENST00000302463.6_Silent_p.V1324V|SETD5_ENST00000407969.1_Silent_p.V1441V|SETD5_ENST00000402198.1_Silent_p.V1422V|SETD5_ENST00000402466.1_Silent_p.V1324V			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1422										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GTGGGGGTGTGCACCAGTACC	0.577																																					p.V1422V		Atlas-SNP	.											.	SETD5	210	.	0			c.G4266A						.						27.0	29.0	28.0					3																	9517712		1964	4153	6117	SO:0001819	synonymous_variant	55209	exon23			GGGTGTGCACCAG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.4266G>A	chr3.hg19:g.9517712G>A		49.0	0.0		46.0	19.0	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Silent	SNP	ENST00000406341.1	hg19	CCDS46741.1																																																																																			.	.		0.577	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
GPD1L	23171	hgsc.bcm.edu	37	3	32181733	32181733	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:32181733G>A	ENST00000282541.5	+	4	581	c.380G>A	c.(379-381)gGc>gAc	p.G127D		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	127					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						ATAGACGAGGGCCCCGAGGGG	0.507																																					p.G127D		Atlas-SNP	.											.	GPD1L	25	.	0			c.G380A						.						175.0	185.0	182.0					3																	32181733		2203	4300	6503	SO:0001583	missense	23171	exon4			ACGAGGGCCCCGA	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.380G>A	chr3.hg19:g.32181733G>A	ENSP00000282541:p.Gly127Asp	76.0	0.0		57.0	16.0	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	hg19	CCDS33729.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641917	0.67244	.	.	ENSG00000152642	ENST00000429432;ENST00000282541;ENST00000425459;ENST00000431009	T;T;T;T	0.56611	0.45;0.45;0.65;0.45	5.46	5.46	0.80206	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.094278	0.64402	D	0.000001	T	0.53254	0.1785	L	0.60067	1.865	0.80722	D	1	P	0.44309	0.832	B	0.40940	0.344	T	0.51803	-0.8659	10	0.30854	T	0.27	-17.0625	19.6998	0.96048	0.0:0.0:1.0:0.0	.	127	Q8N335	GPD1L_HUMAN	D	88;127;80;88	ENSP00000393861:G88D;ENSP00000282541:G127D;ENSP00000408770:G80D;ENSP00000416518:G88D	ENSP00000282541:G127D	G	+	2	0	GPD1L	32156737	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	9.736000	0.98828	2.728000	0.93425	0.655000	0.94253	GGC	.	.		0.507	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64666990	64666990	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:64666990T>A	ENST00000498707.1	-	3	908	c.566A>T	c.(565-567)cAg>cTg	p.Q189L	ADAMTS9_ENST00000459780.1_Missense_Mutation_p.Q189L|ADAMTS9_ENST00000295903.4_Missense_Mutation_p.Q189L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	189					glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ATCCATAGACTGTAGTGGTTC	0.468																																					p.Q189L		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.A566T						.						181.0	168.0	172.0					3																	64666990		2203	4300	6503	SO:0001583	missense	56999	exon3			ATAGACTGTAGTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.566A>T	chr3.hg19:g.64666990T>A	ENSP00000418735:p.Gln189Leu	176.0	0.0		156.0	74.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	3.539	-0.094104	0.07053	.	.	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	T;T;T	0.61392	0.3;0.31;0.11	6.04	2.18	0.27775	Peptidase M12B, propeptide (1);	0.382752	0.24769	N	0.035749	T	0.27933	0.0688	N	0.01800	-0.715	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.17198	-1.0377	10	0.23891	T	0.37	.	11.2942	0.49269	0.6405:0.0:0.0:0.3595	.	189;189;189;189	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	L	189	ENSP00000295903:Q189L;ENSP00000418735:Q189L;ENSP00000419217:Q189L	ENSP00000295903:Q189L	Q	-	2	0	ADAMTS9	64642030	0.911000	0.30947	0.007000	0.13788	0.335000	0.28730	2.693000	0.47027	0.122000	0.18314	-0.527000	0.04329	CAG	.	.		0.468	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
ZBTB38	253461	hgsc.bcm.edu	37	3	141163098	141163098	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:141163098A>G	ENST00000514251.1	+	4	2147	c.1868A>G	c.(1867-1869)aAc>aGc	p.N623S	ZBTB38_ENST00000441582.2_Missense_Mutation_p.N623S|ZBTB38_ENST00000321464.5_Missense_Mutation_p.N624S					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						GATACTGTAAACACCCTGACC	0.453																																					p.N623S		Atlas-SNP	.											.	ZBTB38	92	.	0			c.A1868G						.						88.0	85.0	86.0					3																	141163098		1980	4180	6160	SO:0001583	missense	253461	exon8			CTGTAAACACCCT	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1868A>G	chr3.hg19:g.141163098A>G	ENSP00000426387:p.Asn623Ser	72.0	0.0		52.0	16.0	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	hg19	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	A	5.842	0.339587	0.11069	.	.	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464	T;T;T;T	0.08370	3.58;3.1;3.1;3.1	5.55	-0.817	0.10836	.	0.630837	0.16193	N	0.225297	T	0.04318	0.0119	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.43621	-0.9380	9	.	.	.	-4.4441	11.5098	0.50486	0.4476:0.0:0.5524:0.0	.	624;623	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	S	623;623;623;624	ENSP00000424254:N623S;ENSP00000426387:N623S;ENSP00000406955:N623S;ENSP00000372635:N624S	.	N	+	2	0	ZBTB38	142645788	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.076000	0.11412	-0.138000	0.11434	0.528000	0.53228	AAC	.	.		0.453	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
HS3ST1	9957	hgsc.bcm.edu	37	4	11401189	11401189	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr4:11401189T>C	ENST00000002596.5	-	2	1615	c.441A>G	c.(439-441)cgA>cgG	p.R147R		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	147					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)	p.L146_D148delLRD(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						CCGACGGGTCTCGCAGGATGA	0.592																																					p.R147R		Atlas-SNP	.											.	HS3ST1	41	.	1	Deletion - In frame(1)	liver(1)	c.A441G						.						63.0	59.0	61.0					4																	11401189		2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CGGGTCTCGCAGG	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.441A>G	chr4.hg19:g.11401189T>C		59.0	0.0		46.0	20.0	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	hg19	CCDS3408.1																																																																																			.	.		0.592	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114	
DNAH5	1767	hgsc.bcm.edu	37	5	13700904	13700904	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:13700904T>C	ENST00000265104.4	-	78	13672	c.13568A>G	c.(13567-13569)gAc>gGc	p.D4523G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4523					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAAATGTCGTCCTTCATCCA	0.463									Kartagener syndrome																												p.D4523G		Atlas-SNP	.											.	DNAH5	868	.	0			c.A13568G						.						184.0	170.0	174.0					5																	13700904		2203	4300	6503	SO:0001583	missense	1767	exon78	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATGTCGTCCTTCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13568A>G	chr5.hg19:g.13700904T>C	ENSP00000265104:p.Asp4523Gly	118.0	0.0		88.0	31.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250156	0.80024	.	.	ENSG00000039139	ENST00000265104	T	0.09255	3.0	5.95	5.95	0.96441	Dynein heavy chain (1);	0.049262	0.85682	D	0.000000	T	0.19604	0.0471	L	0.55743	1.74	0.80722	D	1	B	0.28552	0.215	B	0.39465	0.3	T	0.01608	-1.1313	10	0.87932	D	0	.	16.4323	0.83853	0.0:0.0:0.0:1.0	.	4523	Q8TE73	DYH5_HUMAN	G	4523	ENSP00000265104:D4523G	ENSP00000265104:D4523G	D	-	2	0	DNAH5	13753904	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	7.992000	0.88273	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
RAI14	26064	hgsc.bcm.edu	37	5	34823713	34823713	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:34823713A>G	ENST00000265109.3	+	15	2053	c.1766A>G	c.(1765-1767)aAt>aGt	p.N589S	RAI14_ENST00000512629.1_Missense_Mutation_p.N560S|RAI14_ENST00000428746.2_Missense_Mutation_p.N589S|RAI14_ENST00000503673.1_Missense_Mutation_p.N589S|RAI14_ENST00000397449.1_Missense_Mutation_p.N582S|RAI14_ENST00000515799.1_Missense_Mutation_p.N592S|RAI14_ENST00000506376.1_Missense_Mutation_p.N581S	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	589						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GTTATTGAGAATATGAATAAG	0.358																																					p.N592S		Atlas-SNP	.											.	RAI14	100	.	0			c.A1775G						.						58.0	61.0	60.0					5																	34823713		2203	4300	6503	SO:0001583	missense	26064	exon17			TTGAGAATATGAA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1766A>G	chr5.hg19:g.34823713A>G	ENSP00000265109:p.Asn589Ser	96.0	0.0		73.0	26.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289782	0.59976	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.36878	1.26;1.23;1.26;1.26;1.26;1.3;1.3	5.42	5.42	0.78866	.	.	.	.	.	T	0.48537	0.1505	L	0.29908	0.895	0.45035	D	0.998058	D;D;D;D	0.71674	0.998;0.982;0.978;0.982	D;P;P;P	0.80764	0.994;0.473;0.741;0.473	T	0.48854	-0.8998	9	0.52906	T	0.07	-27.1897	15.4697	0.75432	1.0:0.0:0.0:0.0	.	581;560;592;589	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	S	589;560;589;589;592;581;582	ENSP00000265109:N589S;ENSP00000422377:N560S;ENSP00000388725:N589S;ENSP00000422942:N589S;ENSP00000427123:N592S;ENSP00000423854:N581S;ENSP00000380591:N582S	ENSP00000265109:N589S	N	+	2	0	RAI14	34859470	1.000000	0.71417	0.989000	0.46669	0.917000	0.54804	6.348000	0.73009	2.067000	0.61834	0.454000	0.30748	AAT	.	.		0.358	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
HAPLN1	1404	hgsc.bcm.edu	37	5	82940454	82940454	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:82940454C>A	ENST00000274341.4	-	4	1353	c.503G>T	c.(502-504)gGg>gTg	p.G168V		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	168	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	ATTGTAGCGCCCCAGTCGTGG	0.552																																					p.G168V		Atlas-SNP	.											HAPLN1,right_upper_lobe,carcinoma,0,1	HAPLN1	79	.	0			c.G503T						.						34.0	32.0	33.0					5																	82940454		2203	4300	6503	SO:0001583	missense	1404	exon4			TAGCGCCCCAGTC		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"""Immunoglobulin superfamily / V-set domain containing"""	2380	protein-coding gene	gene with protein product	"""Cartilage link protein"", ""hyaluronan and proteoglycan link protein 1"""	115435	"""cartilage linking protein 1"""	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.503G>T	chr5.hg19:g.82940454C>A	ENSP00000274341:p.Gly168Val	68.0	0.0		44.0	20.0	NM_001884	B2R9A9	Missense_Mutation	SNP	ENST00000274341.4	hg19	CCDS4061.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020264	0.93462	.	.	ENSG00000145681	ENST00000274341;ENST00000510978;ENST00000508307;ENST00000503117	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	5.8	5.8	0.92144	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67304	-0.5704	10	0.87932	D	0	.	20.0608	0.97674	0.0:1.0:0.0:0.0	.	168	P10915	HPLN1_HUMAN	V	168;168;168;167	ENSP00000274341:G168V;ENSP00000422592:G168V;ENSP00000421341:G168V;ENSP00000426610:G167V	ENSP00000274341:G168V	G	-	2	0	HAPLN1	82976210	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.466000	0.80914	2.733000	0.93635	0.650000	0.86243	GGG	.	.		0.552	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884	
PCDHA7	56141	hgsc.bcm.edu	37	5	140216124	140216124	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:140216124C>G	ENST00000525929.1	+	1	2156	c.2156C>G	c.(2155-2157)aCg>aGg	p.T719R	PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.T719R|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	719					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCTGTACACGGCGTTGCGG	0.607																																					p.T719R	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.C2156G						.						106.0	88.0	94.0					5																	140216124		2203	4300	6503	SO:0001583	missense	56141	exon1			TGTACACGGCGTT	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2156C>G	chr5.hg19:g.140216124C>G	ENSP00000436426:p.Thr719Arg	50.0	0.0		38.0	14.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257257	0.39896	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.15603	2.41;2.41	3.57	0.749	0.18381	.	0.739382	0.10174	U	0.706779	T	0.44540	0.1298	M	0.93720	3.45	0.09310	N	1	D;P	0.53462	0.96;0.934	P;P	0.58970	0.849;0.71	T	0.24261	-1.0165	10	0.62326	D	0.03	.	8.4633	0.32940	0.0:0.6311:0.0:0.3689	.	719;719	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	R	719	ENSP00000436426:T719R;ENSP00000367365:T719R	ENSP00000367365:T719R	T	+	2	0	PCDHA7	140196308	0.000000	0.05858	0.469000	0.27204	0.694000	0.40290	-1.159000	0.03150	0.304000	0.22809	0.462000	0.41574	ACG	.	.		0.607	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140856286	140856286	+	Silent	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:140856286C>A	ENST00000308177.3	+	1	707	c.603C>A	c.(601-603)gcC>gcA	p.A201A	PCDHGB7_ENST00000398594.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	201	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCGCGCCCTGGACCGAG	0.597																																					p.A201A		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.C603A						.						39.0	33.0	35.0					5																	140856286		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GCGCGCCCTGGAC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.603C>A	chr5.hg19:g.140856286C>A		34.0	0.0		26.0	11.0	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	hg19	CCDS4261.1																																																																																			.	.		0.597	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
OPRM1	4988	hgsc.bcm.edu	37	6	154411035	154411035	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:154411035C>G	ENST00000330432.7	+	2	602	c.365C>G	c.(364-366)aCc>aGc	p.T122S	OPRM1_ENST00000419506.2_Missense_Mutation_p.T122S|OPRM1_ENST00000229768.5_Missense_Mutation_p.T122S|OPRM1_ENST00000452687.2_Missense_Mutation_p.T122S|OPRM1_ENST00000522555.1_Missense_Mutation_p.T22S|OPRM1_ENST00000360422.4_Missense_Mutation_p.T122S|OPRM1_ENST00000414028.2_Missense_Mutation_p.T122S|OPRM1_ENST00000428397.2_Missense_Mutation_p.T122S|OPRM1_ENST00000524163.1_Missense_Mutation_p.T122S|OPRM1_ENST00000434900.2_Missense_Mutation_p.T215S|OPRM1_ENST00000520708.1_Missense_Mutation_p.T22S|OPRM1_ENST00000435918.2_Missense_Mutation_p.T122S|OPRM1_ENST00000522236.1_Missense_Mutation_p.T22S|OPRM1_ENST00000337049.4_Missense_Mutation_p.T122S|OPRM1_ENST00000518759.1_Missense_Mutation_p.T41S	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	122					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GCCACCAGTACCCTGCCCTTC	0.443																																					p.T215S		Atlas-SNP	.											.	OPRM1	241	.	0			c.C644G						.						141.0	135.0	137.0					6																	154411035		2065	4238	6303	SO:0001583	missense	4988	exon4			CCAGTACCCTGCC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"""GPCR / Class A : Opioid receptors"""	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.365C>G	chr6.hg19:g.154411035C>G	ENSP00000328264:p.Thr122Ser	64.0	0.0		63.0	30.0	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422052	0.62622	.	.	ENSG00000112038	ENST00000434900;ENST00000520708;ENST00000518759;ENST00000330432;ENST00000360422;ENST00000428397;ENST00000452687;ENST00000229768;ENST00000419506;ENST00000524163;ENST00000414028;ENST00000435918;ENST00000337049;ENST00000522555;ENST00000522236	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72542	0.3473	L	0.37850	1.14	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;P;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;0.851;1.0;0.994	D;D;D;D;D;D;D;D;D;D;P;D;D	0.97110	0.997;1.0;1.0;0.997;1.0;1.0;1.0;1.0;1.0;1.0;0.673;1.0;0.966	T	0.65874	-0.6062	10	0.20046	T	0.44	.	19.8351	0.96655	0.0:1.0:0.0:0.0	.	122;122;122;122;215;41;122;22;122;122;122;122;122	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;B8Q1L9;P35372-6;Q6UPP1;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	S	215;22;41;122;122;122;122;122;122;122;122;122;122;22;22	ENSP00000394624:T215S;ENSP00000430876:T22S;ENSP00000430260:T41S;ENSP00000328264:T122S;ENSP00000353598:T122S;ENSP00000411903:T122S;ENSP00000410497:T122S;ENSP00000229768:T122S;ENSP00000403549:T122S;ENSP00000430097:T122S;ENSP00000399359:T122S;ENSP00000413752:T122S;ENSP00000338381:T122S;ENSP00000429719:T22S;ENSP00000429373:T22S	ENSP00000229768:T122S	T	+	2	0	OPRM1	154452728	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.687000	0.91594	0.655000	0.94253	ACC	.	.		0.443	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914	
ARID1B	57492	hgsc.bcm.edu	37	6	157150470	157150470	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:157150470G>A	ENST00000350026.5	+	2	1653	c.1652G>A	c.(1651-1653)gGc>gAc	p.G551D	ARID1B_ENST00000275248.4_Missense_Mutation_p.G493D|ARID1B_ENST00000346085.5_Missense_Mutation_p.G551D|ARID1B_ENST00000367148.1_Missense_Mutation_p.G551D	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	551					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGTTCCTATGGCCCTCCAGGC	0.587																																					p.G551D		Atlas-SNP	.											.	ARID1B	320	.	0			c.G1652A						.						93.0	85.0	87.0					6																	157150470		2203	4300	6503	SO:0001583	missense	57492	exon2			CCTATGGCCCTCC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.1652G>A	chr6.hg19:g.157150470G>A	ENSP00000055163:p.Gly551Asp	91.0	0.0		85.0	35.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964519	0.53507	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.03553	4.05;3.89;3.96;3.99;4.07	5.09	5.09	0.68999	.	0.186876	0.33327	N	0.005028	T	0.07863	0.0197	L	0.43923	1.385	0.38507	D	0.948366	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.65323	0.861;0.934;0.934	T	0.22906	-1.0203	10	0.56958	D	0.05	.	18.8734	0.92325	0.0:0.0:1.0:0.0	.	551;551;493	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	D	551;551;551;493;50	ENSP00000344546:G551D;ENSP00000055163:G551D;ENSP00000356116:G551D;ENSP00000275248:G493D;ENSP00000412835:G50D	ENSP00000275248:G493D	G	+	2	0	ARID1B	157192162	1.000000	0.71417	0.960000	0.40013	0.982000	0.71751	6.257000	0.72480	2.515000	0.84797	0.650000	0.86243	GGC	.	.		0.587	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
FNDC1	84624	hgsc.bcm.edu	37	6	159655130	159655130	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:159655130C>T	ENST00000297267.9	+	11	3786	c.3586C>T	c.(3586-3588)Ctg>Ttg	p.L1196L	FNDC1_ENST00000340366.6_Silent_p.L1133L	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1196					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGAAGACCTTCTGTCTTCCTC	0.617																																					p.L1196L		Atlas-SNP	.											.	FNDC1	250	.	0			c.C3586T						.						22.0	25.0	24.0					6																	159655130		1886	4090	5976	SO:0001819	synonymous_variant	84624	exon11			GACCTTCTGTCTT	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3586C>T	chr6.hg19:g.159655130C>T		64.0	0.0		38.0	19.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	5.706	0.314817	0.10789	.	.	ENSG00000164694	ENST00000329629	.	.	.	4.85	0.59	0.17458	.	.	.	.	.	T	0.08846	0.0219	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-7.7516	3.3856	0.07270	0.2295:0.4522:0.229:0.0893	.	.	.	.	F	1091	.	.	S	+	2	0	FNDC1	159575120	0.001000	0.12720	0.000000	0.03702	0.125000	0.20455	0.559000	0.23485	0.415000	0.25817	-0.244000	0.11960	TCT	.	.		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
PTPN12	5782	hgsc.bcm.edu	37	7	77240326	77240326	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr7:77240326A>T	ENST00000248594.6	+	11	1174	c.902A>T	c.(901-903)tAt>tTt	p.Y301F	PTPN12_ENST00000415482.2_Missense_Mutation_p.Y182F|PTPN12_ENST00000435495.2_Missense_Mutation_p.Y171F	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	301					protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CTACAACTATATGAAATTCAT	0.313																																					p.Y301F		Atlas-SNP	.											.	PTPN12	83	.	0			c.A902T						.						129.0	145.0	139.0					7																	77240326		2203	4298	6501	SO:0001583	missense	5782	exon11			AACTATATGAAAT		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.902A>T	chr7.hg19:g.77240326A>T	ENSP00000248594:p.Tyr301Phe	283.0	0.0		203.0	94.0	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	hg19	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361736	0.82353	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.07021	3.83;3.23;3.23	5.47	5.47	0.80525	.	0.208920	0.43579	D	0.000557	T	0.17280	0.0415	M	0.65975	2.015	0.48830	D	0.999714	P	0.50156	0.932	P	0.48304	0.573	T	0.00749	-1.1582	10	0.41790	T	0.15	.	15.8381	0.78814	1.0:0.0:0.0:0.0	.	301	Q05209	PTN12_HUMAN	F	301;182;182;171	ENSP00000248594:Y301F;ENSP00000392429:Y182F;ENSP00000397991:Y171F	ENSP00000248594:Y301F	Y	+	2	0	PTPN12	77078262	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	5.071000	0.64382	2.191000	0.70037	0.533000	0.62120	TAT	.	.		0.313	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
RBM12B	389677	hgsc.bcm.edu	37	8	94748274	94748274	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr8:94748274T>C	ENST00000399300.2	-	3	578	c.365A>G	c.(364-366)tAt>tGt	p.Y122C	RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Missense_Mutation_p.Y122C	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	122							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TGAAGAGCCATATCCAGAATT	0.438																																					p.Y122C		Atlas-SNP	.											.	RBM12B	78	.	0			c.A365G						.						143.0	137.0	139.0					8																	94748274		1856	4091	5947	SO:0001583	missense	389677	exon3			GAGCCATATCCAG		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.365A>G	chr8.hg19:g.94748274T>C	ENSP00000382239:p.Tyr122Cys	111.0	0.0		97.0	31.0	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	hg19	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.250781	0.39797	.	.	ENSG00000183808	ENST00000399300;ENST00000517700;ENST00000519109;ENST00000518597;ENST00000520560	T;T;T;T;T	0.19394	2.72;2.76;2.29;2.32;2.15	5.08	5.08	0.68730	.	0.272209	0.26560	N	0.023700	T	0.31136	0.0787	N	0.24115	0.695	0.30625	N	0.758055	D	0.76494	0.999	D	0.66847	0.947	T	0.15178	-1.0446	10	0.54805	T	0.06	-28.0135	14.6864	0.69052	0.0:0.0:0.0:1.0	.	122	Q8IXT5	RB12B_HUMAN	C	122	ENSP00000382239:Y122C;ENSP00000427729:Y122C;ENSP00000430474:Y122C;ENSP00000428269:Y122C;ENSP00000429807:Y122C	ENSP00000382239:Y122C	Y	-	2	0	RBM12B	94817450	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	2.239000	0.43079	2.132000	0.65825	0.533000	0.62120	TAT	.	.		0.438	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
ACAD8	27034	hgsc.bcm.edu	37	11	134131730	134131730	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr11:134131730T>C	ENST00000281182.4	+	9	1144	c.1038T>C	c.(1036-1038)gaT>gaC	p.D346D	ACAD8_ENST00000543332.1_3'UTR|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000374752.4_Silent_p.D219D|ACAD8_ENST00000537423.1_Silent_p.D269D	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	346					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	AGAGGAAGGATGCAGTGGCCT	0.562																																					p.D346D	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.T1038C						.						140.0	102.0	115.0					11																	134131730		2201	4297	6498	SO:0001819	synonymous_variant	27034	exon9			GAAGGATGCAGTG	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.1038T>C	chr11.hg19:g.134131730T>C		61.0	0.0		25.0	13.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	hg19	CCDS8498.1																																																																																			.	.		0.562	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
TAPBPL	55080	hgsc.bcm.edu	37	12	6570035	6570035	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:6570035T>G	ENST00000266556.7	+	6	1387	c.1222T>G	c.(1222-1224)Ttg>Gtg	p.L408V	TAPBPL_ENST00000545700.1_3'UTR|VAMP1_ENST00000544432.1_5'Flank	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	408					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GAGAACAGCCTTGGGAGTCAT	0.602																																					p.L408V		Atlas-SNP	.											.	TAPBPL	21	.	0			c.T1222G						.						219.0	165.0	183.0					12																	6570035		2203	4300	6503	SO:0001583	missense	55080	exon6			ACAGCCTTGGGAG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.1222T>G	chr12.hg19:g.6570035T>G	ENSP00000266556:p.Leu408Val	49.0	0.0		38.0	16.0	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	hg19	CCDS8546.1	.	.	.	.	.	.	.	.	.	.	T	8.380	0.837234	0.16891	.	.	ENSG00000139192	ENST00000266556	T	0.08102	3.13	5.24	1.35	0.21983	Immunoglobulin-like fold (1);	0.776617	0.12688	N	0.447397	T	0.04998	0.0134	L	0.38175	1.15	0.09310	N	1	B	0.26318	0.146	B	0.21360	0.034	T	0.44528	-0.9322	10	0.07030	T	0.85	-0.11	4.3505	0.11153	0.2938:0.0866:0.0:0.6196	.	408	Q9BX59	TPSNR_HUMAN	V	408	ENSP00000266556:L408V	ENSP00000266556:L408V	L	+	1	2	TAPBPL	6440296	0.001000	0.12720	0.001000	0.08648	0.488000	0.33401	0.454000	0.21827	0.117000	0.18138	0.533000	0.62120	TTG	.	.		0.602	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
R3HDM2	22864	hgsc.bcm.edu	37	12	57663679	57663679	+	Silent	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:57663679A>G	ENST00000347140.3	-	15	1791	c.1401T>C	c.(1399-1401)ctT>ctC	p.L467L	R3HDM2_ENST00000358907.2_Silent_p.L467L|R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000413953.2_Silent_p.L194L|R3HDM2_ENST00000402412.1_Silent_p.L481L|R3HDM2_ENST00000403821.2_Silent_p.L501L|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000441731.2_Silent_p.L162L			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	467	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GCTGGGAGATAAGTGGGGTCT	0.547																																					p.L467L		Atlas-SNP	.											.	R3HDM2	125	.	0			c.T1401C						.						126.0	113.0	117.0					12																	57663679		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon13			GGAGATAAGTGGG	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1401T>C	chr12.hg19:g.57663679A>G		69.0	0.0		63.0	18.0	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	hg19	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	A	14.69	2.611037	0.46631	.	.	ENSG00000179912	ENST00000466401	.	.	.	5.15	2.73	0.32206	.	0.173114	0.42548	N	0.000681	T	0.57007	0.2024	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54886	-0.8226	6	0.56958	D	0.05	-10.9705	3.8692	0.09029	0.5704:0.1795:0.2501:0.0	.	.	.	.	S	65	.	ENSP00000449326:L65S	L	-	2	0	R3HDM2	55949946	0.942000	0.31987	1.000000	0.80357	0.917000	0.54804	0.452000	0.21795	0.500000	0.27991	0.528000	0.53228	TTA	.	.		0.547	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
PAH	5053	hgsc.bcm.edu	37	12	103237549	103237549	+	Silent	SNP	T	T	C	rs376480977		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:103237549T>C	ENST00000553106.1	-	11	1546	c.1074A>G	c.(1072-1074)ttA>ttG	p.L358L	PAH_ENST00000307000.2_Silent_p.L353L	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	358					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCTTCTCTGATAAGCAGTACT	0.483																																					p.L358L		Atlas-SNP	.											.	PAH	77	.	0			c.A1074G						.						85.0	84.0	84.0					12																	103237549		2203	4300	6503	SO:0001819	synonymous_variant	5053	exon11			CTCTGATAAGCAG	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.1074A>G	chr12.hg19:g.103237549T>C		51.0	0.0		51.0	17.0	NM_000277	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	hg19	CCDS9092.1																																																																																			.	.		0.483	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
RPLP0	6175	hgsc.bcm.edu	37	12	120636498	120636498	+	Silent	SNP	G	G	A	rs138718343		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:120636498G>A	ENST00000551150.1	-	5	825	c.510C>T	c.(508-510)agC>agT	p.S170S	PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542265.1_RNA|RPLP0_ENST00000313104.5_Intron|PXN-AS1_ENST00000538804.1_RNA|RPLP0_ENST00000546989.1_Intron|RPLP0_ENST00000550296.1_5'Flank|RPLP0_ENST00000552292.1_5'Flank|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000392514.4_Silent_p.S170S|RPLP0_ENST00000228306.4_Silent_p.S170S			P05388	RLA0_HUMAN	ribosomal protein, large, P0	170					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGTGGCTTCGCTGGCTCCCA	0.527																																					p.S170S		Atlas-SNP	.											.	RPLP0	27	.	0			c.C510T						.	G	,	0,4406		0,0,2203	72.0	69.0	70.0		510,510	-0.5	1.0	12	dbSNP_134	70	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	,	170/318,170/318	120636498	3,12999	2203	4298	6501	SO:0001819	synonymous_variant	6175	exon6			GGCTTCGCTGGCT	AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"""L ribosomal proteins"""	10371	protein-coding gene	gene with protein product	"""acidic ribosomal phosphoprotein P0"""	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.510C>T	chr12.hg19:g.120636498G>A		68.0	0.0		52.0	16.0	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	hg19	CCDS9193.1																																																																																			.	G|1.000;A|0.000		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275	
ALG5	29880	hgsc.bcm.edu	37	13	37524129	37524129	+	Nonsense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:37524129G>A	ENST00000239891.3	-	10	991	c.925C>T	c.(925-927)Cga>Tga	p.R309*	ALG5_ENST00000443765.1_Nonsense_Mutation_p.R279*	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	309					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)	p.R309*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		GTCAAATATCGAAGTCGTATA	0.358																																					p.R309X		Atlas-SNP	.											ALG5,NS,carcinoma,0,3	ALG5	28	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C925T						.						85.0	83.0	84.0					13																	37524129		2203	4300	6503	SO:0001587	stop_gained	29880	exon10			AATATCGAAGTCG	AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"""Glycosyltransferase family 2 domain containing"""	20266	protein-coding gene	gene with protein product		604565	"""asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)"", ""asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"""			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.925C>T	chr13.hg19:g.37524129G>A	ENSP00000239891:p.Arg309*	52.0	0.0		31.0	16.0	NM_013338	B4DR37|Q5TBA6	Nonsense_Mutation	SNP	ENST00000239891.3	hg19	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245912	0.80024	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	.	.	.	5.86	5.01	0.66863	.	0.054432	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6453	0.62277	0.0:0.0:0.6013:0.3987	.	.	.	.	X	279;309	.	ENSP00000239891:R309X	R	-	1	2	ALG5	36422129	1.000000	0.71417	0.984000	0.44739	0.927000	0.56198	3.338000	0.52128	1.462000	0.47948	-0.182000	0.12963	CGA	.	.		0.358	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338	
PCDH17	27253	hgsc.bcm.edu	37	13	58299074	58299074	+	Silent	SNP	G	G	C	rs534412507		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:58299074G>C	ENST00000377918.3	+	4	3152	c.3126G>C	c.(3124-3126)gcG>gcC	p.A1042A		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	1042					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CAACCAAGGCGTGCATCGAGC	0.532																																					p.A1042A	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G3126C						.						85.0	84.0	84.0					13																	58299074		2203	4300	6503	SO:0001819	synonymous_variant	27253	exon4			CAAGGCGTGCATC	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.3126G>C	chr13.hg19:g.58299074G>C		68.0	0.0		37.0	17.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	hg19	CCDS31986.1																																																																																			.	.		0.532	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
TBC1D4	9882	hgsc.bcm.edu	37	13	75884197	75884197	+	Missense_Mutation	SNP	T	T	A	rs531614085	byFrequency	TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:75884197T>A	ENST00000377636.3	-	14	2820	c.2474A>T	c.(2473-2475)gAt>gTt	p.D825V	TBC1D4_ENST00000425511.1_Missense_Mutation_p.D42V|TBC1D4_ENST00000377625.2_Missense_Mutation_p.D762V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.D817V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	825					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TTCTGGGTCATCCTCCCCAGA	0.463													T|||	2	0.000399361	0.0	0.0	5008	,	,		17576	0.0		0.0	False		,,,				2504	0.002				p.D825V		Atlas-SNP	.											.	TBC1D4	142	.	0			c.A2474T						.						107.0	95.0	99.0					13																	75884197		1858	4094	5952	SO:0001583	missense	9882	exon14			GGGTCATCCTCCC	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2474A>T	chr13.hg19:g.75884197T>A	ENSP00000366863:p.Asp825Val	94.0	0.0		60.0	30.0	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	hg19	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392953	0.62066	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511;ENST00000413735	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;1.73	5.93	5.93	0.95920	.	0.244954	0.35436	N	0.003213	T	0.50854	0.1640	L	0.54323	1.7	0.52501	D	0.999954	B;B;B;P	0.40619	0.116;0.404;0.21;0.724	B;B;B;P	0.48063	0.046;0.281;0.124;0.565	T	0.48854	-0.8998	10	0.49607	T	0.09	-9.4382	16.3798	0.83452	0.0:0.0:0.0:1.0	.	42;762;817;825	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	V	825;817;762;42;274	ENSP00000366863:D825V;ENSP00000395986:D817V;ENSP00000366852:D762V;ENSP00000390654:D42V;ENSP00000396932:D274V	ENSP00000366852:D762V	D	-	2	0	TBC1D4	74782198	1.000000	0.71417	0.883000	0.34634	0.956000	0.61745	3.447000	0.52936	2.271000	0.75665	0.533000	0.62120	GAT	.	.		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
MAGEL2	54551	hgsc.bcm.edu	37	15	23889381	23889381	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:23889381C>A	ENST00000532292.1	-	1	1794	c.1700G>T	c.(1699-1701)aGg>aTg	p.R567M		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	450					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		AGGGATTCGCCTGTACTCTAG	0.502																																					p.R1170M		Atlas-SNP	.											.	MAGEL2	108	.	0			c.G3509T						.						49.0	49.0	49.0					15																	23889381		1910	4132	6042	SO:0001583	missense	54551	exon1			ATTCGCCTGTACT	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1700G>T	chr15.hg19:g.23889381C>A	ENSP00000433433:p.Arg567Met	50.0	0.0		27.0	12.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.88	2.963694	0.53507	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.57	3.64	0.41730	.	.	.	.	.	T	0.66307	0.2776	M	0.91406	3.205	0.22737	N	0.998791	.	.	.	.	.	.	T	0.60480	-0.7255	5	.	.	.	.	7.8955	0.29704	0.0:0.8906:0.0:0.1094	.	.	.	.	C	599	.	.	G	-	1	0	MAGEL2	21440474	0.657000	0.27393	0.914000	0.36105	0.909000	0.53808	0.950000	0.29122	2.545000	0.85829	0.462000	0.41574	GGC	.	.		0.502	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
PLCB2	5330	hgsc.bcm.edu	37	15	40584571	40584571	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:40584571C>T	ENST00000260402.3	-	22	2649	c.2400G>A	c.(2398-2400)gaG>gaA	p.E800E	PLCB2_ENST00000456256.2_Silent_p.E800E|PLCB2_ENST00000557821.1_Silent_p.E796E	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	800					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		AGTCCTTCATCTCCAGGAAGA	0.592																																					p.E800E		Atlas-SNP	.											.	PLCB2	177	.	0			c.G2400A						.						68.0	76.0	73.0					15																	40584571		2065	4204	6269	SO:0001819	synonymous_variant	5330	exon22			CTTCATCTCCAGG		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.2400G>A	chr15.hg19:g.40584571C>T		43.0	0.0		32.0	12.0	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	hg19	CCDS42020.1																																																																																			.	.		0.592	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
TP53	7157	hgsc.bcm.edu	37	17	7577509	7577509	+	Missense_Mutation	SNP	C	C	T	rs121912652		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:7577509C>T	ENST00000269305.4	-	7	961	c.772G>A	c.(772-774)Gaa>Aaa	p.E258K	TP53_ENST00000413465.2_Missense_Mutation_p.E258K|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.E258K|TP53_ENST00000359597.4_Missense_Mutation_p.E258K|TP53_ENST00000445888.2_Missense_Mutation_p.E258K|TP53_ENST00000420246.2_Missense_Mutation_p.E258K	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	258	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1978757}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E258K(40)|p.E258*(15)|p.E258Q(9)|p.0?(8)|p.?(1)|p.E258fs*85(1)|p.E258>XX(1)|p.E258fs*71(1)|p.E258fs*2(1)|p.E258_S260delEDS(1)|p.E258del(1)|p.T256fs*87(1)|p.E258L(1)|p.E258fs*87(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGGAGTCTTCCAGTGTGATG	0.587		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E258K	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000455263,brain,glioma,0,1	TP53	33396	.	82	Substitution - Missense(50)|Substitution - Nonsense(15)|Whole gene deletion(8)|Deletion - Frameshift(5)|Deletion - In frame(2)|Unknown(1)|Complex - insertion inframe(1)	large_intestine(14)|urinary_tract(10)|upper_aerodigestive_tract(7)|haematopoietic_and_lymphoid_tissue(7)|skin(7)|lung(6)|oesophagus(5)|central_nervous_system(4)|breast(4)|ovary(4)|bone(4)|stomach(2)|liver(2)|thyroid(1)|soft_tissue(1)|peritoneum(1)|biliary_tract(1)|endometrium(1)|pancreas(1)	c.G772A	GRCh37	CM900213	TP53	M	rs121912652	.						137.0	97.0	111.0					17																	7577509		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGTCTTCCAGTGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.772G>A	chr17.hg19:g.7577509C>T	ENSP00000269305:p.Glu258Lys	67.0	1.0		24.0	18.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896324	0.72639	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	4.62	3.62	0.41486	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99871	0.9939	M	0.92367	3.3	0.80722	A	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;0.999;1.0	D	0.96542	0.9401	9	0.87932	D	0	-21.9865	12.6215	0.56605	0.0:0.8318:0.1682:0.0	.	258;258;258;258;258	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	K	258;258;258;258;258;258;247;126	ENSP00000410739:E258K;ENSP00000352610:E258K;ENSP00000269305:E258K;ENSP00000398846:E258K;ENSP00000391127:E258K;ENSP00000391478:E258K;ENSP00000425104:E126K	ENSP00000269305:E258K	E	-	1	0	TP53	7518234	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	7.609000	0.82925	1.266000	0.44231	0.462000	0.41574	GAA	.	.		0.587	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
MRPL45	84311	hgsc.bcm.edu	37	17	36478418	36478418	+	Silent	SNP	G	G	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:36478418G>C	ENST00000312513.5	+	8	1022	c.861G>C	c.(859-861)ctG>ctC	p.L287L	GPR179_ENST00000584976.1_5'Flank	NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	287						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GCCCTCAGCTGAAACCAGAAG	0.542											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L287L		Atlas-SNP	.											.	MRPL45	27	.	0			c.G861C						.						67.0	67.0	67.0					17																	36478418		2203	4300	6503	SO:0001819	synonymous_variant	84311	exon8			TCAGCTGAAACCA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.861G>C	chr17.hg19:g.36478418G>C		51.0	0.0	863	41.0	20.0	NM_032351	A1L436|Q6ZMJ5	Silent	SNP	ENST00000312513.5	hg19	CCDS11326.1																																																																																			.	.		0.542	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
CISD3	284106	hgsc.bcm.edu	37	17	36887631	36887631	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:36887631A>C	ENST00000439660.2	+	3	267	c.143A>C	c.(142-144)aAg>aCg	p.K48T	RNA5SP440_ENST00000363245.1_RNA|CISD3_ENST00000578573.1_3'UTR	NM_001136498.1	NP_001129970.1	P0C7P0	CISD3_HUMAN	CDGSH iron sulfur domain 3	48						mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			endometrium(2)	2						ACCCCCATCAAGGTGGAGCTG	0.612																																					p.K48T		Atlas-SNP	.											.	CISD3	12	.	0			c.A143C						.						88.0	98.0	95.0					17																	36887631		692	1591	2283	SO:0001583	missense	284106	exon3			CCATCAAGGTGGA	AK097047	CCDS45662.1	17q12	2007-08-10				ENSG00000277972		"""CDGSH iron sulfur domain containing"""	27578	protein-coding gene	gene with protein product	"""mitoNEET related 2"""	611933				17376863, 17584744	Standard	NM_001136498		Approved	Miner2	uc010wds.1	P0C7P0		ENST00000439660.2:c.143A>C	chr17.hg19:g.36887631A>C	ENSP00000391402:p.Lys48Thr	38.0	0.0		22.0	11.0	NM_001136498		Missense_Mutation	SNP	ENST00000439660.2	hg19	CCDS45662.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.405223	0.62288	.	.	ENSG00000230055	ENST00000439660	.	.	.	4.86	2.62	0.31277	Iron sulphur-containing domain, CDGSH-type, subfamily (1);Iron sulphur-containing domain, CDGSH-type (1);	.	.	.	.	T	0.50854	0.1640	L	0.61387	1.9	0.32514	N	0.537194	P	0.43231	0.801	P	0.49012	0.598	T	0.59904	-0.7366	8	0.87932	D	0	-3.5241	6.1161	0.20127	0.7857:0.0:0.2143:0.0	.	48	P0C7P0	CISD3_HUMAN	T	48	.	ENSP00000391402:K48T	K	+	2	0	CISD3	34141157	0.997000	0.39634	0.995000	0.50966	0.816000	0.46133	1.512000	0.35812	0.242000	0.21303	0.454000	0.30748	AAG	.	.		0.612	CISD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441921.1		
FAM104A	84923	hgsc.bcm.edu	37	17	71208818	71208818	+	Intron	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:71208818G>A	ENST00000403627.3	-	3	382				FAM104A_ENST00000405159.3_Splice_Site_p.A128V|FAM104A_ENST00000583178.1_Intron|FAM104A_ENST00000583024.1_Intron|FAM104A_ENST00000580032.1_Splice_Site_p.A17V|FAM104A_ENST00000581110.1_Intron	NM_032837.2	NP_116226.2	Q969W3	F104A_HUMAN	family with sequence similarity 104, member A											endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			LUSC - Lung squamous cell carcinoma(166;0.197)			GAAACCCACCGCGCAGAACGC	0.393																																					p.A128V		Atlas-SNP	.											.	FAM104A	15	.	0			c.C383T						.						145.0	141.0	142.0					17																	71208818		1872	4095	5967	SO:0001627	intron_variant	84923	exon3			CCCACCGCGCAGA	AK027681	CCDS11693.2, CCDS45766.1, CCDS74143.1, CCDS74144.1	17q25.1	2005-12-16			ENSG00000133193	ENSG00000133193			25918	protein-coding gene	gene with protein product							Standard	NM_032837		Approved	FLJ14775	uc002jjj.4	Q969W3	OTTHUMG00000150564	ENST00000403627.3:c.322-2911C>T	chr17.hg19:g.71208818G>A		105.0	0.0		88.0	29.0	NM_001098832	B4E339	Missense_Mutation	SNP	ENST00000403627.3	hg19	CCDS11693.2	.	.	.	.	.	.	.	.	.	.	G	8.869	0.948798	0.18356	.	.	ENSG00000133193	ENST00000405159	T	0.46819	0.86	5.17	-2.07	0.07276	.	.	.	.	.	T	0.33118	0.0852	.	.	.	0.39723	D	0.971497	B	0.15719	0.014	B	0.09377	0.004	T	0.03175	-1.1064	8	0.48119	T	0.1	.	7.2665	0.26232	0.3617:0.1142:0.5241:0.0	.	128	Q969W3-2	.	V	128	ENSP00000384832:A128V	ENSP00000384832:A128V	A	-	2	0	FAM104A	68720413	0.302000	0.24454	0.016000	0.15963	0.653000	0.38743	0.098000	0.15189	-0.849000	0.04158	-1.731000	0.00696	GCG	.	.		0.393	FAM104A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318935.1	NM_032837	
EXOC7	23265	hgsc.bcm.edu	37	17	74085293	74085293	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:74085293T>A	ENST00000335146.7	-	9	1216	c.1163A>T	c.(1162-1164)gAg>gTg	p.E388V	EXOC7_ENST00000411744.2_Missense_Mutation_p.E329V|EXOC7_ENST00000405575.4_Missense_Mutation_p.E360V|EXOC7_ENST00000607838.1_Missense_Mutation_p.E360V|EXOC7_ENST00000467929.2_Missense_Mutation_p.E296V|EXOC7_ENST00000589210.1_Missense_Mutation_p.E337V|EXOC7_ENST00000332065.5_Missense_Mutation_p.E306V			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	388					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTGGTGGTGCTCGGGGATGAT	0.627																																					p.E388V		Atlas-SNP	.											.	EXOC7	47	.	0			c.A1163T						.						105.0	105.0	105.0					17																	74085293		2203	4300	6503	SO:0001583	missense	23265	exon9			TGGTGCTCGGGGA	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1163A>T	chr17.hg19:g.74085293T>A	ENSP00000334100:p.Glu388Val	40.0	0.0		35.0	16.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758980	0.89843	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.98	4.98	0.66077	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.72574	0.3477	M	0.70595	2.14	0.80722	D	1	P;B;D;P;B;P;B	0.57571	0.572;0.24;0.98;0.727;0.03;0.835;0.24	B;B;P;B;B;P;B	0.56088	0.349;0.092;0.791;0.266;0.045;0.65;0.062	T	0.73681	-0.3906	9	0.39692	T	0.17	-34.598	14.6773	0.68989	0.0:0.0:0.0:1.0	.	329;360;296;296;388;306;337	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	V	306;226;360;388;337;296;329	.	ENSP00000333806:E306V	E	-	2	0	EXOC7	71596888	1.000000	0.71417	0.992000	0.48379	0.935000	0.57460	7.571000	0.82399	1.864000	0.54056	0.455000	0.32223	GAG	.	.		0.627	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
MIB1	57534	hgsc.bcm.edu	37	18	19359600	19359600	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr18:19359600A>T	ENST00000261537.6	+	6	1126	c.862A>T	c.(862-864)Att>Ttt	p.I288F	AC091038.1_ENST00000582102.1_RNA|MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	288					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			TGTTTGTGGCATTGATGAAGA	0.378																																					p.I288F		Atlas-SNP	.											.	MIB1	87	.	0			c.A862T						.						303.0	266.0	279.0					18																	19359600		2203	4300	6503	SO:0001583	missense	57534	exon6			TGTGGCATTGATG	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	21086	protein-coding gene	gene with protein product		608677	"""mindbomb homolog 1 (Drosophila)"""				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.862A>T	chr18.hg19:g.19359600A>T	ENSP00000261537:p.Ile288Phe	180.0	0.0		149.0	54.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	hg19	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802349	0.70682	.	.	ENSG00000101752	ENST00000261537	T	0.44482	0.92	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.84326	2.69	0.80722	D	1	P	0.40431	0.717	P	0.49047	0.599	T	0.65335	-0.6193	10	0.62326	D	0.03	-13.8232	14.365	0.66801	1.0:0.0:0.0:0.0	.	288	Q86YT6	MIB1_HUMAN	F	288	ENSP00000261537:I288F	ENSP00000261537:I288F	I	+	1	0	MIB1	17613598	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.279000	0.95777	1.869000	0.54173	0.240000	0.17902	ATT	.	.		0.378	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774	
CDH7	1005	hgsc.bcm.edu	37	18	63526260	63526260	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr18:63526260G>T	ENST00000397968.2	+	9	1898	c.1472G>T	c.(1471-1473)tGt>tTt	p.C491F	CDH7_ENST00000323011.3_Missense_Mutation_p.C491F|CDH7_ENST00000536984.2_Missense_Mutation_p.C491F	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	491	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				ACCACCGTCTGTGAAAATGCC	0.438																																					p.C491F		Atlas-SNP	.											.	CDH7	362	.	0			c.G1472T						.						76.0	74.0	75.0					18																	63526260		2203	4300	6503	SO:0001583	missense	1005	exon9			CCGTCTGTGAAAA	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1472G>T	chr18.hg19:g.63526260G>T	ENSP00000381058:p.Cys491Phe	164.0	0.0		127.0	49.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575129	0.86542	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.53423	0.62;0.62;0.62	5.32	5.32	0.75619	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.75880	-0.3161	10	0.87932	D	0	.	19.347	0.94367	0.0:0.0:1.0:0.0	.	491;491	F5H5X9;Q9ULB5	.;CADH7_HUMAN	F	491	ENSP00000319166:C491F;ENSP00000443030:C491F;ENSP00000381058:C491F	ENSP00000319166:C491F	C	+	2	0	CDH7	61677240	1.000000	0.71417	0.961000	0.40146	0.978000	0.69477	9.666000	0.98612	2.648000	0.89879	0.467000	0.42956	TGT	.	.		0.438	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
SIRT2	22933	hgsc.bcm.edu	37	19	39374291	39374291	+	Missense_Mutation	SNP	C	C	T	rs200953200		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:39374291C>T	ENST00000249396.7	-	9	908	c.607G>A	c.(607-609)Gaa>Aaa	p.E203K	SIRT2_ENST00000392081.2_Missense_Mutation_p.E166K|SIRT2_ENST00000358931.5_Missense_Mutation_p.E203K	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	203	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			AGCGGGTATTCGTGCCGGCAG	0.617																																					p.E203K		Atlas-SNP	.											.	SIRT2	29	.	0			c.G607A						.						88.0	72.0	78.0					19																	39374291		2203	4300	6503	SO:0001583	missense	22933	exon9			GGTATTCGTGCCG	AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2"", ""sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"""	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.607G>A	chr19.hg19:g.39374291C>T	ENSP00000249396:p.Glu203Lys	64.0	0.0		36.0	15.0	NM_012237	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	hg19	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165115	0.38217	.	.	ENSG00000068903	ENST00000249396;ENST00000392081;ENST00000358931;ENST00000456703;ENST00000414941;ENST00000407552	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;2.29	4.31	4.31	0.51392	.	0.197758	0.40554	N	0.001067	T	0.23370	0.0565	N	0.16266	0.395	0.53005	D	0.999969	B;B;B;B	0.32409	0.196;0.125;0.37;0.24	B;B;B;B	0.27262	0.015;0.008;0.078;0.01	T	0.06625	-1.0816	10	0.25106	T	0.35	-9.9569	10.3892	0.44158	0.0:0.9032:0.0:0.0968	.	203;166;203;183	Q8IXJ6-4;Q8IXJ6-2;Q8IXJ6;Q8IXJ6-3	.;.;SIRT2_HUMAN;.	K	203;166;203;188;166;166	ENSP00000249396:E203K;ENSP00000375931:E166K;ENSP00000351809:E203K;ENSP00000404309:E166K;ENSP00000385146:E166K	ENSP00000249396:E203K	E	-	1	0	SIRT2	44066131	0.960000	0.32886	0.736000	0.30914	0.274000	0.26718	2.146000	0.42216	2.405000	0.81733	0.491000	0.48974	GAA	.	.		0.617	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1		
PLD3	23646	hgsc.bcm.edu	37	19	40872766	40872766	+	Silent	SNP	C	C	T	rs375652785		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:40872766C>T	ENST00000409587.1	+	5	586	c.189C>T	c.(187-189)ggC>ggT	p.G63G	PLD3_ENST00000356508.5_Silent_p.G63G|PLD3_ENST00000409419.1_Silent_p.G63G|PLD3_ENST00000409735.4_Silent_p.G63G|PLD3_ENST00000409281.1_Silent_p.G63G			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	63					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			GGGAATACGGCGACTTGCATC	0.627																																					p.G63G		Atlas-SNP	.											.	PLD3	71	.	0			c.C189T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	73.0	69.0	71.0		189,189	-5.5	0.9	19		71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLD3	NM_001031696.2,NM_012268.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	63/491,63/491	40872766	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23646	exon5			ATACGGCGACTTG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.189C>T	chr19.hg19:g.40872766C>T		49.0	0.0		33.0	16.0	NM_012268	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	hg19	CCDS33027.1																																																																																			.	.		0.627	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
CEACAM8	1088	hgsc.bcm.edu	37	19	43098033	43098033	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:43098033C>A	ENST00000244336.5	-	2	185	c.84G>T	c.(82-84)tgG>tgT	p.W28C	LIPE-AS1_ENST00000594688.1_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	28					immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				TGGGCGGGTTCCAGAAGGTGA	0.502																																					p.W28C		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G84T						.						105.0	98.0	100.0					19																	43098033		2203	4300	6503	SO:0001583	missense	1088	exon2			CGGGTTCCAGAAG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.84G>T	chr19.hg19:g.43098033C>A	ENSP00000244336:p.Trp28Cys	42.0	0.0		44.0	19.0	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	hg19	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.157915	0.38119	.	.	ENSG00000124469	ENST00000244336	T	0.22336	1.96	1.63	1.63	0.23807	.	.	.	.	.	T	0.35740	0.0942	M	0.66939	2.045	0.20638	N	0.999872	D	0.56035	0.974	P	0.60117	0.869	T	0.07462	-1.0771	9	0.87932	D	0	.	6.707	0.23257	0.0:1.0:0.0:0.0	.	28	P31997	CEAM8_HUMAN	C	28	ENSP00000244336:W28C	ENSP00000244336:W28C	W	-	3	0	CEACAM8	47789873	0.516000	0.26218	0.146000	0.22360	0.618000	0.37518	1.947000	0.40293	1.205000	0.43262	0.313000	0.20887	TGG	.	.		0.502	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
PSG9	5678	hgsc.bcm.edu	37	19	43762554	43762554	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:43762554T>C	ENST00000270077.3	-	5	1139	c.1043A>G	c.(1042-1044)gAa>gGa	p.E348G	PSG9_ENST00000418820.2_Missense_Mutation_p.E255G|PSG9_ENST00000443718.3_Missense_Mutation_p.E255G|PSG9_ENST00000244293.7_Missense_Mutation_p.E255G|PSG9_ENST00000593948.1_Missense_Mutation_p.E255G|PSG9_ENST00000596730.1_Missense_Mutation_p.E162G|PSG9_ENST00000291752.5_Missense_Mutation_p.E162G	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	348	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GTCGAGGTTTTCTCCTGAACG	0.453																																					p.E348G		Atlas-SNP	.											.	PSG9	77	.	0			c.A1043G						.						134.0	163.0	153.0					19																	43762554		2137	4278	6415	SO:0001583	missense	5678	exon5			AGGTTTTCTCCTG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.1043A>G	chr19.hg19:g.43762554T>C	ENSP00000270077:p.Glu348Gly	32.0	0.0		20.0	13.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	10.10	1.257419	0.22965	.	.	ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	1.58	-2.54	0.06307	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19446	0.0467	L	0.43757	1.38	0.09310	N	1	P;D;P;P;B;P	0.53745	0.729;0.962;0.87;0.951;0.001;0.602	P;D;P;P;B;P	0.64410	0.791;0.925;0.654;0.823;0.053;0.73	T	0.13872	-1.0493	9	0.59425	D	0.04	.	2.2184	0.03966	0.2161:0.0:0.4831:0.3008	.	255;204;255;162;348;348	E7EW65;Q15225;Q15227;G3XAA7;Q6LEU7;Q00887	.;.;.;.;.;PSG9_HUMAN	G	348;162;255;309;255	ENSP00000270077:E348G;ENSP00000291752:E162G;ENSP00000396753:E255G;ENSP00000244293:E255G	ENSP00000244293:E255G	E	-	2	0	PSG9	48454394	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.759000	0.04761	-0.634000	0.05538	0.163000	0.16589	GAA	.	.		0.453	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
ZNF677	342926	hgsc.bcm.edu	37	19	53740390	53740390	+	Silent	SNP	G	G	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:53740390G>C	ENST00000598513.1	-	5	1740	c.1590C>G	c.(1588-1590)ctC>ctG	p.L530L	ZNF677_ENST00000333952.4_Silent_p.L530L	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GGTGTCTAGTGAGGTTTGCAA	0.333																																					p.L530L		Atlas-SNP	.											.	ZNF677	94	.	0			c.C1590G						.						134.0	127.0	130.0					19																	53740390		2203	4299	6502	SO:0001819	synonymous_variant	342926	exon5			TCTAGTGAGGTTT	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1590C>G	chr19.hg19:g.53740390G>C		229.0	0.0		157.0	68.0	NM_182609		Silent	SNP	ENST00000598513.1	hg19	CCDS12861.1																																																																																			.	.		0.333	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
NLRP12	91662	hgsc.bcm.edu	37	19	54307234	54307234	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:54307234G>T	ENST00000324134.6	-	6	2725	c.2557C>A	c.(2557-2559)Cac>Aac	p.H853N	NLRP12_ENST00000354278.3_Missense_Mutation_p.H853N|NLRP12_ENST00000535162.1_Missense_Mutation_p.H853N|NLRP12_ENST00000345770.5_Missense_Mutation_p.H854N|NLRP12_ENST00000391773.1_Missense_Mutation_p.H854N|NLRP12_ENST00000391772.1_Missense_Mutation_p.H854N|NLRP12_ENST00000351894.4_Missense_Mutation_p.H853N|NLRP12_ENST00000391775.3_Missense_Mutation_p.H853N	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	853					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CAGACTGGGTGCCTCAGTCCC	0.478																																					p.C853S		Atlas-SNP	.											.	NLRP12	236	.	0			c.T2557A						.						85.0	70.0	75.0					19																	54307234		2203	4300	6503	SO:0001583	missense	91662	exon6			CTGGGTGCCTCAG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2557C>A	chr19.hg19:g.54307234G>T	ENSP00000319377:p.His853Asn	50.0	0.0		30.0	10.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533586	0.27387	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000358661;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.49432	1.05;1.05;0.78;0.78;1.05;1.05;0.78	4.52	2.3	0.28687	.	0.458810	0.15793	N	0.244365	T	0.40909	0.1136	L	0.45698	1.435	0.09310	N	1	B;B;B;B;B	0.20368	0.009;0.044;0.005;0.009;0.006	B;B;B;B;B	0.24155	0.012;0.051;0.011;0.012;0.023	T	0.39057	-0.9632	10	0.56958	D	0.05	.	10.1919	0.43032	0.0:0.0:0.6431:0.3569	.	854;136;853;853;853	F2Z321;P59046-5;A8K407;A8MTQ2;P59046	.;.;.;.;NAL12_HUMAN	N	853;853;853;853;136;853;854;854;854	ENSP00000319377:H853N;ENSP00000438030:H853N;ENSP00000340473:H853N;ENSP00000346231:H853N;ENSP00000375655:H853N;ENSP00000375653:H854N;ENSP00000375652:H854N	ENSP00000319377:H853N	H	-	1	0	NLRP12	58999046	0.167000	0.22975	0.014000	0.15608	0.640000	0.38277	1.890000	0.39728	0.576000	0.29452	0.442000	0.29010	CAC	.	.		0.478	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
TCF15	6939	hgsc.bcm.edu	37	20	585251	585251	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:585251C>A	ENST00000246080.3	-	2	744	c.584G>T	c.(583-585)cGa>cTa	p.R195L		NM_004609.3	NP_004600.2	Q12870	TCF15_HUMAN	transcription factor 15 (basic helix-loop-helix)	195					death (GO:0016265)|ear development (GO:0043583)|eating behavior (GO:0042755)|establishment of epithelial cell apical/basal polarity (GO:0045198)|mesenchymal to epithelial transition (GO:0060231)|mesoderm development (GO:0007498)|muscle organ morphogenesis (GO:0048644)|neuromuscular process controlling posture (GO:0050884)|paraxial mesoderm development (GO:0048339)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression involved in extracellular matrix organization (GO:1901311)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|lung(2)|prostate(1)	4		Breast(17;0.231)				CCGTGGCCCTCGAAGGGGGGC	0.642																																					p.R195L		Atlas-SNP	.											.	TCF15	6	.	0			c.G584T						.						11.0	12.0	12.0					20																	585251		2121	4169	6290	SO:0001583	missense	6939	exon2			GGCCCTCGAAGGG		CCDS33432.1	20p13	2013-05-21			ENSG00000125878	ENSG00000125878		"""Basic helix-loop-helix proteins"""	11627	protein-coding gene	gene with protein product		601010				8825648, 8041747	Standard	NM_004609		Approved	EC2, PARAXIS, bHLHa40	uc002wdz.3	Q12870	OTTHUMG00000031640	ENST00000246080.3:c.584G>T	chr20.hg19:g.585251C>A	ENSP00000246080:p.Arg195Leu	82.0	0.0		80.0	36.0	NM_004609	Q9NQQ1	Missense_Mutation	SNP	ENST00000246080.3	hg19	CCDS33432.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190772	0.78789	.	.	ENSG00000125878	ENST00000246080	D	0.96265	-3.96	5.08	4.13	0.48395	.	0.000000	0.64402	D	0.000003	D	0.96975	0.9012	L	0.55481	1.735	0.30769	N	0.743195	D	0.63880	0.993	D	0.67725	0.953	D	0.95442	0.8526	10	0.72032	D	0.01	-1.0614	13.52	0.61561	0.0:0.8441:0.1559:0.0	.	195	Q12870	TCF15_HUMAN	L	195	ENSP00000246080:R195L	ENSP00000246080:R195L	R	-	2	0	TCF15	533251	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	4.235000	0.58666	1.489000	0.48450	0.655000	0.94253	CGA	.	.		0.642	TCF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077475.2	NM_004609	
SLC4A11	83959	hgsc.bcm.edu	37	20	3209657	3209657	+	Splice_Site	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:3209657C>A	ENST00000380056.3	-	16	2114	c.2067G>T	c.(2065-2067)agG>agT	p.R689S	SLC4A11_ENST00000488544.1_5'UTR|SLC4A11_ENST00000380059.3_Splice_Site_p.R716S|SLC4A11_ENST00000539553.2_Splice_Site_p.R673S	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	689	Membrane (bicarbonate transporter).				bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						CCTTCACCAGCCTGCAGCAGA	0.657																																					p.R716S	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G2148T						.						85.0	71.0	76.0					20																	3209657		2202	4300	6502	SO:0001630	splice_region_variant	83959	exon17			CACCAGCCTGCAG	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2067-1G>T	chr20.hg19:g.3209657C>A		18.0	0.0		21.0	10.0	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	hg19	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085299	0.76642	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	T;T;T	0.78924	-1.22;-1.22;-1.22	4.93	2.99	0.34606	Bicarbonate transporter, C-terminal (1);	0.096978	0.64402	D	0.000001	D	0.82600	0.5072	M	0.69185	2.1	0.80722	D	1	P;P;P	0.49635	0.909;0.926;0.844	P;P;P	0.56612	0.701;0.802;0.73	T	0.82961	-0.0197	10	0.87932	D	0	.	11.3086	0.49351	0.0:0.8502:0.0:0.1498	.	673;716;689	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	S	716;689;673	ENSP00000369399:R716S;ENSP00000369396:R689S;ENSP00000441370:R673S	ENSP00000369396:R689S	R	-	3	2	SLC4A11	3157657	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	4.877000	0.63086	0.606000	0.29965	0.462000	0.41574	AGG	.	.		0.657	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		Missense_Mutation
AAR2	25980	hgsc.bcm.edu	37	20	34828481	34828481	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:34828481G>A	ENST00000373932.3	+	2	1037	c.691G>A	c.(691-693)Gac>Aac	p.D231N	AAR2_ENST00000320849.4_Missense_Mutation_p.D231N|AAR2_ENST00000397286.3_Missense_Mutation_p.D231N	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	231																	GCACAGCATGGACCTGAGCTA	0.592																																					p.D231N		Atlas-SNP	.											.	.	.	.	0			c.G691A						.						36.0	36.0	36.0					20																	34828481		2203	4300	6503	SO:0001583	missense	25980	exon2			AGCATGGACCTGA		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 4"""	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.691G>A	chr20.hg19:g.34828481G>A	ENSP00000363043:p.Asp231Asn	55.0	0.0		40.0	13.0	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	hg19	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184603	0.94885	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.70045	-0.45;-0.45;-0.45	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.84862	0.5566	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87452	0.2402	10	0.87932	D	0	.	17.8963	0.88890	0.0:0.0:1.0:0.0	.	231;231	A2A2Q9;Q9Y312	.;CT004_HUMAN	N	231	ENSP00000380455:D231N;ENSP00000313674:D231N;ENSP00000363043:D231N	ENSP00000313674:D231N	D	+	1	0	C20orf4	34291895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.959000	0.93110	2.775000	0.95449	0.655000	0.94253	GAC	.	.		0.592	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511	
NLGN3	54413	hgsc.bcm.edu	37	X	70389592	70389592	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:70389592A>G	ENST00000358741.3	+	8	2495	c.2192A>G	c.(2191-2193)tAc>tGc	p.Y731C	NLGN3_ENST00000536169.1_Missense_Mutation_p.Y691C|NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000374051.3_Missense_Mutation_p.Y711C	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	731					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					GCCCTCTACTACCGTAAGGAC	0.642																																					p.Y731C	Esophageal Squamous(103;760 1488 16849 22250 40351)	Atlas-SNP	.											.	NLGN3	159	.	0			c.A2192G						.						28.0	25.0	26.0					X																	70389592		2203	4300	6503	SO:0001583	missense	54413	exon8			TCTACTACCGTAA	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.2192A>G	chrX.hg19:g.70389592A>G	ENSP00000351591:p.Tyr731Cys	36.0	0.0		23.0	20.0	NM_181303	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Missense_Mutation	SNP	ENST00000358741.3	hg19	CCDS55441.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.373920	0.61735	.	.	ENSG00000196338	ENST00000536169;ENST00000374051;ENST00000358741	T;T;T	0.78481	-1.18;-1.18;-1.18	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.88698	0.6507	M	0.86268	2.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.90571	0.4522	10	0.87932	D	0	.	14.0645	0.64819	1.0:0.0:0.0:0.0	.	691;731;711	D3DVV1;Q9NZ94;Q9NZ94-2	.;NLGN3_HUMAN;.	C	691;711;731	ENSP00000445298:Y691C;ENSP00000363163:Y711C;ENSP00000351591:Y731C	ENSP00000351591:Y731C	Y	+	2	0	NLGN3	70306317	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	9.139000	0.94554	1.897000	0.54924	0.352000	0.21897	TAC	.	.		0.642	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977	
MAGEC3	139081	hgsc.bcm.edu	37	X	140953292	140953292	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:140953292C>T	ENST00000298296.1	+	2	159	c.159C>T	c.(157-159)gcC>gcT	p.A53A		NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	53								p.A53A(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					ACTATTCTGCCTTTCATCTTG	0.512																																					p.A53A		Atlas-SNP	.											.	MAGEC3	228	.	1	Substitution - coding silent(1)	kidney(1)	c.C159T						.						190.0	150.0	164.0					X																	140953292		2203	4300	6503	SO:0001819	synonymous_variant	139081	exon2			TTCTGCCTTTCAT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.159C>T	chrX.hg19:g.140953292C>T		59.0	0.0		30.0	23.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.512	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
MT-ND5	4540	hgsc.bcm.edu	37	M	12419	12419	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrM:12419A>T	ENST00000361567.2	+	1	83	c.83A>T	c.(82-84)aAa>aTa	p.K28I	MT-TE_ENST00000387459.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	28					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TAACCCTAACAAAAAAAACTC	0.413																																					p.K28M		Atlas-SNP	.											.	.	.	.	0			c.A83T						.																																			SO:0001583	missense	0	exon1			CTAACAAAAAAAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.83A>T	chrM.hg19:g.12419A>T	ENSP00000354813:p.Lys28Ile	201.0	1.0		119.0	107.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.413	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MTSS1	9788	hgsc.bcm.edu	37	8	125565827	125565828	+	In_Frame_Ins	INS	-	-	TAT			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr8:125565827_125565828insTAT	ENST00000518547.1	-	14	2146_2147	c.1673_1674insATA	c.(1672-1674)tac>taATAc	p.557_558ins*	MTSS1_ENST00000354184.4_In_Frame_Ins_p.275_276ins*|MTSS1_ENST00000524090.1_In_Frame_Ins_p.447_448ins*|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000395508.2_In_Frame_Ins_p.331_332ins*|MTSS1_ENST00000378017.3_In_Frame_Ins_p.532_533ins*|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000431961.2_In_Frame_Ins_p.275_276ins*|MTSS1_ENST00000325064.5_In_Frame_Ins_p.561_562ins*	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	557					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ACATCCGTCGGTAGGACTGGCT	0.55																																					p.Y558delinsX	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-Indel,Pindel	.											.	MTSS1	79	.	0			c.1674_1675insATA						.																																			SO:0001652	inframe_insertion	9788	exon14			.	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1673_1674insATA	chr8.hg19:g.125565827_125565828insTAT	ENSP00000429064:p.Tyr558*	121.0	0.0		96.0	33.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	In_Frame_Ins	INS	ENST00000518547.1	hg19	CCDS6353.1																																																																																			.	.		0.550	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
CAPN3	825	hgsc.bcm.edu	37	15	42698136	42698151	+	Splice_Site	DEL	ACCAAGGTAGGTGTGT	ACCAAGGTAGGTGTGT	-	rs373194123		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	ACCAAGGTAGGTGTGT	ACCAAGGTAGGTGTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:42698136_42698151delACCAAGGTAGGTGTGT	ENST00000397163.3	+	15	2014_2019	c.1795_1800delACCAAGGTAGGTGTGT	c.(1795-1800)accaagdel	p.TK599fs	CAPN3_ENST00000397200.4_Splice_Site_p.TK87fs|CAPN3_ENST00000349748.3_Intron|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000569136.1_5'UTR|CAPN3_ENST00000561817.1_Intron|CAPN3_ENST00000357568.3_Intron|CAPN3_ENST00000397204.4_5'UTR|CAPN3_ENST00000337571.4_Intron|CAPN3_ENST00000318023.7_Intron|CAPN3_ENST00000356316.3_Intron	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	599	Linker.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AAAGAAAAAAACCAAGGTAGGTGTGTGGGTAGAGAG	0.431																																					p.598_600del		Atlas-Indel,Pindel	.											.	CAPN3	172	.	0			c.1794_1800del	GRCh37	CI983047|CS052038	CAPN3	I|S	rs80338803	.																																			SO:0001630	splice_region_variant	825	exon15			.	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1800+1ACCAAGGTAGGTGTGT>-	chr15.hg19:g.42698136_42698151delACCAAGGTAGGTGTGT		148.0	0.0		57.0	17.0	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Frame_Shift_Del	DEL	ENST00000397163.3	hg19	CCDS45245.1																																																																																			.	.		0.431	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		Frame_Shift_Del
KMT2D	8085	hgsc.bcm.edu	37	12	49425062	49425062	+	Frame_Shift_Del	DEL	T	T	-			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:49425062delT	ENST00000301067.7	-	39	13425	c.13426delA	c.(13426-13428)actfs	p.T4476fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4476					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCCCGCCCAGTGCTGAGTTGC	0.607																																					p.T4476fs		Atlas-Indel,Pindel	.											.	MLL2	1173	.	0			c.13427delC						.						71.0	77.0	75.0					12																	49425062		2049	4201	6250	SO:0001589	frameshift_variant	8085	exon39			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.13426delA	chr12.hg19:g.49425062delT	ENSP00000301067:p.Thr4476fs	53.0	0.0		40.0	20.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.607	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
CCDC73	493860	hgsc.bcm.edu	37	11	32657339	32657339	+	Frame_Shift_Del	DEL	T	T	-			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr11:32657339delT	ENST00000335185.5	-	14	1131	c.1088delA	c.(1087-1089)aatfs	p.N363fs	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	363										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TGATAATTCATTTTTAATCTT	0.244																																					p.X363X		Atlas-Indel,Pindel	.											.	CCDC73	136	.	0			c.1089delA						.						38.0	35.0	36.0					11																	32657339		1763	4012	5775	SO:0001589	frameshift_variant	493860	exon14			.	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1088delA	chr11.hg19:g.32657339delT	ENSP00000335325:p.Asn363fs	118.0	0.0		67.0	38.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	In_Frame_Del	DEL	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.244	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
BBX	56987	hgsc.bcm.edu	37	3	107491784	107491817	+	Frame_Shift_Del	DEL	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	-	rs113054196|rs566303124|rs557240456		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:107491784_107491817delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	ENST00000325805.8	+	11	1503_1536	c.1216_1249delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	c.(1216-1251)tttcctgatttttcttattctgccagtagcaagatafs	p.FPDFSYSASSKI406fs	BBX_ENST00000406780.1_Frame_Shift_Del_p.FPDFSYSASSKI406fs|BBX_ENST00000416476.2_Intron|BBX_ENST00000402543.1_Frame_Shift_Del_p.FPDFSYSASSKI406fs|BBX_ENST00000415149.2_Frame_Shift_Del_p.FPDFSYSASSKI406fs			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	406					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			ATGTAGTCATTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGATAATAATTAG	0.355																																					p.405_416del		Pindel	.											.	BBX	156	.	0			c.1215_1248del						.																																			SO:0001589	frameshift_variant	56987	exon11			.	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1216_1249delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	chr3.hg19:g.107491784_107491817delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	ENSP00000319974:p.Phe406fs	129.0	0.0		69.0	19.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Frame_Shift_Del	DEL	ENST00000325805.8	hg19	CCDS46881.1																																																																																			.	.		0.355	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
FMR1	2332	hgsc.bcm.edu	37	X	147014260	147014260	+	Frame_Shift_Del	DEL	A	A	-			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:147014260delA	ENST00000370475.4	+	9	986	c.858delA	c.(856-858)atafs	p.I286fs	FMR1_ENST00000439526.2_Frame_Shift_Del_p.I286fs|FMR1_ENST00000370470.1_Frame_Shift_Del_p.I286fs|FMR1_ENST00000370477.1_Frame_Shift_Del_p.I286fs|FMR1_ENST00000370471.3_Frame_Shift_Del_p.I286fs|FMR1_ENST00000334557.6_Frame_Shift_Del_p.I286fs|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000218200.8_Frame_Shift_Del_p.I286fs	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	286	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AAGATGTAATACAAGTTCCAA	0.338									Fragile X syndrome																												p.I286fs		Pindel	.											.	FMR1	93	.	0			c.857delT						.						66.0	63.0	64.0					X																	147014260		2202	4300	6502	SO:0001589	frameshift_variant	2332	exon9	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	.	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.858delA	chrX.hg19:g.147014260delA	ENSP00000359506:p.Ile286fs	171.0	0.0		137.0	63.0	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Frame_Shift_Del	DEL	ENST00000370475.4	hg19	CCDS14682.1																																																																																			.	.		0.338	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
