#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_PopFreq	i_dbSNP_Strength	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
RALGPS2	55103	hgsc.bcm.edu	37	1	178863074	178863074	+	Nonsense_Mutation	SNP	T	T	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr1:178863074T>A	ENST00000367635.3	+	16	1684	c.1346T>A	c.(1345-1347)tTg>tAg	p.L449*	RALGPS2_ENST00000477383.1_3'UTR|RALGPS2_ENST00000367634.2_Nonsense_Mutation_p.L423*	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	449					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TCAGAAGATTTGGCAGTACAT	0.318																																					p.L449X		Atlas-SNP	.											.	RALGPS2	69	.	0			c.T1346A						PASS	.						61.0	61.0	61.0					1																	178863074		2203	4293	6496	SO:0001587	stop_gained	55103	exon16			AAGATTTGGCAGT	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.1346T>A	chr1.hg19:g.178863074T>A	ENSP00000356607:p.Leu449*	62.0	0.0	.		54.0	18.0	.	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Nonsense_Mutation	SNP	ENST00000367635.3	hg19	CCDS1325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	39|39	7.409622|7.409622	0.98265|0.98265	.|.	.|.	ENSG00000116191|ENSG00000116191	ENST00000367635;ENST00000367634;ENST00000324778;ENST00000535251|ENST00000367632	.|.	.|.	.|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	0.248036|.	0.33875|.	N|.	0.004461|.	.|T	.|0.67655	.|0.2916	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70974	.|-0.4726	.|3	0.02654|.	T|.	1|.	.|.	15.3383|15.3383	0.74277|0.74277	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|R	449;423;414;98|40	.|.	ENSP00000313613:L414X|.	L|W	+|+	2|1	0|0	RALGPS2|RALGPS2	177129697|177129697	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.143000|7.143000	0.77348|0.77348	2.102000|2.102000	0.63906|0.63906	0.454000|0.454000	0.30748|0.30748	TTG|TGG	.	.	.	none		0.318	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
PRR30	339779	hgsc.bcm.edu	37	2	27360426	27360426	+	Missense_Mutation	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:27360426G>A	ENST00000335524.3	-	3	1297	c.772C>T	c.(772-774)Ccc>Tcc	p.P258S	PREB_ENST00000416802.1_5'Flank|PREB_ENST00000260643.2_5'Flank|PREB_ENST00000406567.3_5'Flank	NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		258										cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGCTGCGGGGCCGGAGGCAC	0.657																																					p.P258S		Atlas-SNP	.											.	C2orf53	45	.	0			c.C772T						PASS	.						20.0	22.0	21.0					2																	27360426		2081	4142	6223	SO:0001583	missense	339779	exon3			TGCGGGGCCGGAG																												ENST00000335524.3:c.772C>T	chr2.hg19:g.27360426G>A	ENSP00000335017:p.Pro258Ser	156.0	0.0	.		173.0	50.0	.	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	hg19	CCDS1739.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.302|9.302	1.053391|1.053391	0.19907|0.19907	.|.	.|.	ENSG00000186143|ENSG00000186143	ENST00000432962|ENST00000335524	.|T	.|0.32753	.|1.44	4.67|4.67	3.78|3.78	0.43462|0.43462	.|.	.|0.958574	.|0.08507	.|N	.|0.935541	T|T	0.34774|0.34774	0.0909|0.0909	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|D	.|0.53312	.|0.959	.|P	.|0.51615	.|0.675	T|T	0.21381|0.21381	-1.0247|-1.0247	6|10	0.87932|0.59425	D|D	0|0.04	-2.4184|-2.4184	10.6794|10.6794	0.45804|0.45804	0.0:0.1934:0.8066:0.0|0.0:0.1934:0.8066:0.0	.|.	.|258	.|Q53SZ7	.|CB053_HUMAN	V|S	93|258	.|ENSP00000335017:P258S	ENSP00000393468:A93V|ENSP00000335017:P258S	A|P	-|-	2|1	0|0	C2orf53|C2orf53	27213930|27213930	0.971000|0.971000	0.33674|0.33674	0.163000|0.163000	0.22734|0.22734	0.184000|0.184000	0.23303|0.23303	2.911000|2.911000	0.48774|0.48774	1.153000|1.153000	0.42468|0.42468	0.561000|0.561000	0.74099|0.74099	GCC|CCC	.	.	.	none		0.657	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1		
DPP10	57628	hgsc.bcm.edu	37	2	116593770	116593770	+	Nonsense_Mutation	SNP	C	C	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:116593770C>A	ENST00000410059.1	+	22	2468	c.1988C>A	c.(1987-1989)tCa>tAa	p.S663*	DPP10_ENST00000393147.2_Nonsense_Mutation_p.S667*|DPP10_ENST00000409163.1_Nonsense_Mutation_p.S613*|DPP10_ENST00000310323.8_Nonsense_Mutation_p.S656*	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	663						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						ATCTTAAAATCAGATGAAAAG	0.343																																					p.S667X		Atlas-SNP	.											.	DPP10	415	.	0			c.C2000A						PASS	.						84.0	82.0	83.0					2																	116593770		2203	4300	6503	SO:0001587	stop_gained	57628	exon22			TAAAATCAGATGA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1988C>A	chr2.hg19:g.116593770C>A	ENSP00000386565:p.Ser663*	146.0	0.0	.		125.0	30.0	.	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Nonsense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	C	41	8.960916	0.99018	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	.	.	.	5.67	5.67	0.87782	.	0.066573	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.2616	18.7538	0.91825	0.0:1.0:0.0:0.0	.	.	.	.	X	663;613;667;656	.	ENSP00000309066:S656X	S	+	2	0	DPP10	116310240	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.472000	0.60189	2.649000	0.89929	0.655000	0.94253	TCA	.	.	.	none		0.343	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
NOP58	51602	hgsc.bcm.edu	37	2	203165004	203165004	+	Missense_Mutation	SNP	G	G	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:203165004G>C	ENST00000264279.5	+	13	1542	c.1316G>C	c.(1315-1317)tGt>tCt	p.C439S		NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	439					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						CTTCCAACCTGTTCTAAAAAA	0.333																																					p.C439S		Atlas-SNP	.											.	NOP58	41	.	0			c.G1316C						PASS	.						85.0	89.0	87.0					2																	203165004		2203	4299	6502	SO:0001583	missense	51602	exon13			CAACCTGTTCTAA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"""NOP58 ribonucleoprotein homolog (yeast)"""			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.1316G>C	chr2.hg19:g.203165004G>C	ENSP00000264279:p.Cys439Ser	468.0	0.0	.		554.0	177.0	.	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Missense_Mutation	SNP	ENST00000264279.5	hg19	CCDS2353.1	.	.	.	.	.	.	.	.	.	.	G	4.364	0.067124	0.08388	.	.	ENSG00000055044	ENST00000264279	T	0.58210	0.35	6.04	3.99	0.46301	.	0.334108	0.36815	N	0.002398	T	0.23410	0.0566	N	0.03608	-0.345	0.31765	N	0.6328	B	0.10296	0.003	B	0.01281	0.0	T	0.22521	-1.0214	10	0.07813	T	0.8	-8.107	8.6349	0.33941	0.0899:0.0:0.7125:0.1977	.	439	Q9Y2X3	NOP58_HUMAN	S	439	ENSP00000264279:C439S	ENSP00000264279:C439S	C	+	2	0	NOP58	202873249	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.010000	0.40913	1.457000	0.47850	0.563000	0.77884	TGT	.	.	.	none		0.333	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44369747	44369747	+	Missense_Mutation	SNP	C	C	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr3:44369747C>G	ENST00000309765.4	+	19	4849	c.4681C>G	c.(4681-4683)Ctt>Gtt	p.L1561V		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	1561						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)										TTCAGGTGCTCTTTCCTTGGG	0.338																																					p.L1561V		Atlas-SNP	.											.	.	.	.	0			c.C4681G						PASS	.						80.0	67.0	71.0					3																	44369747		692	1591	2283	SO:0001583	missense	375337	exon19			GGTGCTCTTTCCT	AK093476	CCDS46809.1	3p21.33	2012-10-08	2012-10-08	2012-10-08	ENSG00000173769	ENSG00000173769			24746	protein-coding gene	gene with protein product		614412	"""chromosome 3 open reading frame 77"""	C3orf77		22069478	Standard	NM_001145030		Approved	FLJ36157	uc003cna.4	Q8N9V7	OTTHUMG00000156172	ENST00000309765.4:c.4681C>G	chr3.hg19:g.44369747C>G	ENSP00000310303:p.Leu1561Val	98.0	0.0	.		115.0	49.0	.	NM_001145030		Missense_Mutation	SNP	ENST00000309765.4	hg19	CCDS46809.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328068	0.60743	.	.	ENSG00000173769	ENST00000309765	T	0.16457	2.34	5.91	4.06	0.47325	.	.	.	.	.	T	0.10937	0.0267	N	0.24115	0.695	0.33686	D	0.612714	P	0.50617	0.937	B	0.40165	0.321	T	0.18618	-1.0331	9	0.45353	T	0.12	-3.4146	8.1854	0.31335	0.0:0.4478:0.4564:0.0958	.	1561	Q8N9V7	CC077_HUMAN	V	1561	ENSP00000310303:L1561V	ENSP00000310303:L1561V	L	+	1	0	C3orf77	44344751	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.138000	0.31491	0.782000	0.33613	0.655000	0.94253	CTT	.	.	.	none		0.338	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	
TRIM42	287015	hgsc.bcm.edu	37	3	140409996	140409996	+	Missense_Mutation	SNP	A	A	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr3:140409996A>C	ENST00000286349.3	+	4	2238	c.2047A>C	c.(2047-2049)Aat>Cat	p.N683H		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	683	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TAGAGCCATCAATGATAATGG	0.438																																					p.N683H		Atlas-SNP	.											.	TRIM42	143	.	0			c.A2047C						PASS	.						152.0	148.0	149.0					3																	140409996		2203	4300	6503	SO:0001583	missense	287015	exon4			GCCATCAATGATA	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.2047A>C	chr3.hg19:g.140409996A>C	ENSP00000286349:p.Asn683His	118.0	0.0	.		118.0	30.0	.	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	hg19	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699132	0.68501	.	.	ENSG00000155890	ENST00000286349	T	0.62232	0.04	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.084638	0.49916	D	0.000130	T	0.66703	0.2816	N	0.24115	0.695	0.36090	D	0.843388	D	0.89917	1.0	D	0.91635	0.999	T	0.75739	-0.3212	10	0.87932	D	0	-29.3416	11.9122	0.52745	1.0:0.0:0.0:0.0	.	683	Q8IWZ5	TRI42_HUMAN	H	683	ENSP00000286349:N683H	ENSP00000286349:N683H	N	+	1	0	TRIM42	141892686	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	5.754000	0.68743	2.074000	0.62210	0.528000	0.53228	AAT	.	.	.	none		0.438	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
EIF4G1	1981	hgsc.bcm.edu	37	3	184042785	184042785	+	Silent	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr3:184042785G>A	ENST00000346169.2	+	18	3010	c.2739G>A	c.(2737-2739)gaG>gaA	p.E913E	EIF4G1_ENST00000350481.5_Silent_p.E749E|EIF4G1_ENST00000342981.4_Silent_p.E914E|EIF4G1_ENST00000352767.3_Silent_p.E920E|EIF4G1_ENST00000382330.3_Silent_p.E920E|EIF4G1_ENST00000435046.2_Silent_p.E717E|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000424196.1_Silent_p.E920E|EIF4G1_ENST00000414031.1_Silent_p.E873E|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.E750E|EIF4G1_ENST00000427845.1_Silent_p.E827E|EIF4G1_ENST00000392537.2_Silent_p.E826E|EIF4G1_ENST00000434061.2_Silent_p.E718E|EIF4G1_ENST00000411531.1_Silent_p.E874E|EIF4G1_ENST00000319274.6_Silent_p.E913E	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	913	eIF3/EIF4A-binding.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGTTAACAGAGGCAATAATGC	0.478																																					p.E920E		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G2760A						PASS	.						111.0	114.0	113.0					3																	184042785		2203	4300	6503	SO:0001819	synonymous_variant	1981	exon19			AACAGAGGCAATA	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.2739G>A	chr3.hg19:g.184042785G>A		71.0	0.0	.		67.0	25.0	.	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.	.	none		0.478	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
NKX3-2	579	hgsc.bcm.edu	37	4	13543692	13543692	+	Silent	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr4:13543692G>A	ENST00000382438.5	-	2	1562	c.927C>T	c.(925-927)ccC>ccT	p.P309P		NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	309					determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						AATAGTAGGAGGGCTGCAGTG	0.657																																					p.P309P		Atlas-SNP	.											.	NKX3-2	15	.	0			c.C927T						PASS	.						41.0	36.0	38.0					4																	13543692		2200	4299	6499	SO:0001819	synonymous_variant	579	exon2			GTAGGAGGGCTGC	AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"""Homeoboxes / ANTP class : NKL subclass"""	951	protein-coding gene	gene with protein product		602183	"""bagpipe homeobox homolog 1 (Drosophila)"""	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.927C>T	chr4.hg19:g.13543692G>A		280.0	0.0	.		335.0	90.0	.	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	hg19	CCDS3410.1																																																																																			.	.	.	none		0.657	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3		
RUFY3	22902	hgsc.bcm.edu	37	4	71660584	71660584	+	IGR	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr4:71660584G>A	ENST00000226328.4	+	0	4233				RUFY3_ENST00000381006.3_Silent_p.R510R|RUFY3_ENST00000502653.1_Silent_p.R457R	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3						negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TCCCAGGAAGGGGTTCCCAGA	0.388																																					p.R510R		Atlas-SNP	.											.	RUFY3	61	.	0			c.G1530A						PASS	.						132.0	137.0	135.0					4																	71660584		2203	4300	6503	SO:0001628	intergenic_variant	22902	exon14			AGGAAGGGGTTCC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910		chr4.hg19:g.71660584G>A		126.0	0.0	.		137.0	49.0	.	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Silent	SNP	ENST00000226328.4	hg19	CCDS3547.1																																																																																			.	.	.	none		0.388	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961	
HNRNPDL	9987	hgsc.bcm.edu	37	4	83350614	83350614	+	Missense_Mutation	SNP	C	C	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr4:83350614C>G	ENST00000295470.5	-	1	405	c.230G>C	c.(229-231)gGa>gCa	p.G77A	HNRNPDL_ENST00000602300.1_5'Flank|HNRNPDL_ENST00000514511.1_5'Flank|HNRNPDL_ENST00000349655.4_5'Flank|ENOPH1_ENST00000509635.1_5'Flank|ENOPH1_ENST00000273920.3_5'Flank|HNRNPDL_ENST00000502762.1_Missense_Mutation_p.G77A	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	77					regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										CCTGCGCCCTCCCTTTATAGC	0.741																																					p.G77A		Atlas-SNP	.											.	HNRPDL	35	.	0			c.G230C						PASS	.						7.0	10.0	9.0					4																	83350614		2072	4194	6266	SO:0001583	missense	9987	exon1			CGCCCTCCCTTTA	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.230G>C	chr4.hg19:g.83350614C>G	ENSP00000295470:p.Gly77Ala	68.0	0.0	.		87.0	32.0	.	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Missense_Mutation	SNP	ENST00000295470.5	hg19	CCDS3593.1	.	.	.	.	.	.	.	.	.	.	c	19.68	3.873638	0.72180	.	.	ENSG00000152795	ENST00000295470;ENST00000502762	T;T	0.66460	-0.21;-0.21	4.37	3.5	0.40072	.	0.357050	0.20341	N	0.094229	T	0.42877	0.1222	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44877	-0.9299	10	0.87932	D	0	.	6.9493	0.24536	0.0:0.7224:0.1789:0.0988	.	77	O14979	HNRDL_HUMAN	A	77	ENSP00000295470:G77A;ENSP00000422040:G77A	ENSP00000295470:G77A	G	-	2	0	HNRPDL	83569638	0.998000	0.40836	1.000000	0.80357	0.803000	0.45373	0.789000	0.26886	2.132000	0.65825	0.305000	0.20034	GGA	.	.	.	none		0.741	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463	
NNT	23530	hgsc.bcm.edu	37	5	43613093	43613093	+	Missense_Mutation	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr5:43613093G>A	ENST00000264663.5	+	3	456	c.235G>A	c.(235-237)Gtt>Att	p.V79I	NNT_ENST00000512996.2_5'UTR|NNT_ENST00000344920.4_Missense_Mutation_p.V79I	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	79					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TCCTGCTGGTGTTCAGAACTT	0.473																																					p.V79I		Atlas-SNP	.											.	NNT	92	.	0			c.G235A						PASS	.						168.0	169.0	169.0					5																	43613093		2203	4300	6503	SO:0001583	missense	23530	exon3			GCTGGTGTTCAGA	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.235G>A	chr5.hg19:g.43613093G>A	ENSP00000264663:p.Val79Ile	132.0	0.0	.		126.0	54.0	.	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598252	0.87055	.	.	ENSG00000112992	ENST00000505678;ENST00000512422;ENST00000264663;ENST00000344920	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.7	5.7	0.88788	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-1 (1);Alanine dehydrogenase/PNT, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88451	0.6440	M	0.81179	2.53	0.80722	D	1	P	0.46859	0.885	P	0.48901	0.594	D	0.89154	0.3525	10	0.59425	D	0.04	-29.0904	19.8481	0.96728	0.0:0.0:1.0:0.0	.	79	Q13423	NNTM_HUMAN	I	79	ENSP00000427670:V79I;ENSP00000421886:V79I;ENSP00000264663:V79I;ENSP00000343873:V79I	ENSP00000264663:V79I	V	+	1	0	NNT	43648850	1.000000	0.71417	0.979000	0.43373	0.954000	0.61252	9.584000	0.98220	2.705000	0.92388	0.650000	0.86243	GTT	.	.	.	none		0.473	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
CSF1R	1436	hgsc.bcm.edu	37	5	149459890	149459890	+	Missense_Mutation	SNP	C	C	T	rs535129002		TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr5:149459890C>T	ENST00000286301.3	-	4	608	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	CSF1R_ENST00000543093.1_Missense_Mutation_p.R106Q	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	106					cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GTTCCAGGGCCGGGCAGGGTC	0.617																																					p.R106Q		Atlas-SNP	.											.	CSF1R	250	.	0			c.G317A						PASS	.						36.0	35.0	35.0					5																	149459890		2203	4299	6502	SO:0001583	missense	1436	exon4			CAGGGCCGGGCAG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.317G>A	chr5.hg19:g.149459890C>T	ENSP00000286301:p.Arg106Gln	49.0	0.0	.		67.0	5.0	.	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	hg19	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.892951	0.33442	.	.	ENSG00000182578	ENST00000286301;ENST00000543093	T;T	0.04758	3.56;3.56	4.92	1.53	0.23141	.	0.583037	0.14309	N	0.327833	T	0.07863	0.0197	L	0.56769	1.78	0.09310	N	1	D;D;P	0.63880	0.993;0.987;0.929	P;B;B	0.50049	0.629;0.396;0.211	T	0.28996	-1.0026	10	0.29301	T	0.29	.	5.7207	0.17985	0.0:0.5844:0.0:0.4156	.	106;106;106	B4DG86;B5A955;P07333	.;.;CSF1R_HUMAN	Q	106	ENSP00000286301:R106Q;ENSP00000445282:R106Q	ENSP00000286301:R106Q	R	-	2	0	CSF1R	149440083	0.000000	0.05858	0.015000	0.15790	0.087000	0.18053	-0.169000	0.09911	0.445000	0.26639	0.561000	0.74099	CGG	.	.	.	none		0.617	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
CLPSL2	389383	hgsc.bcm.edu	37	6	35745347	35745347	+	Missense_Mutation	SNP	T	T	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr6:35745347T>C	ENST00000403376.3	+	2	196	c.196T>C	c.(196-198)Tgc>Cgc	p.C66R	CLPSL2_ENST00000360454.2_Missense_Mutation_p.C66R|CLPSL2_ENST00000481904.1_3'UTR	NM_207409.2	NP_997292.2	Q6UWE3	COLL2_HUMAN	colipase-like 2	66					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										AACCATGATCTGCTTGCCCCA	0.557																																					p.C66R		Atlas-SNP	.											.	.	.	.	0			c.T196C						PASS	.						42.0	41.0	41.0					6																	35745347		2203	4300	6503	SO:0001583	missense	389383	exon2			ATGATCTGCTTGC		CCDS4810.2, CCDS69095.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000196748	ENSG00000196748			21250	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 126"""	C6orf126			Standard	NM_001286550		Approved	dJ510O8.5, UNQ3045	uc010jvz.1	Q6UWE3	OTTHUMG00000014581	ENST00000403376.3:c.196T>C	chr6.hg19:g.35745347T>C	ENSP00000385898:p.Cys66Arg	73.0	0.0	.		70.0	19.0	.	NM_207409	B0QZ45|Q5T9G3	Missense_Mutation	SNP	ENST00000403376.3	hg19	CCDS4810.2	.	.	.	.	.	.	.	.	.	.	T	14.54	2.565760	0.45694	.	.	ENSG00000196748	ENST00000360454;ENST00000403376	.	.	.	3.41	2.2	0.27929	.	0.000000	0.39759	N	0.001275	T	0.61502	0.2352	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.982;0.987	T	0.64428	-0.6410	9	0.87932	D	0	-20.7405	6.6191	0.22792	0.0:0.0:0.2463:0.7537	.	66;66	Q6UWE3;Q6UWE3-2	CF126_HUMAN;.	R	66	.	ENSP00000353639:C66R	C	+	1	0	C6orf126	35853325	0.936000	0.31750	0.532000	0.27989	0.271000	0.26615	1.611000	0.36879	0.645000	0.30675	0.459000	0.35465	TGC	.	.	.	none		0.557	CLPSL2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280618.2	NM_207409	
SLC22A7	10864	hgsc.bcm.edu	37	6	43268946	43268946	+	Missense_Mutation	SNP	T	T	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr6:43268946T>C	ENST00000372585.5	+	6	996	c.901T>C	c.(901-903)Tgt>Cgt	p.C301R	SLC22A7_ENST00000372574.3_Missense_Mutation_p.C299R|SLC22A7_ENST00000372589.3_Missense_Mutation_p.C299R|SLC22A7_ENST00000487175.1_3'UTR	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	301					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	CTTGCTCCACTGTGCCAGGCT	0.577																																					p.C301R		Atlas-SNP	.											.	SLC22A7	69	.	0			c.T901C						PASS	.						174.0	158.0	163.0					6																	43268946		2203	4300	6503	SO:0001583	missense	10864	exon5			CTCCACTGTGCCA	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"""Solute carriers"""	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.901T>C	chr6.hg19:g.43268946T>C	ENSP00000361666:p.Cys301Arg	35.0	0.0	.		47.0	20.0	.	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	17.37	3.373115	0.61624	.	.	ENSG00000137204	ENST00000372589;ENST00000372585;ENST00000372574	T;T;T	0.55413	0.52;0.52;0.52	4.95	4.95	0.65309	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.100743	0.64402	D	0.000001	T	0.66848	0.2831	M	0.86028	2.79	0.80722	D	1	D;D;D	0.67145	0.987;0.984;0.996	D;D;D	0.68943	0.961;0.935;0.96	T	0.74222	-0.3735	10	0.87932	D	0	.	12.1803	0.54208	0.0:0.0:0.0:1.0	.	301;299;299	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	R	299;301;299	ENSP00000361670:C299R;ENSP00000361666:C301R;ENSP00000361655:C299R	ENSP00000361655:C299R	C	+	1	0	SLC22A7	43376924	1.000000	0.71417	0.980000	0.43619	0.525000	0.34531	5.033000	0.64146	1.871000	0.54225	0.374000	0.22700	TGT	.	.	.	none		0.577	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152589267	152589267	+	Missense_Mutation	SNP	G	G	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr6:152589267G>T	ENST00000367255.5	-	100	19340	c.18739C>A	c.(18739-18741)Ctc>Atc	p.L6247I	SYNE1_ENST00000356820.4_Missense_Mutation_p.L771I|SYNE1_ENST00000265368.4_Missense_Mutation_p.L6247I|SYNE1_ENST00000448038.1_Missense_Mutation_p.L6176I|SYNE1_ENST00000423061.1_Missense_Mutation_p.L6176I|SYNE1_ENST00000341594.5_Missense_Mutation_p.L5859I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6247					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGCGAAGGAGACTCTTCTGC	0.443										HNSCC(10;0.0054)																											p.L6247I		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C18739A						PASS	.						100.0	100.0	100.0					6																	152589267		2203	4300	6503	SO:0001583	missense	23345	exon100			GAAGGAGACTCTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18739C>A	chr6.hg19:g.152589267G>T	ENSP00000356224:p.Leu6247Ile	83.0	0.0	.		87.0	30.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534749	0.64972	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.73681	-0.68;-0.7;-0.77;-0.69;-0.4;0.88	5.74	5.74	0.90152	.	0.000000	0.50627	D	0.000101	T	0.70298	0.3208	M	0.72894	2.215	0.49687	D	0.999816	P;P;P	0.46912	0.818;0.818;0.886	B;B;P	0.48677	0.382;0.382;0.586	T	0.70306	-0.4908	10	0.34782	T	0.22	.	11.0403	0.47827	0.0687:0.0:0.8012:0.1301	.	6247;6247;6176	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	I	6247;6176;6247;6176;5859;771	ENSP00000356224:L6247I;ENSP00000396024:L6176I;ENSP00000265368:L6247I;ENSP00000390975:L6176I;ENSP00000341887:L5859I;ENSP00000349276:L771I	ENSP00000265368:L6247I	L	-	1	0	SYNE1	152630960	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	4.624000	0.61254	2.873000	0.98535	0.563000	0.77884	CTC	.	.	.	none		0.443	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
DNAJB9	4189	hgsc.bcm.edu	37	7	108213747	108213747	+	Nonsense_Mutation	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr7:108213747C>T	ENST00000249356.3	+	3	1168	c.622C>T	c.(622-624)Caa>Taa	p.Q208*	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	208					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						GACTGTCACTCAACGAAGAGG	0.378																																					p.Q208X		Atlas-SNP	.											.	DNAJB9	25	.	0			c.C622T						PASS	.						103.0	102.0	102.0					7																	108213747		2203	4300	6503	SO:0001587	stop_gained	4189	exon3			GTCACTCAACGAA	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"""Heat shock proteins / DNAJ (HSP40)"""	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.622C>T	chr7.hg19:g.108213747C>T	ENSP00000249356:p.Gln208*	46.0	0.0	.		74.0	36.0	.	NM_012328		Nonsense_Mutation	SNP	ENST00000249356.3	hg19	CCDS5752.1	.	.	.	.	.	.	.	.	.	.	C	41	8.877952	0.98988	.	.	ENSG00000128590	ENST00000249356	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1901	0.93663	0.0:1.0:0.0:0.0	.	.	.	.	X	208	.	.	Q	+	1	0	DNAJB9	108000983	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.377000	0.79668	2.776000	0.95493	0.655000	0.94253	CAA	.	.	.	none		0.378	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1		
SGK223	157285	hgsc.bcm.edu	37	8	8234618	8234618	+	Missense_Mutation	SNP	G	G	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr8:8234618G>T	ENST00000520004.1	-	3	1565	c.1301C>A	c.(1300-1302)gCa>gAa	p.A434E	SGK223_ENST00000330777.4_Missense_Mutation_p.A434E			Q86YV5	SG223_HUMAN		436							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGCAGCAGCTGCATGTTCTAT	0.617																																					p.A434E	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1301A						PASS	.						61.0	67.0	65.0					8																	8234618		2053	4200	6253	SO:0001583	missense	0	exon2			GCAGCTGCATGTT																												ENST00000520004.1:c.1301C>A	chr8.hg19:g.8234618G>T	ENSP00000428054:p.Ala434Glu	42.0	0.0	.		54.0	15.0	.	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.703006	0.00719	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.56444	0.46;0.46	4.76	-0.32	0.12721	.	1.566350	0.03920	N	0.283453	T	0.36908	0.0984	L	0.36672	1.1	0.09310	N	1	B	0.31125	0.309	B	0.32289	0.143	T	0.13202	-1.0518	10	0.02654	T	1	.	5.1422	0.14965	0.3301:0.2621:0.4078:0.0	.	434	Q86YV5	SG223_HUMAN	E	434	ENSP00000330930:A434E;ENSP00000428054:A434E	ENSP00000330930:A434E	A	-	2	0	AC068353.1	8272028	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	1.166000	0.31834	-0.162000	0.10964	-0.175000	0.13238	GCA	.	.	.	none		0.617	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ECD	11319	hgsc.bcm.edu	37	10	74920311	74920311	+	Splice_Site	SNP	T	T	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:74920311T>G	ENST00000372979.4	-	3	412		c.e3-2		ECD_ENST00000610256.1_Splice_Site|ECD_ENST00000454759.2_Splice_Site|ECD_ENST00000430082.2_Splice_Site	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)						cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					GAACACCTCCTAAAAACAAGA	0.338																																					.		Atlas-SNP	.											.	ECD	50	.	0			c.206-2A>C						PASS	.						75.0	69.0	71.0					10																	74920311		2203	4300	6503	SO:0001630	splice_region_variant	11319	exon4			ACCTCCTAAAAAC	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.206-2A>C	chr10.hg19:g.74920311T>G		175.0	0.0	.		204.0	49.0	.	NM_001135753	C9JX46|E9PAW8	Splice_Site	SNP	ENST00000372979.4	hg19	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.063343	0.76187	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759;ENST00000413026	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7558	0.57335	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ECD	74590317	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	7.209000	0.77916	1.907000	0.55213	0.533000	0.62120	.	.	.	.	none		0.338	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Intron
MCMBP	79892	hgsc.bcm.edu	37	10	121586617	121586617	+	IGR	SNP	T	T	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:121586617T>C	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Silent_p.L908L|INPP5F_ENST00000369080.3_Silent_p.L298L	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CCCAGTCTCTTAGCAGCACAG	0.478																																					p.L908L		Atlas-SNP	.											.	INPP5F	112	.	0			c.T2724C						PASS	.						127.0	102.0	111.0					10																	121586617		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			GTCTCTTAGCAGC	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		chr10.hg19:g.121586617T>C		60.0	0.0	.		51.0	14.0	.	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	hg19	CCDS7617.1																																																																																			.	.	.	none		0.478	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
AP2A2	161	hgsc.bcm.edu	37	11	977190	977190	+	Missense_Mutation	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:977190C>T	ENST00000448903.2	+	5	710	c.569C>T	c.(568-570)tCc>tTc	p.S190F	AP2A2_ENST00000534328.1_Missense_Mutation_p.S190F|AP2A2_ENST00000332231.5_Missense_Mutation_p.S190F	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	190					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		GACTGGACATCCCGAGTGGTG	0.602																																					p.S190F		Atlas-SNP	.											.	AP2A2	50	.	0			c.C569T						PASS	.						59.0	67.0	65.0					11																	977190		2122	4216	6338	SO:0001583	missense	161	exon5			GGACATCCCGAGT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.569C>T	chr11.hg19:g.977190C>T	ENSP00000413234:p.Ser190Phe	53.0	0.0	.		80.0	21.0	.	NM_012305	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.158320	0.38119	.	.	ENSG00000183020	ENST00000525796;ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000534485;ENST00000329626	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.7	2.8	2.8	0.32819	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.075573	0.56097	D	0.000038	T	0.63616	0.2526	M	0.83603	2.65	0.58432	D	0.999998	P;D;D	0.71674	0.943;0.998;0.997	P;P;D	0.64237	0.86;0.856;0.923	T	0.73161	-0.4070	10	0.72032	D	0.01	-32.6353	14.8145	0.70020	0.0:1.0:0.0:0.0	.	83;190;190	Q59FN8;O94973-2;O94973	.;.;AP2A2_HUMAN	F	30;190;190;190;190;190;180;63	ENSP00000437228:S30F;ENSP00000436059:S190F;ENSP00000413234:S190F;ENSP00000327694:S190F;ENSP00000435756:S180F	ENSP00000328024:S63F	S	+	2	0	AP2A2	967190	1.000000	0.71417	0.102000	0.21198	0.011000	0.07611	7.541000	0.82084	1.895000	0.54865	0.586000	0.80456	TCC	.	.	.	none		0.602	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305	
CSNK2A3	283106	hgsc.bcm.edu	37	11	11373596	11373596	+	Silent	SNP	T	T	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:11373596T>C	ENST00000528848.2	-	1	1308	c.1071A>G	c.(1069-1071)tcA>tcG	p.S357S	GALNT18_ENST00000227756.4_Intron|RP11-567I13.1_ENST00000526867.1_RNA	NM_001256686.1	NP_001243615.1	Q8NEV1	CSK23_HUMAN	casein kinase 2, alpha 3 polypeptide	357					positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)										GAGTTGGCACTGAAGAAATCC	0.587																																					p.S357S		Atlas-SNP	.											.	.	.	.	0			c.A1071G						PASS	.																																			SO:0001819	synonymous_variant	283106	exon1			TGGCACTGAAGAA	X64692	CCDS59224.1	11p15.3	2013-01-18	2013-01-17	2013-01-17	ENSG00000254598	ENSG00000254598			2458	protein-coding gene	gene with protein product			"""casein kinase 2, alpha 1 polypeptide pseudogene"""	CSNK2A1P		12102635, 1610905, 20625391	Standard	NM_001256686		Approved		uc001mjp.4	Q8NEV1	OTTHUMG00000165708	ENST00000528848.2:c.1071A>G	chr11.hg19:g.11373596T>C		109.0	0.0	.		111.0	26.0	.	NM_001256686		Silent	SNP	ENST00000528848.2	hg19	CCDS59224.1																																																																																			.	.	.	none		0.587	CSNK2A3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385850.3	NM_001256686	
TPH1	7166	hgsc.bcm.edu	37	11	18051107	18051107	+	Missense_Mutation	SNP	T	T	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:18051107T>C	ENST00000250018.2	-	4	984	c.422A>G	c.(421-423)tAc>tGc	p.Y141C	TPH1_ENST00000341556.2_Missense_Mutation_p.Y141C	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	141					aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	ACGTTTACGGTAGACATTGTC	0.264																																					p.Y141C		Atlas-SNP	.											.	TPH1	44	.	0			c.A422G						PASS	.						57.0	61.0	60.0					11																	18051107		2198	4285	6483	SO:0001583	missense	7166	exon4			TTACGGTAGACAT	X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"""tryptophan 5-monooxygenase"""	191060	"""tryptophan hydroxylase (tryptophan 5-monooxygenase)"""	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.422A>G	chr11.hg19:g.18051107T>C	ENSP00000250018:p.Tyr141Cys	54.0	0.0	.		54.0	10.0	.	NM_004179	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Missense_Mutation	SNP	ENST00000250018.2	hg19	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860327	0.71834	.	.	ENSG00000129167	ENST00000250018;ENST00000341556;ENST00000528338	D;D;D	0.99795	-6.78;-6.78;-6.78	5.75	5.75	0.90469	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99873	0.9940	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96375	0.9277	10	0.87932	D	0	-15.8182	16.0614	0.80839	0.0:0.0:0.0:1.0	.	141	P17752	TPH1_HUMAN	C	141;141;151	ENSP00000250018:Y141C;ENSP00000343550:Y141C;ENSP00000436081:Y151C	ENSP00000250018:Y141C	Y	-	2	0	TPH1	18007683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.136000	0.71703	2.191000	0.70037	0.528000	0.53228	TAC	.	.	.	none		0.264	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179	
ZPR1	8882	hgsc.bcm.edu	37	11	116655623	116655623	+	Silent	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:116655623G>A	ENST00000227322.3	-	8	827	c.768C>T	c.(766-768)agC>agT	p.S256S		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		256					apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		GGCAGTTTGTGCTGAACTGGA	0.507																																					p.S256S		Atlas-SNP	.											.	ZNF259	27	.	0			c.C768T						PASS	.						121.0	104.0	110.0					11																	116655623		2201	4296	6497	SO:0001819	synonymous_variant	8882	exon8			GTTTGTGCTGAAC																												ENST00000227322.3:c.768C>T	chr11.hg19:g.116655623G>A		98.0	0.0	.		94.0	38.0	.	NM_003904	Q2TAA0	Silent	SNP	ENST00000227322.3	hg19	CCDS8375.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.834|7.834	0.720560|0.720560	0.15372|0.15372	.|.	.|.	ENSG00000109917|ENSG00000109917	ENST00000444935|ENST00000429220	.|.	.|.	.|.	5.92|5.92	3.07|3.07	0.35406|0.35406	.|.	.|.	.|.	.|.	.|.	T|T	0.54143|0.54143	0.1840|0.1840	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.47873|0.47873	-0.9083|-0.9083	4|4	.|.	.|.	.|.	-17.5691|-17.5691	5.7069|5.7069	0.17913|0.17913	0.2102:0.0:0.6522:0.1376|0.2102:0.0:0.6522:0.1376	.|.	.|.	.|.	.|.	V|Y	256|183	.|.	.|.	A|H	-|-	2|1	0|0	ZNF259|ZNF259	116160833|116160833	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.685000|0.685000	0.39939|0.39939	0.961000|0.961000	0.29267|0.29267	0.845000|0.845000	0.35118|0.35118	0.655000|0.655000	0.94253|0.94253	GCA|CAC	.	.	.	none		0.507	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2		
B4GALNT3	283358	hgsc.bcm.edu	37	12	668503	668503	+	Missense_Mutation	SNP	A	A	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr12:668503A>T	ENST00000266383.5	+	19	2817	c.2804A>T	c.(2803-2805)aAg>aTg	p.K935M		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	935					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GGCATCTACAAGTCTGACCTG	0.602																																					p.K935M		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A2804T						PASS	.						127.0	132.0	130.0					12																	668503		2203	4300	6503	SO:0001583	missense	283358	exon19			TCTACAAGTCTGA	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2804A>T	chr12.hg19:g.668503A>T	ENSP00000266383:p.Lys935Met	125.0	0.0	.		117.0	30.0	.	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.539637	0.85917	.	.	ENSG00000139044	ENST00000266383	T	0.40756	1.02	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.69531	0.3121	M	0.89095	3.005	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.77024	-0.2741	10	0.87932	D	0	-40.3422	14.6956	0.69118	1.0:0.0:0.0:0.0	.	935	Q6L9W6	B4GN3_HUMAN	M	935	ENSP00000266383:K935M	ENSP00000266383:K935M	K	+	2	0	B4GALNT3	538764	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.223000	0.95203	1.930000	0.55929	0.379000	0.24179	AAG	.	.	.	none		0.602	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
C2CD5	9847	hgsc.bcm.edu	37	12	22606969	22606969	+	Missense_Mutation	SNP	C	C	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr12:22606969C>A	ENST00000333957.4	-	24	2987	c.2732G>T	c.(2731-2733)gGa>gTa	p.G911V	C2CD5_ENST00000545552.1_Missense_Mutation_p.G965V|C2CD5_ENST00000396028.2_Missense_Mutation_p.G953V|C2CD5_ENST00000544930.1_Missense_Mutation_p.G767V|C2CD5_ENST00000536386.1_Missense_Mutation_p.G964V|C2CD5_ENST00000542676.1_Missense_Mutation_p.G962V|C2CD5_ENST00000446597.1_Missense_Mutation_p.G962V	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	911					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										ACCACTGACTCCTCCTTCCTA	0.358																																					p.G911V		Atlas-SNP	.											.	.	.	.	0			c.G2732T						PASS	.						90.0	80.0	83.0					12																	22606969		2203	4300	6503	SO:0001583	missense	9847	exon24			CTGACTCCTCCTT	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.2732G>T	chr12.hg19:g.22606969C>A	ENSP00000334229:p.Gly911Val	49.0	0.0	.		60.0	16.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.3|21.3	4.123537|4.123537	0.77436|0.77436	.|.	.|.	ENSG00000111731|ENSG00000111731	ENST00000539615|ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930	.|T;T;T;T;T;T	.|0.74209	.|-0.79;-0.79;-0.82;-0.8;-0.79;-0.8	5.41|5.41	4.53|4.53	0.55603|0.55603	.|.	.|0.062767	.|0.64402	.|D	.|0.000005	.|D	.|0.85221	.|0.5647	M|M	0.76170|0.76170	2.325|2.325	0.80722|0.80722	D|D	1|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	.|1.0;0.999;0.999;1.0;0.988	.|D	.|0.86983	.|0.2105	.|10	.|0.87932	.|D	.|0	-20.1497|-20.1497	14.1353|14.1353	0.65284|0.65284	0.0:0.9278:0.0:0.0722|0.0:0.9278:0.0:0.0722	.|.	.|964;962;767;953;911	.|F5H2A1;B4DRN7;F5H3N1;Q86YS7-2;Q86YS7	.|.;.;.;.;K0528_HUMAN	X|V	212|911;962;964;953;962;965;767	.|ENSP00000334229:G911V;ENSP00000388756:G962V;ENSP00000439392:G964V;ENSP00000379345:G953V;ENSP00000441951:G962V;ENSP00000443204:G965V	.|ENSP00000334229:G911V	E|G	-|-	1|2	0|0	KIAA0528|KIAA0528	22498236|22498236	1.000000|1.000000	0.71417|0.71417	0.934000|0.934000	0.37439|0.37439	0.972000|0.972000	0.66771|0.66771	7.493000|7.493000	0.81493|0.81493	1.281000|1.281000	0.44480|0.44480	0.561000|0.561000	0.74099|0.74099	GAG|GGA	.	.	.	none		0.358	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
KRT84	3890	hgsc.bcm.edu	37	12	52776299	52776299	+	Silent	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr12:52776299G>A	ENST00000257951.3	-	4	900	c.834C>T	c.(832-834)ttC>ttT	p.F278F	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	278	Coil 1B.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		ACTTGTTCATGAAAGCTGCAT	0.458																																					p.F278F		Atlas-SNP	.											.	KRT84	61	.	0			c.C834T						PASS	.						131.0	117.0	122.0					12																	52776299		2203	4300	6503	SO:0001819	synonymous_variant	3890	exon4			GTTCATGAAAGCT	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.834C>T	chr12.hg19:g.52776299G>A		45.0	0.0	.		61.0	16.0	.	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	hg19	CCDS8825.1																																																																																			.	.	.	none		0.458	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
OR4E2	26686	hgsc.bcm.edu	37	14	22133689	22133689	+	Silent	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr14:22133689C>T	ENST00000408935.1	+	1	393	c.393C>T	c.(391-393)caC>caT	p.H131H		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		CTCCACTCCACTACCCCAATG	0.483																																					p.H131H		Atlas-SNP	.											.	OR4E2	44	.	0			c.C393T						PASS	.						191.0	180.0	184.0					14																	22133689		2042	4205	6247	SO:0001819	synonymous_variant	26686	exon1			ACTCCACTACCCC		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.393C>T	chr14.hg19:g.22133689C>T		60.0	0.0	.		56.0	18.0	.	NM_001001912	Q6IET6|Q96R62	Silent	SNP	ENST00000408935.1	hg19	CCDS41916.1																																																																																			.	.	.	none		0.483	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
G2E3	55632	hgsc.bcm.edu	37	14	31085631	31085631	+	Missense_Mutation	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr14:31085631C>T	ENST00000206595.6	+	15	2166	c.2012C>T	c.(2011-2013)gCa>gTa	p.A671V	G2E3_ENST00000438909.2_Missense_Mutation_p.A625V|G2E3_ENST00000553504.1_Missense_Mutation_p.A701V	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	671	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						AACTGTTTAGCAATTCCCATC	0.368																																					p.A671V		Atlas-SNP	.											.	G2E3	82	.	0			c.C2012T						PASS	.						65.0	60.0	62.0					14																	31085631		2203	4300	6503	SO:0001583	missense	55632	exon15			GTTTAGCAATTCC	AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"""Zinc fingers, PHD-type"""	20338	protein-coding gene	gene with protein product	"""PHD finger protein 7B"""	611299	"""KIAA1333"""	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.2012C>T	chr14.hg19:g.31085631C>T	ENSP00000206595:p.Ala671Val	150.0	0.0	.		139.0	44.0	.	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	hg19	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	C	2.276	-0.365809	0.05069	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504	T;T;T	0.57752	0.38;0.38;0.38	5.8	1.92	0.25849	HECT (3);	0.807701	0.12051	N	0.504113	T	0.27349	0.0671	N	0.17474	0.49	0.09310	N	0.999996	B;B	0.14438	0.01;0.001	B;B	0.17433	0.018;0.003	T	0.29792	-1.0000	10	0.02654	T	1	-1.326	4.2841	0.10846	0.2379:0.4554:0.0:0.3066	.	183;671	Q49AD9;Q7L622	.;G2E3_HUMAN	V	671;625;701	ENSP00000206595:A671V;ENSP00000391068:A625V;ENSP00000451653:A701V	ENSP00000206595:A671V	A	+	2	0	G2E3	30155382	0.968000	0.33430	0.995000	0.50966	0.629000	0.37895	1.333000	0.33816	0.353000	0.24079	0.591000	0.81541	GCA	.	.	.	none		0.368	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769	
BTBD7	55727	hgsc.bcm.edu	37	14	93761032	93761032	+	Missense_Mutation	SNP	T	T	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr14:93761032T>G	ENST00000334746.5	-	3	641	c.334A>C	c.(334-336)Aag>Cag	p.K112Q	BTBD7_ENST00000554565.1_Intron|BTBD7_ENST00000555525.1_Missense_Mutation_p.K112Q|BTBD7_ENST00000393170.2_5'Flank|BTBD7_ENST00000298896.3_Missense_Mutation_p.K112Q	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	112					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GAAAGCTCCTTTAATGCTGAT	0.453																																					p.K112Q		Atlas-SNP	.											.	BTBD7	112	.	0			c.A334C						PASS	.						87.0	77.0	81.0					14																	93761032		2203	4300	6503	SO:0001583	missense	55727	exon3			GCTCCTTTAATGC	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.334A>C	chr14.hg19:g.93761032T>G	ENSP00000335615:p.Lys112Gln	80.0	0.0	.		71.0	19.0	.	NM_018167	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.174317	0.78452	.	.	ENSG00000011114	ENST00000334746;ENST00000298896;ENST00000555525	T	0.46819	0.86	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.66096	0.2755	L	0.57536	1.79	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.991;0.991	T	0.68265	-0.5454	10	0.72032	D	0.01	.	16.3224	0.82956	0.0:0.0:0.0:1.0	.	112;112;112	Q9P203-3;G3V3T2;Q9P203	.;.;BTBD7_HUMAN	Q	112	ENSP00000335615:K112Q	ENSP00000298896:K112Q	K	-	1	0	BTBD7	92830785	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.263000	0.75096	0.533000	0.62120	AAG	.	.	.	none		0.453	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860	
FAM98B	283742	hgsc.bcm.edu	37	15	38776827	38776827	+	IGR	SNP	T	T	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr15:38776827T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G423G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gtggtggtggtggtggtggag	0.443																																					p.G423G		Atlas-SNP	.											FAM98B_ENST00000397609,NS,carcinoma,0,1	FAM98B	53	.	0			c.T1269A						PASS	.						19.0	18.0	18.0					15																	38776827		1515	3413	4928	SO:0001628	intergenic_variant	283742	exon8			TGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776827T>A		78.0	0.0	.		80.0	10.0	.	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.443	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611	
TGFB1I1	7041	hgsc.bcm.edu	37	16	31488254	31488254	+	Missense_Mutation	SNP	G	G	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr16:31488254G>T	ENST00000394863.3	+	10	1172	c.1042G>T	c.(1042-1044)Ggc>Tgc	p.G348C	TGFB1I1_ENST00000361773.3_Missense_Mutation_p.G331C|TGFB1I1_ENST00000394858.2_Missense_Mutation_p.G331C|TGFB1I1_ENST00000567607.1_Missense_Mutation_p.G331C	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	348	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						GCGCTGCCAGGGCTGCCAGGG	0.692																																					p.G348C		Atlas-SNP	.											.	TGFB1I1	60	.	0			c.G1042T						PASS	.						10.0	11.0	11.0					16																	31488254		2183	4269	6452	SO:0001583	missense	7041	exon10			TGCCAGGGCTGCC	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.1042G>T	chr16.hg19:g.31488254G>T	ENSP00000378332:p.Gly348Cys	43.0	0.0	.		44.0	26.0	.	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Missense_Mutation	SNP	ENST00000394863.3	hg19	CCDS42156.1	.	.	.	.	.	.	.	.	.	.	G	33	5.216196	0.95104	.	.	ENSG00000140682	ENST00000394863;ENST00000361773;ENST00000394858	D;D;D	0.89050	-2.46;-2.46;-2.46	5.35	4.39	0.52855	Zinc finger, LIM-type (5);	0.049439	0.85682	D	0.000000	D	0.95111	0.8416	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95618	0.8678	10	0.87932	D	0	.	12.2376	0.54524	0.0837:0.0:0.9163:0.0	.	348	O43294	TGFI1_HUMAN	C	348;331;331	ENSP00000378332:G348C;ENSP00000355117:G331C;ENSP00000378327:G331C	ENSP00000355117:G331C	G	+	1	0	TGFB1I1	31395755	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.737000	0.98831	1.391000	0.46566	0.484000	0.47621	GGC	.	.	.	none		0.692	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3		
COG4	25839	hgsc.bcm.edu	37	16	70543137	70543137	+	Silent	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr16:70543137C>T	ENST00000323786.5	-	7	1020	c.999G>A	c.(997-999)caG>caA	p.Q333Q	COG4_ENST00000393612.4_Silent_p.Q329Q	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	329					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				TGCTCACCTGCTGGTGGTAGT	0.458																																					p.Q333Q		Atlas-SNP	.											.	COG4	64	.	0			c.G999A						PASS	.						163.0	146.0	152.0					16																	70543137		2198	4300	6498	SO:0001819	synonymous_variant	25839	exon7			CACCTGCTGGTGG	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.999G>A	chr16.hg19:g.70543137C>T		47.0	0.0	.		97.0	47.0	.	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Silent	SNP	ENST00000323786.5	hg19	CCDS10892.2																																																																																			.	.	.	none		0.458	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
METTL16	79066	hgsc.bcm.edu	37	17	2405596	2405596	+	Missense_Mutation	SNP	T	T	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:2405596T>G	ENST00000263092.6	-	2	157	c.30A>C	c.(28-30)agA>agC	p.R10S	METTL16_ENST00000571669.2_Intron|METTL16_ENST00000538844.1_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	10							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						TGTATCTATTTCTTGCATGCA	0.393																																					p.R10S		Atlas-SNP	.											.	METTL16	75	.	0			c.A30C						PASS	.						179.0	156.0	164.0					17																	2405596		1852	4101	5953	SO:0001583	missense	79066	exon2			TCTATTTCTTGCA	AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"""methyltransferase 10 domain containing"""	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.30A>C	chr17.hg19:g.2405596T>G	ENSP00000263092:p.Arg10Ser	57.0	0.0	.		72.0	31.0	.	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.810352	0.70797	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.58940	0.3	5.63	-0.311	0.12761	.	0.000000	0.85682	D	0.000000	T	0.75057	0.3798	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.91635	0.972;0.999	T	0.72074	-0.4400	10	0.87932	D	0	-8.5176	5.0389	0.14449	0.1296:0.2868:0.0:0.5836	.	10;10	Q86W50-2;Q86W50	.;MET16_HUMAN	S	10	ENSP00000263092:R10S	ENSP00000263092:R10S	R	-	3	2	METTL16	2352346	0.998000	0.40836	0.999000	0.59377	0.962000	0.63368	0.343000	0.19944	0.081000	0.16988	-0.444000	0.05651	AGA	.	.	.	none		0.393	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086	
MYH10	4628	hgsc.bcm.edu	37	17	8438748	8438748	+	Silent	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:8438748C>T	ENST00000269243.4	-	15	1959	c.1821G>A	c.(1819-1821)ttG>ttA	p.L607L	MYH10_ENST00000360416.3_Silent_p.L617L|MYH10_ENST00000396239.1_Silent_p.L607L|MYH10_ENST00000379980.4_Silent_p.L623L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	607	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						ATGACTGGTGCAAAAGGGTGG	0.443																																					p.L617L		Atlas-SNP	.											.	MYH10	148	.	0			c.G1851A						PASS	.						103.0	94.0	97.0					17																	8438748		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon16			CTGGTGCAAAAGG	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.1821G>A	chr17.hg19:g.8438748C>T		67.0	0.0	.		85.0	47.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.	.	none		0.443	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
RAI1	10743	hgsc.bcm.edu	37	17	17697096	17697096	+	Missense_Mutation	SNP	G	G	C	rs113303801|rs398124422|rs371983878|rs571229335|rs587780431	byFrequency	TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:17697096G>C	ENST00000353383.1	+	3	1303	c.834G>C	c.(832-834)caG>caC	p.Q278H	RAI1_ENST00000261641.6_Missense_Mutation_p.Q278H	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	278	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GCTATGACcagcagcagcagc	0.637																																					p.Q278H		Atlas-SNP	.											.	RAI1	121	.	0			c.G834C						PASS	.						18.0	23.0	22.0					17																	17697096		2081	4107	6188	SO:0001583	missense	10743	exon3			TGACCAGCAGCAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.834G>C	chr17.hg19:g.17697096G>C	ENSP00000323074:p.Gln278His	45.0	0.0	.		82.0	6.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	g	0.076	-1.192861	0.01607	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.69806	-0.43;1.41;0.17	4.53	-9.06	0.00727	.	0.597522	0.15390	N	0.264894	T	0.43743	0.1261	L	0.39898	1.24	0.18873	N	0.999987	P	0.37864	0.61	B	0.37198	0.243	T	0.31392	-0.9945	10	0.35671	T	0.21	.	4.0515	0.09798	0.4386:0.1326:0.3468:0.0819	.	278	Q7Z5J4	RAI1_HUMAN	H	278;278;278;278;278;255	ENSP00000323074:Q278H;ENSP00000379120:Q278H;ENSP00000261641:Q278H	ENSP00000261641:Q278H	Q	+	3	2	RAI1	17637821	0.953000	0.32496	0.000000	0.03702	0.311000	0.27955	0.063000	0.14410	-2.722000	0.00388	-1.461000	0.01025	CAG	.	.	.	none		0.637	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36623021	36623021	+	Missense_Mutation	SNP	G	G	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:36623021G>T	ENST00000431231.2	+	7	1165	c.1097G>T	c.(1096-1098)gGg>gTg	p.G366V	ARHGAP23_ENST00000443378.1_Missense_Mutation_p.G272V|ARHGAP23_ENST00000437668.3_Missense_Mutation_p.G366V	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	366					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						GAGGCACTGGGGCCAGGGGCA	0.692																																					p.G366V		Atlas-SNP	.											.	ARHGAP23	48	.	0			c.G1097T						PASS	.						10.0	16.0	14.0					17																	36623021		690	1584	2274	SO:0001583	missense	57636	exon7			CACTGGGGCCAGG	AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.1097G>T	chr17.hg19:g.36623021G>T	ENSP00000393539:p.Gly366Val	85.0	0.0	.		113.0	57.0	.	NM_001199417		Missense_Mutation	SNP	ENST00000431231.2	hg19	CCDS56027.1	.	.	.	.	.	.	.	.	.	.	G	9.403	1.078473	0.20227	.	.	ENSG00000225485	ENST00000437668;ENST00000431231;ENST00000443378	T;T;T	0.15017	2.46;2.83;2.78	4.61	4.61	0.57282	.	.	.	.	.	T	0.10294	0.0252	N	0.22421	0.69	0.40687	D	0.982361	P;P	0.44734	0.842;0.615	B;B	0.37888	0.24;0.26	T	0.03651	-1.1016	9	0.59425	D	0.04	.	6.8498	0.24008	0.1906:0.0:0.8094:0.0	.	366;366	Q9P227;Q9P227-2	RHG23_HUMAN;.	V	366;366;272	ENSP00000394153:G366V;ENSP00000393539:G366V;ENSP00000407333:G272V	ENSP00000393539:G366V	G	+	2	0	ARHGAP23	33876547	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	3.391000	0.52530	2.408000	0.81797	0.555000	0.69702	GGG	.	.	.	none		0.692	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274461	39274461	+	Missense_Mutation	SNP	C	C	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:39274461C>G	ENST00000391413.2	-	1	145	c.107G>C	c.(106-108)aGg>aCg	p.R36T		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	36	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GTAGGTGGTCCTGCAGCAGGT	0.662																																					p.R36T		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G107C						PASS	.						21.0	24.0	23.0					17																	39274461		692	1591	2283	SO:0001583	missense	653240	exon1			GTGGTCCTGCAGC	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.107G>C	chr17.hg19:g.39274461C>G	ENSP00000375232:p.Arg36Thr	54.0	0.0	.		71.0	10.0	.	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	hg19	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	8.971	0.972966	0.18736	.	.	ENSG00000212721	ENST00000391413	T	0.01379	4.96	4.17	0.917	0.19380	.	.	.	.	.	T	0.02727	0.0082	M	0.90145	3.09	0.09310	N	1	B	0.22983	0.078	B	0.25614	0.062	T	0.48410	-0.9038	9	0.14252	T	0.57	.	3.4615	0.07535	0.3471:0.4506:0.0:0.2022	.	36	Q9BYQ6	KR411_HUMAN	T	36	ENSP00000375232:R36T	ENSP00000375232:R36T	R	-	2	0	KRTAP4-11	36527987	0.000000	0.05858	0.607000	0.28956	0.268000	0.26511	-0.865000	0.04250	0.397000	0.25310	-0.243000	0.11985	AGG	.	.	.	none		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
TOM1L1	10040	hgsc.bcm.edu	37	17	52990171	52990171	+	Missense_Mutation	SNP	A	A	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:52990171A>G	ENST00000575882.1	+	4	720	c.367A>G	c.(367-369)Att>Gtt	p.I123V	TOM1L1_ENST00000348161.4_Missense_Mutation_p.I46V|TOM1L1_ENST00000540336.1_Missense_Mutation_p.I46V|TOM1L1_ENST00000572158.1_Missense_Mutation_p.I116V|TOM1L1_ENST00000536554.1_Missense_Mutation_p.I46V|TOM1L1_ENST00000575333.1_Missense_Mutation_p.I123V|TOM1L1_ENST00000570371.1_Missense_Mutation_p.I123V|TOM1L1_ENST00000572405.1_Missense_Mutation_p.I88V|TOM1L1_ENST00000445275.2_Missense_Mutation_p.I123V	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	123	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				activation of protein kinase activity (GO:0032147)|intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|positive regulation of protein autophosphorylation (GO:0031954)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	clathrin binding (GO:0030276)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|ubiquitin binding (GO:0043130)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	15						CTTGAATTTCATTAAGGTAAG	0.313																																					p.I123V		Atlas-SNP	.											.	TOM1L1	33	.	0			c.A367G						PASS	.						56.0	58.0	57.0					17																	52990171		2203	4299	6502	SO:0001583	missense	10040	exon4			AATTTCATTAAGG	AJ010071	CCDS11582.1	17q23.2	2008-01-03	2007-01-12			ENSG00000141198			11983	protein-coding gene	gene with protein product		604701	"""target of myb1 (chicken) homolog-like 1"""			10329004, 15611048, 17977829	Standard	NM_005486		Approved	SRCASM	uc002iud.2	O75674		ENST00000575882.1:c.367A>G	chr17.hg19:g.52990171A>G	ENSP00000460823:p.Ile123Val	71.0	0.0	.		74.0	8.0	.	NM_005486	Q53G06|Q8N749	Missense_Mutation	SNP	ENST00000575882.1	hg19	CCDS11582.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309181	0.40895	.	.	ENSG00000141198	ENST00000445275;ENST00000540336;ENST00000348161;ENST00000536554	T;T;T;T	0.27104	1.69;1.69;1.69;1.69	5.72	4.65	0.58169	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.244803	0.33916	N	0.004422	T	0.26919	0.0659	M	0.63428	1.95	0.43673	D	0.996109	P;P;P;P;B;P	0.45396	0.826;0.647;0.685;0.647;0.043;0.857	B;B;B;B;B;B	0.41412	0.338;0.176;0.356;0.19;0.037;0.356	T	0.05053	-1.0909	10	0.56958	D	0.05	-12.0729	9.2264	0.37410	0.9156:0.0:0.0844:0.0	.	46;116;46;123;123;46	B4DUW5;B4E1N0;B7Z9E2;O75674;Q8N749;B4E1M9	.;.;.;TM1L1_HUMAN;.;.	V	123;46;46;46	ENSP00000408958:I123V;ENSP00000441242:I46V;ENSP00000343901:I46V;ENSP00000443099:I46V	ENSP00000343901:I46V	I	+	1	0	TOM1L1	50345170	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.061000	0.64319	2.184000	0.69523	0.460000	0.39030	ATT	.	.	.	none		0.313	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486	
TEX14	56155	hgsc.bcm.edu	37	17	56670954	56670954	+	Missense_Mutation	SNP	C	C	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:56670954C>A	ENST00000240361.8	-	15	2641	c.2556G>T	c.(2554-2556)aaG>aaT	p.K852N	TEX14_ENST00000389934.3_Missense_Mutation_p.K846N|TEX14_ENST00000349033.5_Missense_Mutation_p.K846N			Q8IWB6	TEX14_HUMAN	testis expressed 14	852					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCAAACTGTCCTTGGCTCCTT	0.418																																					p.K852N		Atlas-SNP	.											.	TEX14	343	.	0			c.G2556T						PASS	.						210.0	158.0	176.0					17																	56670954		2203	4300	6503	SO:0001583	missense	56155	exon15			ACTGTCCTTGGCT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2556G>T	chr17.hg19:g.56670954C>A	ENSP00000240361:p.Lys852Asn	109.0	0.0	.		152.0	35.0	.	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352807	0.24512	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.80566	-1.39;-1.39;-1.34	4.78	0.311	0.15831	.	0.716733	0.13889	N	0.355726	T	0.74253	0.3692	L	0.57536	1.79	0.09310	N	1	P;P;P	0.46142	0.704;0.873;0.804	B;B;P	0.44860	0.162;0.436;0.462	T	0.63065	-0.6720	10	0.38643	T	0.18	-8.5367	4.1126	0.10065	0.0:0.5389:0.1727:0.2884	.	852;846;846	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	N	852;846;846	ENSP00000240361:K852N;ENSP00000374584:K846N;ENSP00000268910:K846N	ENSP00000240361:K852N	K	-	3	2	TEX14	54025953	0.050000	0.20438	0.705000	0.30386	0.036000	0.12997	0.098000	0.15189	0.336000	0.23639	-0.251000	0.11542	AAG	.	.	.	none		0.418	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
SMCHD1	23347	hgsc.bcm.edu	37	18	2729383	2729383	+	Silent	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr18:2729383G>A	ENST00000320876.6	+	24	3362	c.3024G>A	c.(3022-3024)acG>acA	p.T1008T	SMCHD1_ENST00000261598.8_Silent_p.T1008T|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1008					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AAGACCAGACGCTTAAAGCAA	0.313																																					p.T1008T		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G3024A						PASS	.						43.0	40.0	41.0					18																	2729383		1791	4050	5841	SO:0001819	synonymous_variant	23347	exon24			CCAGACGCTTAAA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3024G>A	chr18.hg19:g.2729383G>A		57.0	0.0	.		65.0	23.0	.	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.	.	none		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
C18orf8	29919	hgsc.bcm.edu	37	18	21106695	21106695	+	Missense_Mutation	SNP	A	A	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr18:21106695A>C	ENST00000269221.3	+	13	1265	c.1155A>C	c.(1153-1155)gaA>gaC	p.E385D	C18orf8_ENST00000590868.1_Missense_Mutation_p.E337D	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	385						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGAGAAAGGAATGCAAGATGG	0.463																																					p.E385D		Atlas-SNP	.											.	C18orf8	58	.	0			c.A1155C						PASS	.						121.0	113.0	116.0					18																	21106695		2203	4300	6503	SO:0001583	missense	29919	exon13			AAAGGAATGCAAG	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1155A>C	chr18.hg19:g.21106695A>C	ENSP00000269221:p.Glu385Asp	55.0	0.0	.		61.0	22.0	.	NM_013326	Q9BU17|Q9Y5M0	Missense_Mutation	SNP	ENST00000269221.3	hg19	CCDS32803.1	.	.	.	.	.	.	.	.	.	.	A	9.126	1.010228	0.19277	.	.	ENSG00000141452	ENST00000269221;ENST00000544799;ENST00000540942;ENST00000542734	.	.	.	4.86	-9.72	0.00515	.	0.162119	0.53938	N	0.000044	T	0.08537	0.0212	N	0.00327	-1.64	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.40887	-0.9539	9	0.08179	T	0.78	-8.5287	9.6011	0.39605	0.3022:0.2706:0.4272:0.0	.	228;385	B7Z2Y1;Q96DM3	.;MIC1_HUMAN	D	385;228;337;228	.	ENSP00000269221:E385D	E	+	3	2	C18orf8	19360693	0.997000	0.39634	0.870000	0.34147	0.995000	0.86356	0.548000	0.23314	-1.505000	0.01807	0.533000	0.62120	GAA	.	.	.	none		0.463	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
ZNF562	54811	hgsc.bcm.edu	37	19	9763811	9763811	+	Silent	SNP	A	A	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr19:9763811A>G	ENST00000448622.1	-	6	1257	c.1095T>C	c.(1093-1095)aaT>aaC	p.N365N	ZNF562_ENST00000453372.2_Silent_p.N365N|ZNF562_ENST00000537617.1_Silent_p.N249N|ZNF562_ENST00000293648.4_Silent_p.N293N|ZNF562_ENST00000590155.1_Silent_p.N364N|ZNF562_ENST00000541032.1_Silent_p.N328N|ZNF562_ENST00000453792.2_Silent_p.N296N	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						CTCCAGTGTGATTTCGTATGT	0.428																																					p.N365N		Atlas-SNP	.											.	ZNF562	72	.	0			c.T1095C						PASS	.						137.0	129.0	132.0					19																	9763811		2203	4300	6503	SO:0001819	synonymous_variant	54811	exon6			AGTGTGATTTCGT	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"""Zinc fingers, C2H2-type"", ""-"""	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.1095T>C	chr19.hg19:g.9763811A>G		69.0	0.0	.		84.0	27.0	.	NM_001130032	Q32MN2|Q9NXS5	Silent	SNP	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.	.	none		0.428	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656	
AP2S1	1175	hgsc.bcm.edu	37	19	47341743	47341743	+	Silent	SNP	C	C	T			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr19:47341743C>T	ENST00000263270.6	-	5	615	c.390G>A	c.(388-390)aaG>aaA	p.K130K	AP2S1_ENST00000593442.1_Silent_p.K80K|AP2S1_ENST00000352203.4_Silent_p.K144K|AP2S1_ENST00000601498.1_Silent_p.K146K|AP2S1_ENST00000601649.1_Silent_p.K92K|AP2S1_ENST00000597020.1_Silent_p.K110K|AP2S1_ENST00000599990.1_Silent_p.K132K	NM_004069.3	NP_004060.2	P53680	AP2S1_HUMAN	adaptor-related protein complex 2, sigma 1 subunit	130					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|regulation of endocytosis (GO:0030100)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(1)|urinary_tract(1)	3		all_cancers(25;1.24e-06)|all_epithelial(76;1.09e-05)|all_lung(116;0.00019)|Lung NSC(112;0.000601)|Ovarian(192;0.0221)|all_neural(266;0.0459)|Breast(70;0.128)		OV - Ovarian serous cystadenocarcinoma(262;3.86e-05)|all cancers(93;0.000107)|Epithelial(262;0.00325)|GBM - Glioblastoma multiforme(486;0.0336)		GTTTCAGCACCTTCGTCTGGC	0.657																																					p.K130K		Atlas-SNP	.											.	AP2S1	12	.	0			c.G390A						PASS	.						54.0	45.0	48.0					19																	47341743		2203	4300	6503	SO:0001819	synonymous_variant	1175	exon5			CAGCACCTTCGTC	AJ010148	CCDS12693.1, CCDS33062.1	19q13.2-q13.3	2014-02-04				ENSG00000042753			565	protein-coding gene	gene with protein product		602242	"""hypocalciuric hypercalcemia 3 (Oklahoma type)"""	CLAPS2, HHC3		9040778, 9767099, 23222959	Standard	XM_005258500		Approved	FBHOk, FBH3	uc002pft.1	P53680		ENST00000263270.6:c.390G>A	chr19.hg19:g.47341743C>T		88.0	0.0	.		96.0	35.0	.	NM_004069	B2R4Z4|O75977|Q6PK67	Silent	SNP	ENST00000263270.6	hg19	CCDS33062.1																																																																																			.	.	.	none		0.657	AP2S1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466643.1		
ACSS1	84532	hgsc.bcm.edu	37	20	25004243	25004243	+	Silent	SNP	T	T	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr20:25004243T>C	ENST00000323482.4	-	4	745	c.666A>G	c.(664-666)ggA>ggG	p.G222G	ACSS1_ENST00000542618.1_Silent_p.G101G|ACSS1_ENST00000537502.1_Silent_p.G139G|ACSS1_ENST00000432802.2_Silent_p.G222G	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	222					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CACCCCGGAGTCCTTGGTTGA	0.537																																					p.G222G		Atlas-SNP	.											.	ACSS1	46	.	0			c.A666G						PASS	.						75.0	65.0	69.0					20																	25004243		2203	4300	6503	SO:0001819	synonymous_variant	84532	exon4			CCGGAGTCCTTGG		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.666A>G	chr20.hg19:g.25004243T>C		24.0	0.0	.		57.0	21.0	.	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	hg19	CCDS13167.1																																																																																			.	.	.	none		0.537	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
CCM2L	140706	hgsc.bcm.edu	37	20	30602782	30602782	+	Missense_Mutation	SNP	C	C	T	rs545553537		TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr20:30602782C>T	ENST00000300415.8	+	2	119	c.106C>T	c.(106-108)Cgc>Tgc	p.R36C	CCM2L_ENST00000262659.8_Missense_Mutation_p.R36C			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	36																	CAGCGTGAGCCGCCGGCCCCT	0.637													C|||	1	0.000199681	0.0	0.0014	5008	,	,		15977	0.0		0.0	False		,,,				2504	0.0				p.R36C		Atlas-SNP	.											.	.	.	.	0			c.C106T						PASS	.						72.0	72.0	72.0					20																	30602782		2203	4300	6503	SO:0001583	missense	140706	exon2			GTGAGCCGCCGGC	AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 160"""	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.106C>T	chr20.hg19:g.30602782C>T	ENSP00000300415:p.Arg36Cys	89.0	0.0	.		113.0	42.0	.	NM_080625	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	hg19		.	.	.	.	.	.	.	.	.	.	C	29.4	5.007033	0.93287	.	.	ENSG00000101331	ENST00000300415;ENST00000339619;ENST00000262659	T;T	0.60171	0.21;0.21	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.77377	0.4121	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81328	-0.0982	10	0.87932	D	0	-39.7528	16.7122	0.85388	0.0:1.0:0.0:0.0	.	36	Q9NUG4-2	.	C	36	ENSP00000300415:R36C;ENSP00000262659:R36C	ENSP00000262659:R36C	R	+	1	0	C20orf160	30066443	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.299000	0.65716	2.418000	0.82041	0.655000	0.94253	CGC	.	.	.	none		0.637	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625	
MAPK1	5594	hgsc.bcm.edu	37	22	22160189	22160189	+	Missense_Mutation	SNP	G	G	A			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr22:22160189G>A	ENST00000215832.6	-	3	630	c.442C>T	c.(442-444)Cgt>Tgt	p.R148C	MAPK1_ENST00000398822.3_Missense_Mutation_p.R148C|MAPK1_ENST00000544786.1_Missense_Mutation_p.R148C	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	TTGAGGTCACGGTGCAGAACG	0.428																																					p.R148C		Atlas-SNP	.											.	MAPK1	38	.	0			c.C442T						PASS	.						195.0	175.0	182.0					22																	22160189		2203	4300	6503	SO:0001583	missense	5594	exon3			GGTCACGGTGCAG	M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.442C>T	chr22.hg19:g.22160189G>A	ENSP00000215832:p.Arg148Cys	113.0	0.0	.		116.0	37.0	.	NM_002745	A8CZ64	Missense_Mutation	SNP	ENST00000215832.6	hg19	CCDS13795.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.583812	0.86748	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	T;T;T	0.64803	-0.12;-0.12;-0.12	4.77	3.76	0.43208	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050300	0.85682	N	0.000000	T	0.78117	0.4233	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.81491	-0.0909	10	0.87932	D	0	0.4712	13.3578	0.60638	0.0765:0.0:0.9235:0.0	.	148;148	A8CZ64;P28482	.;MK01_HUMAN	C	148;136;148;148	ENSP00000215832:R148C;ENSP00000381803:R148C;ENSP00000440842:R148C	ENSP00000215832:R148C	R	-	1	0	MAPK1	20490189	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.654000	0.83653	1.374000	0.46228	0.650000	0.86243	CGT	.	.	.	none		0.428	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2		
PRR14L	253143	hgsc.bcm.edu	37	22	32108919	32108919	+	Silent	SNP	T	T	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr22:32108919T>G	ENST00000327423.6	-	4	5095	c.4906A>C	c.(4906-4908)Aga>Cga	p.R1636R	PRR14L_ENST00000434485.1_Silent_p.R1636R|PRR14L_ENST00000397493.2_Silent_p.R1636R	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1636										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						CGTCGGTATCTTAGCTTCTGA	0.468											OREG0003533	type=REGULATORY REGION|Gene=BC040859|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R1636R		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4906C						PASS	.						34.0	27.0	29.0					22																	32108919		692	1591	2283	SO:0001819	synonymous_variant	253143	exon4			GGTATCTTAGCTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.4906A>C	chr22.hg19:g.32108919T>G		92.0	0.0	.	829	110.0	41.0	.	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Silent	SNP	ENST00000327423.6	hg19	CCDS13900.2																																																																																			.	.	.	none		0.468	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
CXorf23	256643	hgsc.bcm.edu	37	X	19973668	19973668	+	Missense_Mutation	SNP	A	A	C			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chrX:19973668A>C	ENST00000379682.4	-	4	1324	c.1291T>G	c.(1291-1293)Tcc>Gcc	p.S431A	CXorf23_ENST00000379687.3_Missense_Mutation_p.S431A|CXorf23_ENST00000356980.3_Missense_Mutation_p.S431A			A2AJT9	CX023_HUMAN	chromosome X open reading frame 23	431						mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(6)|skin(1)|urinary_tract(1)	11						CTCTCTGTGGAATAGCTAGAA	0.333																																					p.S431A		Atlas-SNP	.											.	CXorf23	75	.	0			c.T1291G						PASS	.						97.0	86.0	90.0					X																	19973668		2203	4300	6503	SO:0001583	missense	256643	exon4			CTGTGGAATAGCT	AL833278	CCDS14194.2	Xp22.13	2012-11-27			ENSG00000173681	ENSG00000173681			27413	protein-coding gene	gene with protein product						14702039	Standard	NM_198279		Approved		uc004czp.3	A2AJT9	OTTHUMG00000021226	ENST00000379682.4:c.1291T>G	chrX.hg19:g.19973668A>C	ENSP00000369004:p.Ser431Ala	24.0	0.0	.		18.0	12.0	.	NM_198279	A1A4E8|Q5VSM7|Q5VSN1|Q6ZS60|Q8N1W7	Missense_Mutation	SNP	ENST00000379682.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.73|10.73	1.433061|1.433061	0.25813|0.25813	.|.	.|.	ENSG00000173681|ENSG00000173681	ENST00000340625|ENST00000379687;ENST00000379682;ENST00000356980;ENST00000539038	.|T;T;T	.|0.12774	.|2.65;2.65;2.65	5.05|5.05	3.87|3.87	0.44632|0.44632	.|.	.|.	.|.	.|.	.|.	T|T	0.07638|0.07638	0.0192|0.0192	N|N	0.17800|0.17800	0.525|0.525	0.26427|0.26427	N|N	0.976006|0.976006	.|B;B	.|0.23377	.|0.017;0.084	.|B;B	.|0.18561	.|0.011;0.022	T|T	0.39078|0.39078	-0.9631|-0.9631	5|8	.|.	.|.	.|.	.|.	4.3281|4.3281	0.11050|0.11050	0.6669:0.0:0.0972:0.2358|0.6669:0.0:0.0972:0.2358	.|.	.|431;431	.|A2AJT9-2;A2AJT9	.|.;CX023_HUMAN	C|A	39|431;431;431;319	.|ENSP00000369009:S431A;ENSP00000369004:S431A;ENSP00000349470:S431A	.|.	F|S	-|-	2|1	0|0	CXorf23|CXorf23	19883589|19883589	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.551000|1.551000	0.36233|0.36233	0.578000|0.578000	0.29487|0.29487	0.486000|0.486000	0.48141|0.48141	TTC|TCC	.	.	.	none		0.333	CXorf23-006	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000055991.2	NM_198279	
HTATSF1	27336	hgsc.bcm.edu	37	X	135593689	135593689	+	Missense_Mutation	SNP	T	T	G			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chrX:135593689T>G	ENST00000218364.4	+	9	1959	c.1785T>G	c.(1783-1785)aaT>aaG	p.N595K	HTATSF1_ENST00000535601.1_Missense_Mutation_p.N595K	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	595	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					TAGAAGAAAATGACTCTGAAA	0.383																																					p.N595K		Atlas-SNP	.											.	HTATSF1	66	.	0			c.T1785G						PASS	.						55.0	60.0	59.0					X																	135593689		2201	4298	6499	SO:0001583	missense	27336	exon10			AGAAAATGACTCT	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1785T>G	chrX.hg19:g.135593689T>G	ENSP00000218364:p.Asn595Lys	133.0	0.0	.		154.0	111.0	.	NM_001163280	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	hg19	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	T	4.431	0.079832	0.08533	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.04049	3.72;3.72	3.82	2.65	0.31530	.	0.148955	0.31589	N	0.007382	T	0.03011	0.0089	N	0.19112	0.55	0.09310	N	1	B	0.33694	0.421	B	0.27500	0.08	T	0.41875	-0.9484	10	0.87932	D	0	-11.1441	6.7729	0.23604	0.0:0.1179:0.0:0.8821	.	595	O43719	HTSF1_HUMAN	K	595	ENSP00000442699:N595K;ENSP00000218364:N595K	ENSP00000218364:N595K	N	+	3	2	HTATSF1	135421355	0.295000	0.24389	0.047000	0.18901	0.018000	0.09664	1.393000	0.34497	0.653000	0.30826	0.425000	0.28330	AAT	.	.	.	none		0.383	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500	
PKN3	29941	hgsc.bcm.edu	37	9	131477092	131477093	+	Frame_Shift_Ins	INS	-	-	AT			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr9:131477092_131477093insAT	ENST00000291906.4	+	13	1993_1994	c.1600_1601insAT	c.(1600-1602)catfs	p.H534fs	PKN3_ENST00000485301.1_3'UTR	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	534	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CAAACGTCCCCATATGGAGCCT	0.609																																					p.H534fs		Atlas-Indel,Pindel	.											PKN3,neck,malignant_melanoma,0,1	PKN3	62	.	0			c.1600_1601insAT						PASS	.																																			SO:0001589	frameshift_variant	29941	exon13			.	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1603_1604dupAT	chr9.hg19:g.131477095_131477096dupAT	ENSP00000291906:p.His534fs	136.0	0.0	0		144.0	41.0	0.284722	NM_013355	Q9UM03	Frame_Shift_Ins	INS	ENST00000291906.4	hg19	CCDS6908.1																																																																																			.	.	.	none		0.609	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
C19orf18	147685	hgsc.bcm.edu	37	19	58472818	58472818	+	Frame_Shift_Del	DEL	C	C	-			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr19:58472818delC	ENST00000314391.3	-	5	574	c.473delG	c.(472-474)ggtfs	p.G158fs		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18	158						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)		CGTGGACTCACCCTCGTCCTC	0.493																																					p.G158fs		Atlas-Indel,Pindel	.											.	C19orf18	27	.	0			c.474delT						PASS	.						176.0	139.0	152.0					19																	58472818		2203	4300	6503	SO:0001589	frameshift_variant	147685	exon5			.	BC033933	CCDS12967.1	19q13.43	2013-03-11			ENSG00000177025	ENSG00000177025			28642	protein-coding gene	gene with protein product						12477932	Standard	NM_152474		Approved	MGC41906	uc002qqv.3	Q8NEA5	OTTHUMG00000183450	ENST00000314391.3:c.473delG	chr19.hg19:g.58472818delC	ENSP00000321519:p.Gly158fs	62.0	0.0	0		81.0	25.0	0.308642	NM_152474		Frame_Shift_Del	DEL	ENST00000314391.3	hg19	CCDS12967.1																																																																																			.	.	.	none		0.493	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	NM_152474	
LRP2	4036	hgsc.bcm.edu	37	2	169999196	169999197	+	Frame_Shift_Ins	INS	-	-	A	rs367958079		TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:169999196_169999197insA	ENST00000263816.3	-	71	13380_13381	c.13095_13096insT	c.(13093-13098)actgagfs	p.E4366fs		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4366	EGF-like 16. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GCATCACACTCAGTGGTGCTCC	0.574																																					p.E4366_C4367delinsX		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.13096_13097insT						PASS	.																																			SO:0001589	frameshift_variant	4036	exon71			.		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.13096dupT	chr2.hg19:g.169999197_169999197dupA	ENSP00000263816:p.Glu4366fs	53.0	0.0	0		56.0	18.0	0.321429	NM_004525	O00711|Q16215	Frame_Shift_Ins	INS	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.574	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ECD	11319	hgsc.bcm.edu	37	10	74920304	74920308	+	Splice_Site	DEL	CACCT	CACCT	-			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	CACCT	CACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:74920304_74920308delCACCT	ENST00000372979.4	-	3	413_417	c.207_211delAGGTG	c.(205-213)ggaggtgtt>ggtt	p.GV70fs	ECD_ENST00000610256.1_5'UTR|ECD_ENST00000454759.2_Splice_Site_p.GV70fs|ECD_ENST00000430082.2_Splice_Site_p.GV70fs	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	70					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TGAGCAGGAACACCTCCTAAAAACA	0.337																																					p.70_71del		Atlas-INDEL	.											.	ECD	50	.	0			c.208_212del						PASS	.																																			SO:0001630	splice_region_variant	11319	exon3			.	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.206-1AGGTG>-	chr10.hg19:g.74920304_74920308delCACCT		182.0	0.0	0		210.0	48.0	0.228571	NM_001135752	C9JX46|E9PAW8	Frame_Shift_Del	DEL	ENST00000372979.4	hg19	CCDS7321.1																																																																																			.	.	.	none		0.337	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Frame_Shift_Del
HMGCS2	3158	hgsc.bcm.edu	37	1	120301769	120301769	+	Frame_Shift_Del	DEL	A	A	-			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr1:120301769delA	ENST00000369406.3	-	4	871	c.822delT	c.(820-822)cgtfs	p.R274fs	HMGCS2_ENST00000544913.2_Frame_Shift_Del_p.R232fs|HMGCS2_ENST00000476640.1_Intron	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	274					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		GGATTTTTTTACGGTATGATG	0.468																																					p.K275fs		Atlas-Indel,Pindel	.											.	HMGCS2	58	.	0			c.823delA						PASS	.						130.0	130.0	130.0					1																	120301769		2203	4300	6503	SO:0001589	frameshift_variant	3158	exon4			.	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.822delT	chr1.hg19:g.120301769delA	ENSP00000358414:p.Arg274fs	100.0	0.0	0		92.0	23.0	0.25	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Frame_Shift_Del	DEL	ENST00000369406.3	hg19	CCDS905.1																																																																																			.	.	.	none		0.468	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518	
ECD	11319	hgsc.bcm.edu	37	10	74920305	74920311	+	Splice_Site	DEL	ACCTCCT	ACCTCCT	-			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	ACCTCCT	ACCTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:74920305_74920311delACCTCCT	ENST00000372979.4	-	3	412_416	c.206_210delAGGAGGT	c.(205-210)gaggag>g	p.EE69fs	ECD_ENST00000610256.1_5'UTR|ECD_ENST00000454759.2_Splice_Site_p.EE69fs|ECD_ENST00000430082.2_Splice_Site_p.EE69fs	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	69					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					GAGCAGGAACACCTCCTAAAAACAAGA	0.343																																					p.69_71del		Pindel	.											.	ECD	50	.	0			c.206_211del						PASS	.																																			SO:0001630	splice_region_variant	11319	exon3			.	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.206-1AGGAGGT>-	chr10.hg19:g.74920305_74920311delACCTCCT		179.0	0.0	.		205.0	34.0	0.166	NM_001135752	C9JX46|E9PAW8	In_Frame_Del	DEL	ENST00000372979.4	hg19	CCDS7321.1																																																																																			.	.	.	none		0.343	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Frame_Shift_Del
SP8	221833	hgsc.bcm.edu	37	7	20824939	20825106	+	In_Frame_Del	DEL	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	-	rs185796187|rs550042701|rs372591893|rs201180283	byFrequency	TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr7:20824939_20825106delGAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	ENST00000361443.4	-	3	513_680	c.276_443delGCCTGGCTCCAGCGCCTTCTCCCTCACCTCCAGCAGCGCCGCAGCCGCCGCCGCCGCCGCCGCAGCCGCCGCCTCCAGCTCGCCCTTCGCCAACGACTACTCTGTTTTCCAGGCCCCCGGAGTTTCCGGGGGCAGCGGCGGCGGCGGCGGGGGCGGCGGCGGCGGCTC	c.(274-444)tcgcctggctccagcgccttctccctcacctccagcagcgccgcagccgccgccgccgccgccgcagccgccgcctccagctcgcccttcgccaacgactactctgttttccaggcccccggagtttccgggggcagcggcggcggcggcgggggcggcggcggcggctcc>tcc	p.92_148SPGSSAFSLTSSSAAAAAAAAAAAASSSPFANDYSVFQAPGVSGGSGGGGGGGGGGS>S	SP8_ENST00000418710.2_In_Frame_Del_p.110_166SPGSSAFSLTSSSAAAAAAAAAAAASSSPFANDYSVFQAPGVSGGSGGGGGGGGGGS>S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	92	Ser-rich.				dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G165delG(1)|p.G147delG(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						GTGCGCGGAGGAgccgccgccgccgcccccgccgccgccgccgctgcccccgGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAggcggcggctgcggcggcggcggcggcggctgcggcgCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGCGAGCCGCCGC	0.758																																					p.111_166del		Pindel	.											.	SP8	43	.	2	Deletion - In frame(2)	central_nervous_system(2)	c.331_498del						PASS	.																																			SO:0001651	inframe_deletion	221833	exon2			.		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.276_443delGCCTGGCTCCAGCGCCTTCTCCCTCACCTCCAGCAGCGCCGCAGCCGCCGCCGCCGCCGCCGCAGCCGCCGCCTCCAGCTCGCCCTTCGCCAACGACTACTCTGTTTTCCAGGCCCCCGGAGTTTCCGGGGGCAGCGGCGGCGGCGGCGGGGGCGGCGGCGGCGGCTC	chr7.hg19:g.20824939_20825106delGAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	ENSP00000354482:p.Ser92_Gly147del	50.0	0.0	.		99.0	10.0	0.101	NM_182700	Q7Z615|Q7Z616|Q96MJ1	In_Frame_Del	DEL	ENST00000361443.4	hg19	CCDS5372.1																																																																																			.	.	.	none		0.758	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
