#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_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
ZNF343	79175	hgsc.bcm.edu	37	20	2473385	2473385	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr20:2473385delT	ENST00000278772.4	-	5	751	c.264delA	c.(262-264)aaafs	p.K88fs	ZNF343_ENST00000358413.2_Frame_Shift_Del_p.K88fs|ZNF343_ENST00000381253.1_Frame_Shift_Del_p.K88fs|RP4-734P14.4_ENST00000461548.1_Frame_Shift_Del_p.K88fs	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						GCATCACTTCTTTGTATAGAT	0.408																																					p.E89fs		Atlas-Indel	.											ZNF343,NS,carcinoma,0,1	ZNF343	47	1	0			c.265delG						PASS	.						234.0	216.0	222.0					20																	2473385		2203	4300	6503	SO:0001589	frameshift_variant	79175	exon5			.	AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"""Zinc fingers, C2H2-type"", ""-"""	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.264delA	20.37:g.2473385delT	ENSP00000278772:p.Lys88fs	88.0	0.0	0		116.0	15.0	0.12931	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Frame_Shift_Del	DEL	ENST00000278772.4	37	CCDS13028.1																																																																																			.	.	none		0.408	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325	
ZNF223	7766	hgsc.bcm.edu	37	19	44570830	44570831	+	Frame_Shift_Del	DEL	AG	AG	-	rs568496344	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:44570830_44570831delAG	ENST00000434772.3	+	5	1104_1105	c.849_850delAG	c.(847-852)acagggfs	p.G284fs	ZNF223_ENST00000591793.1_Frame_Shift_Del_p.G394fs	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GAATTCACACAGGGGAGAAGCC	0.421														7	0.00139776	0.0	0.0	5008	,	,		22779	0.0069		0.0	False		,,,				2504	0.0				p.283_283del		Pindel,Atlas-Indel	.											.	ZNF223	61	.	0			c.848_849del						PASS	.																																			SO:0001589	frameshift_variant	7766	exon5			.	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.849_850delAG	19.37:g.44570830_44570831delAG	ENSP00000401947:p.Gly284fs	91.0	0.0	.		226.0	39.0	0.173	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Frame_Shift_Del	DEL	ENST00000434772.3	37	CCDS12635.1																																																																																			.	.	none		0.421	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
GAST	2520	hgsc.bcm.edu	37	17	39872062	39872064	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:39872062_39872064delGAA	ENST00000329402.3	+	3	311_313	c.244_246delGAA	c.(244-246)gaadel	p.E85del	JUP_ENST00000540235.1_Intron|RNA5SP442_ENST00000365050.1_RNA	NM_000805.4	NP_000796.1	P01350	GAST_HUMAN	gastrin	85					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			ATGGCTGGAGGAAGAAGAAGAAG	0.562																																					p.81_82del		Atlas-Indel	.											.	GAST	13	.	0			c.243_245del						PASS	.																																			SO:0001651	inframe_deletion	2520	exon3			.		CCDS11404.1	17q21.2	2013-02-26	2005-06-14	2005-06-14	ENSG00000184502	ENSG00000184502		"""Endogenous ligands"""	4164	protein-coding gene	gene with protein product	"""preprogastrin"""	137250		GAS			Standard	NM_000805		Approved		uc002hxl.3	P01350	OTTHUMG00000133496	ENST00000329402.3:c.244_246delGAA	17.37:g.39872071_39872073delGAA	ENSP00000331358:p.Glu85del	94.0	0.0	0		113.0	15.0	0.132743	NM_000805	P78463|P78464	In_Frame_Del	DEL	ENST00000329402.3	37	CCDS11404.1																																																																																			.	.	none		0.562	GAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257409.1		
ATAD5	79915	hgsc.bcm.edu	37	17	29221631	29221635	+	Frame_Shift_Del	DEL	TCTCT	TCTCT	-			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	TCTCT	TCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:29221631_29221635delTCTCT	ENST00000321990.4	+	22	5725_5729	c.5347_5351delTCTCT	c.(5347-5352)tctcttfs	p.SL1783fs	TEFM_ENST00000579183.1_5'Flank	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1783					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TTCGAGTCGATCTCTTCTCTATGTG	0.341																																					p.1782_1784del		Pindel,Atlas-Indel	.											.	ATAD5	150	.	0			c.5346_5350del						PASS	.																																			SO:0001589	frameshift_variant	79915	exon22			.		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.5347_5351delTCTCT	17.37:g.29221636_29221640delTCTCT	ENSP00000313171:p.Ser1783fs	65.0	0.0	.		55.0	14.0	0.255	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Frame_Shift_Del	DEL	ENST00000321990.4	37	CCDS11260.1																																																																																			.	.	none		0.341	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
P2RY10	27334	hgsc.bcm.edu	37	X	78216808	78216808	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:78216808delT	ENST00000171757.2	+	4	1071	c.791delT	c.(790-792)attfs	p.I264fs	P2RY10_ENST00000544091.1_Frame_Shift_Del_p.I264fs	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						ATTAACTTTATTTTTTACACC	0.458																																					p.I264fs		Pindel,Atlas-Indel	.											.	P2RY10	99	.	0			c.790delA						PASS	.						145.0	137.0	140.0					X																	78216808		2203	4300	6503	SO:0001589	frameshift_variant	27334	exon2			.	AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.791delT	X.37:g.78216808delT	ENSP00000171757:p.Ile264fs	25.0	0.0	.		36.0	20.0	0.556	NM_198333	D3DTE5|Q4VBN7|Q86V16	Frame_Shift_Del	DEL	ENST00000171757.2	37	CCDS14442.1																																																																																			.	.	none		0.458	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1		
NFKBIE	4794	hgsc.bcm.edu	37	6	44229563	44229564	+	In_Frame_Ins	INS	-	-	GTACAGCCAGATGGA	rs375743668		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:44229563_44229564insGTACAGCCAGATGGA	ENST00000275015.5	-	3	906_907	c.907_908insTCCATCTGGCTGTAC	c.(907-909)cat>cTCCATCTGGCTGTACat	p.302_303insLHLAV		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	302					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTGGTCCAGATGTACAGCCAGA	0.614																																					p.H303delinsLHLAVH		Pindel	.											.	NFKBIE	31	.	0			c.908_909insTCCATCTGGCTGTAC						PASS	.																																			SO:0001652	inframe_insertion	4794	exon3			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.893_907dupTCCATCTGGCTGTAC	6.37:g.44229563_44229564insGTACAGCCAGATGGA	ENSP00000275015:p.Leu298_Val302dup	35.0	0.0	.		36.0	10.0	0.278	NM_004556	Q5T9V9	In_Frame_Ins	INS	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.614	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
GP2	2813	hgsc.bcm.edu	37	16	20329589	20329589	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:20329589A>C	ENST00000381362.4	-	8	1256	c.1180T>G	c.(1180-1182)Ttt>Gtt	p.F394V	GP2_ENST00000302555.5_Missense_Mutation_p.F391V|GP2_ENST00000381360.5_Missense_Mutation_p.F247V|GP2_ENST00000341642.5_Missense_Mutation_p.F244V|GP2_ENST00000573897.1_5'Flank	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	394	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ACCAGGTTAAACCGGGAGGTG	0.498																																					p.F394V		Atlas-SNP	.											.	GP2	122	.	0			c.T1180G						PASS	.						203.0	164.0	178.0					16																	20329589		2203	4300	6503	SO:0001583	missense	2813	exon8			GGTTAAACCGGGA	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.1180T>G	16.37:g.20329589A>C	ENSP00000370767:p.Phe394Val	199.0	0.0	0		184.0	37.0	0.201087	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	ENST00000381362.4	37	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.246113	0.59103	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	5.8	4.69	0.59074	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	.	.	.	.	D	0.91620	0.7352	M	0.90595	3.13	0.09310	N	0.999993	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.85130	0.987;0.997;0.997;0.995	D	0.83676	0.0169	9	0.41790	T	0.15	-14.0034	10.2265	0.43229	0.9209:0.0:0.0791:0.0	.	244;372;391;394	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	V	391;394;247;244;372	ENSP00000304044:F391V;ENSP00000370767:F394V;ENSP00000370765:F247V;ENSP00000343861:F244V	ENSP00000304044:F391V	F	-	1	0	GP2	20237090	0.853000	0.29707	0.007000	0.13788	0.754000	0.42855	1.836000	0.39191	0.989000	0.38761	0.528000	0.53228	TTT	.	.	none		0.498	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
MYO18B	84700	hgsc.bcm.edu	37	22	26422889	26422889	+	Missense_Mutation	SNP	G	G	A	rs187337528		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:26422889G>A	ENST00000407587.2	+	43	7121	c.6952G>A	c.(6952-6954)Gct>Act	p.A2318T	MYO18B_ENST00000536101.1_Missense_Mutation_p.A2317T|MYO18B_ENST00000335473.7_Missense_Mutation_p.A2317T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2317						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A2318T(2)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CGAAGGGGCCGCTGGTGGTCT	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		16066	0.001		0.0	False		,,,				2504	0.0				p.A2317T		Atlas-SNP	.											MYO18B,NS,haematopoietic_neoplasm,0,2	MYO18B	322	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G6949A						PASS	.						28.0	34.0	32.0					22																	26422889		1894	4096	5990	SO:0001583	missense	84700	exon43			GGGGCCGCTGGTG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.6952G>A	22.37:g.26422889G>A	ENSP00000386096:p.Ala2318Thr	31.0	0.0	0		38.0	13.0	0.342105	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.012	-1.691334	0.00731	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86956	-2.17;-2.17;-2.19	4.43	-7.52	0.01341	.	7739.210000	0.00166	N	0.000002	T	0.64294	0.2585	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.001	T	0.58284	-0.7663	10	0.23891	T	0.37	.	0.11	0.00055	0.3104:0.2229:0.2234:0.2433	.	1830;2319;2317;2318;2317	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	T	2317;2317;2318	ENSP00000441229:A2317T;ENSP00000334563:A2317T;ENSP00000386096:A2318T	ENSP00000334563:A2317T	A	+	1	0	MYO18B	24752889	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-1.861000	0.01654	-1.216000	0.02607	-0.448000	0.05591	GCT	G|1.000;A|0.000	0.000	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
NBEA	26960	hgsc.bcm.edu	37	13	35782857	35782857	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:35782857A>G	ENST00000400445.3	+	32	5921	c.5387A>G	c.(5386-5388)aAg>aGg	p.K1796R	NBEA_ENST00000540320.1_Missense_Mutation_p.K1796R|NBEA_ENST00000310336.4_Missense_Mutation_p.K1796R|NBEA_ENST00000379939.2_Missense_Mutation_p.K1793R	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1796					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GTGCCTGTAAAGAAACCACCT	0.428																																					p.K1796R		Atlas-SNP	.											.	NBEA	340	.	0			c.A5387G						PASS	.						63.0	60.0	61.0					13																	35782857		1837	4085	5922	SO:0001583	missense	26960	exon32			CTGTAAAGAAACC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5387A>G	13.37:g.35782857A>G	ENSP00000383295:p.Lys1796Arg	89.0	0.0	0		68.0	26.0	0.382353	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.708964	0.68615	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.60171	0.21;0.22;0.22;0.21	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.54854	0.1884	M	0.65975	2.015	0.80722	D	1	P;P	0.42409	0.779;0.666	B;B	0.34346	0.141;0.18	T	0.61768	-0.6995	10	0.52906	T	0.07	.	16.056	0.80805	1.0:0.0:0.0:0.0	.	1796;1793	Q8NFP9;Q5T321	NBEA_HUMAN;.	R	1796;1796;1793;1796;423	ENSP00000440951:K1796R;ENSP00000383295:K1796R;ENSP00000369271:K1793R;ENSP00000308534:K1796R	ENSP00000308534:K1796R	K	+	2	0	NBEA	34680857	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.855000	0.92236	2.178000	0.69098	0.533000	0.62120	AAG	.	.	none		0.428	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
CACNA1C	775	hgsc.bcm.edu	37	12	2676736	2676736	+	Splice_Site	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:2676736C>T	ENST00000347598.4	+	13	1671	c.1671C>T	c.(1669-1671)gaC>gaT	p.D557D	CACNA1C_ENST00000399595.1_Splice_Site_p.D557D|CACNA1C_ENST00000399629.1_Splice_Site_p.D557D|CACNA1C_ENST00000399606.1_Splice_Site_p.D557D|CACNA1C_ENST00000399621.1_Splice_Site_p.D557D|CACNA1C_ENST00000399638.1_Splice_Site_p.D557D|CACNA1C_ENST00000399641.1_Splice_Site_p.D557D|CACNA1C_ENST00000480911.1_Splice_Site_p.D557D|CACNA1C_ENST00000327702.7_Splice_Site_p.D557D|CACNA1C_ENST00000335762.5_Splice_Site_p.D582D|CACNA1C_ENST00000399634.1_Splice_Site_p.D557D|CACNA1C_ENST00000399617.1_Splice_Site_p.D557D|CACNA1C_ENST00000406454.3_Splice_Site_p.D557D|CACNA1C_ENST00000399603.1_Splice_Site_p.D557D|CACNA1C_ENST00000399597.1_Splice_Site_p.D557D|CACNA1C_ENST00000399644.1_Splice_Site_p.D557D|CACNA1C_ENST00000399591.1_Splice_Site_p.D557D|CACNA1C_ENST00000399601.1_Splice_Site_p.D557D|CACNA1C_ENST00000402845.3_Splice_Site_p.D557D|CACNA1C_ENST00000399649.1_Splice_Site_p.D557D|CACNA1C_ENST00000344100.3_Splice_Site_p.D557D|CACNA1C_ENST00000399655.1_Splice_Site_p.D557D|CACNA1C_ENST00000399637.1_Splice_Site_p.D557D	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	557					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCTGCCAGACACGGCAAACA	0.567																																					p.D557D		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C1671T						PASS	.						18.0	20.0	19.0					12																	2676736		2095	4247	6342	SO:0001630	splice_region_variant	775	exon13			GCCAGACACGGCA	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1670-1C>T	12.37:g.2676736C>T		41.0	0.0	0		38.0	16.0	0.421053	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																			.	.	none		0.567	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	Silent
STAT3	6774	hgsc.bcm.edu	37	17	40474470	40474470	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:40474470T>C	ENST00000264657.5	-	21	2243	c.1931A>G	c.(1930-1932)cAg>cGg	p.Q644R	STAT3_ENST00000404395.3_Missense_Mutation_p.Q644R|STAT3_ENST00000585517.1_Missense_Mutation_p.Q644R|STAT3_ENST00000389272.3_Missense_Mutation_p.Q546R|STAT3_ENST00000588969.1_Missense_Mutation_p.Q644R	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	644	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		Missing (in AD-HIES). {ECO:0000269|PubMed:17881745}.		acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		GTTGTTCAGCTGCTGCTTTGT	0.458									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.Q644R		Atlas-SNP	.											.	STAT3	268	.	0			c.A1931G	GRCh37	CM083172	STAT3	M		PASS	.						255.0	223.0	234.0					17																	40474470		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTCAGCTGCTGCT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"""SH2 domain containing"""	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1931A>G	17.37:g.40474470T>C	ENSP00000264657:p.Gln644Arg	237.0	0.0	0		283.0	137.0	0.484099	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.266403	0.59540	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.88354	-2.37;-2.37;-2.37	4.64	4.64	0.57946	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.87557	0.6207	N	0.11313	0.125	0.58432	D	0.999996	P;P;P	0.49559	0.908;0.925;0.925	D;D;D	0.67900	0.922;0.954;0.954	D	0.87438	0.2393	10	0.33141	T	0.24	-36.6451	14.2314	0.65895	0.0:0.0:0.0:1.0	.	644;644;644	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	R	644;546;644	ENSP00000264657:Q644R;ENSP00000373923:Q546R;ENSP00000384943:Q644R	ENSP00000264657:Q644R	Q	-	2	0	STAT3	37727996	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.128000	0.71650	1.953000	0.56701	0.460000	0.39030	CAG	.	.	none		0.458	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
C5	727	hgsc.bcm.edu	37	9	123719614	123719614	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:123719614C>T	ENST00000223642.1	-	39	4740	c.4711G>A	c.(4711-4713)Gaa>Aaa	p.E1571K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1571	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	AAAACATTTTCTACAGTGATG	0.348																																					p.E1571K		Atlas-SNP	.											.	C5	124	.	0			c.G4711A						PASS	.						197.0	191.0	193.0					9																	123719614		2203	4300	6503	SO:0001583	missense	727	exon39			CATTTTCTACAGT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4711G>A	9.37:g.123719614C>T	ENSP00000223642:p.Glu1571Lys	92.0	0.0	0		83.0	5.0	0.060241	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357662	0.61293	.	.	ENSG00000106804	ENST00000223642	T	0.22336	1.96	5.86	4.96	0.65561	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.150336	0.64402	D	0.000016	T	0.29061	0.0722	L	0.43923	1.385	0.38310	D	0.943213	D	0.61080	0.989	P	0.57620	0.824	T	0.09596	-1.0667	10	0.21014	T	0.42	.	10.9448	0.47294	0.0:0.9142:0.0:0.0858	.	1571	P01031	CO5_HUMAN	K	1571	ENSP00000223642:E1571K	ENSP00000223642:E1571K	E	-	1	0	C5	122759435	1.000000	0.71417	0.920000	0.36463	0.417000	0.31264	4.611000	0.61162	1.486000	0.48398	0.655000	0.94253	GAA	.	.	none		0.348	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
TCL1A	8115	hgsc.bcm.edu	37	14	96180291	96180291	+	Missense_Mutation	SNP	G	G	A	rs201228671	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:96180291G>A	ENST00000402399.1	-	1	242	c.113C>T	c.(112-114)aCc>aTc	p.T38I	TCL1A_ENST00000554012.1_Missense_Mutation_p.T38I|RP11-164H13.1_ENST00000553445.1_RNA|TCL1A_ENST00000555202.1_Missense_Mutation_p.T38I|RP11-164H13.1_ENST00000547644.2_RNA|RP11-164H13.1_ENST00000556386.1_RNA|TCL1A_ENST00000556450.1_Missense_Mutation_p.T38I	NM_021966.2	NP_068801.1	P56279	TCL1A_HUMAN	T-cell leukemia/lymphoma 1A	38					multicellular organismal development (GO:0007275)|stem cell maintenance (GO:0019827)	cell cortex (GO:0005938)|endoplasmic reticulum (GO:0005783)|pronucleus (GO:0045120)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		TACCTCGATGGTTAAGGGCAG	0.647			T	TRA@	T-CLL																																p.T38I	Ovarian(96;1068 2019 35393 39316)	Atlas-SNP	.		Dom	yes		14	14q32.1	8115	T-cell leukemia/lymphoma 1A		L	.	TCL1A	26	.	0			c.C113T						PASS	.						86.0	81.0	83.0					14																	96180291		2203	4300	6503	SO:0001583	missense	8115	exon1			TCGATGGTTAAGG	X82240	CCDS9941.1	14q32.1	2008-07-03				ENSG00000100721			11648	protein-coding gene	gene with protein product		186960				2783489, 7809072	Standard	NM_021966		Approved	TCL1	uc001yfb.4	P56279		ENST00000402399.1:c.113C>T	14.37:g.96180291G>A	ENSP00000385036:p.Thr38Ile	59.0	0.0	0		61.0	32.0	0.52459	NM_001098725	Q6IBK7	Missense_Mutation	SNP	ENST00000402399.1	37	CCDS9941.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.242016	0.22796	.	.	ENSG00000100721	ENST00000554012;ENST00000402399;ENST00000556450;ENST00000555202	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	3.15	-2.77	0.05877	.	1.693040	0.03527	N	0.221932	T	0.20170	0.0485	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.22487	-1.0215	10	0.31617	T	0.26	-11.297	7.6786	0.28500	0.4562:0.0:0.5438:0.0	.	38	P56279	TCL1A_HUMAN	I	38	ENSP00000451506:T38I;ENSP00000385036:T38I;ENSP00000450701:T38I;ENSP00000450496:T38I	ENSP00000385036:T38I	T	-	2	0	TCL1A	95250044	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.190000	0.03058	-0.453000	0.07076	-1.090000	0.02178	ACC	G|0.999;C|0.001	.	alt		0.647	TCL1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413246.1		
ARMCX5	64860	hgsc.bcm.edu	37	X	101858323	101858323	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:101858323G>A	ENST00000604957.1	+	1	3876	c.1254G>A	c.(1252-1254)ggG>ggA	p.G418G	ARMCX5_ENST00000537008.1_Silent_p.G418G|ARMCX5_ENST00000246174.2_Silent_p.G418G|ARMCX5_ENST00000372742.1_Silent_p.G418G|RP4-769N13.7_ENST00000602441.1_RNA|ARMCX5_ENST00000536530.1_Silent_p.G418G|RP4-769N13.6_ENST00000476910.2_RNA|ARMCX5_ENST00000541409.1_Silent_p.G418G	NM_001168478.1	NP_001161950.1	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	418										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	22						AATTACTAGGGCACTTGAGTA	0.388																																					p.G418G		Atlas-SNP	.											.	ARMCX5	55	.	0			c.G1254A						PASS	.						53.0	53.0	53.0					X																	101858323		2203	4300	6503	SO:0001819	synonymous_variant	64860	exon3			ACTAGGGCACTTG		CCDS14500.1	Xq22.1-q22.3	2014-03-21			ENSG00000125962	ENSG00000125962		"""Armadillo repeat containing"""	25772	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_022838		Approved	FLJ12969, GASP5	uc004ejh.3	Q6P1M9	OTTHUMG00000022062	ENST00000604957.1:c.1254G>A	X.37:g.101858323G>A		97.0	0.0	0		92.0	11.0	0.119565	NM_022838	B3KU88|D3DX99|Q68DB4|Q9BVZ3|Q9H969	Silent	SNP	ENST00000604957.1	37	CCDS14500.1																																																																																			.	.	none		0.388	ARMCX5-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469659.1	NM_022838	
FNIP2	57600	hgsc.bcm.edu	37	4	159789387	159789387	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:159789387C>T	ENST00000264433.6	+	13	1674	c.1599C>T	c.(1597-1599)aaC>aaT	p.N533N	FNIP2_ENST00000379346.3_Silent_p.N556N	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	533					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TACAAGAGAACCAGCTGACCT	0.493																																					p.N533N		Atlas-SNP	.											.	FNIP2	90	.	0			c.C1599T						PASS	.						92.0	94.0	94.0					4																	159789387		2077	4216	6293	SO:0001819	synonymous_variant	57600	exon13			AGAGAACCAGCTG	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 1"""	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.1599C>T	4.37:g.159789387C>T		80.0	0.0	0		78.0	4.0	0.0512821	NM_020840	Q05DC3|Q96I31|Q9H994	Silent	SNP	ENST00000264433.6	37	CCDS47155.1																																																																																			.	.	none		0.493	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	
FN1	2335	hgsc.bcm.edu	37	2	216289966	216289966	+	Missense_Mutation	SNP	G	G	A	rs145123731	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:216289966G>A	ENST00000359671.1	-	7	1152	c.887C>T	c.(886-888)cCg>cTg	p.P296L	FN1_ENST00000432072.2_Missense_Mutation_p.P296L|FN1_ENST00000446046.1_Missense_Mutation_p.P296L|FN1_ENST00000356005.4_Missense_Mutation_p.P296L|FN1_ENST00000426059.1_Missense_Mutation_p.P296L|FN1_ENST00000354785.4_Missense_Mutation_p.P296L|FN1_ENST00000357009.2_Missense_Mutation_p.P296L|FN1_ENST00000336916.4_Missense_Mutation_p.P296L|FN1_ENST00000323926.6_Missense_Mutation_p.P296L|FN1_ENST00000346544.3_Missense_Mutation_p.P296L|FN1_ENST00000421182.1_Missense_Mutation_p.P296L|FN1_ENST00000345488.5_Missense_Mutation_p.P296L|FN1_ENST00000357867.4_Missense_Mutation_p.P296L|FN1_ENST00000443816.1_Missense_Mutation_p.P296L			P02751	FINC_HUMAN	fibronectin 1	296					acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GTGAGGCTGCGGTTGGTAAAC	0.517																																					p.P296L		Atlas-SNP	.											FN1_ENST00000354785,colon,carcinoma,+1,2	FN1	521	2	0			c.C887T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400	12.9+/-30.5	0,6,2197	122.0	119.0	120.0		887,887,887,887,887,887	5.8	1.0	2	dbSNP_134	120	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	FN1	NM_002026.2,NM_054034.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	98,98,98,98,98,98	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	296/2356,296/658,296/2177,296/2297,296/2331,296/2478	216289966	6,13000	2203	4300	6503	SO:0001583	missense	2335	exon7			GGCTGCGGTTGGT		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.887C>T	2.37:g.216289966G>A	ENSP00000352696:p.Pro296Leu	117.0	0.0	0		96.0	33.0	0.34375	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	G	24.1	4.491508	0.84962	0.001362	0.0	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.48836	0.8;2.19;2.34;0.88;2.4;2.04;2.39;2.04;2.34;2.08;1.57;0.88;1.47;1.46	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000002	T	0.68100	0.2964	L	0.59436	1.845	0.80722	D	1	D;D;P;D;D;D;D;D;D;D;P	0.89917	0.989;1.0;0.885;0.982;1.0;1.0;1.0;1.0;1.0;1.0;0.936	P;D;P;P;D;D;D;D;D;D;B	0.91635	0.592;0.998;0.477;0.688;0.999;0.998;0.983;0.996;0.999;0.999;0.396	T	0.68108	-0.5496	10	0.72032	D	0.01	.	20.1374	0.98035	0.0:0.0:1.0:0.0	.	296;296;296;296;296;296;296;296;296;296;296	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	L	296	ENSP00000394423:P296L;ENSP00000323534:P296L;ENSP00000338200:P296L;ENSP00000350534:P296L;ENSP00000346839:P296L;ENSP00000352696:P296L;ENSP00000265312:P296L;ENSP00000273049:P296L;ENSP00000349509:P296L;ENSP00000410422:P296L;ENSP00000415018:P296L;ENSP00000399538:P296L;ENSP00000348285:P296L;ENSP00000398907:P296L	ENSP00000265313:P296L	P	-	2	0	FN1	215998211	1.000000	0.71417	0.999000	0.59377	0.682000	0.39822	2.458000	0.45014	2.763000	0.94921	0.563000	0.77884	CCG	G|1.000;A|0.000	0.000	strong		0.517	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
COL16A1	1307	hgsc.bcm.edu	37	1	32149326	32149326	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:32149326C>T	ENST00000373672.3	-	34	2877	c.2361G>A	c.(2359-2361)agG>agA	p.R787R	COL16A1_ENST00000271069.6_Silent_p.R786R|COL16A1_ENST00000373668.3_Silent_p.R787R	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	787	Triple-helical region 5 (COL5) with 3 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CCTGGACTCCCCTTCCTGGAG	0.602																																					p.R787R	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G2361A						PASS	.						73.0	92.0	86.0					1																	32149326		1979	4151	6130	SO:0001819	synonymous_variant	1307	exon34			GACTCCCCTTCCT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.2361G>A	1.37:g.32149326C>T		64.0	0.0	0		73.0	31.0	0.424658	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			.	.	none		0.602	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
PLXNA2	5362	hgsc.bcm.edu	37	1	208216497	208216497	+	Missense_Mutation	SNP	C	C	T	rs572241200		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:208216497C>T	ENST00000367033.3	-	21	4683	c.3926G>A	c.(3925-3927)cGc>cAc	p.R1309H		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1309					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GATTCCTGAGCGGTCCAGGTC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19355	0.001		0.0	False		,,,				2504	0.0				p.R1309H		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	0			c.G3926A						PASS	.						94.0	89.0	91.0					1																	208216497		2203	4300	6503	SO:0001583	missense	5362	exon21			CCTGAGCGGTCCA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.3926G>A	1.37:g.208216497C>T	ENSP00000356000:p.Arg1309His	110.0	0.0	0		117.0	38.0	0.324786	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.774387	0.96922	.	.	ENSG00000076356	ENST00000367033	T	0.00932	5.53	5.42	5.42	0.78866	.	0.048395	0.85682	D	0.000000	T	0.01835	0.0058	N	0.24115	0.695	0.80722	D	1	D	0.67145	0.996	P	0.50970	0.655	T	0.70963	-0.4729	10	0.87932	D	0	.	19.2386	0.93873	0.0:1.0:0.0:0.0	.	1309	O75051	PLXA2_HUMAN	H	1309	ENSP00000356000:R1309H	ENSP00000356000:R1309H	R	-	2	0	PLXNA2	206283120	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.454000	0.80714	2.543000	0.85770	0.650000	0.86243	CGC	.	.	none		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
TTK	7272	hgsc.bcm.edu	37	6	80744802	80744802	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:80744802T>A	ENST00000369798.2	+	15	1826	c.1715T>A	c.(1714-1716)aTa>aAa	p.I572K	TTK_ENST00000509894.1_Missense_Mutation_p.I571K|TTK_ENST00000230510.3_Missense_Mutation_p.I571K	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	572	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CGGAACGAAATAGCTTATTTG	0.279																																					p.I572K		Atlas-SNP	.											.	TTK	199	.	0			c.T1715A						PASS	.						77.0	83.0	81.0					6																	80744802		2199	4288	6487	SO:0001583	missense	7272	exon15			ACGAAATAGCTTA		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1715T>A	6.37:g.80744802T>A	ENSP00000358813:p.Ile572Lys	190.0	0.0	0		127.0	49.0	0.385827	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135303	0.77662	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	T;T;T	0.76448	-1.02;-1.02;-1.02	5.67	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043215	0.85682	D	0.000000	T	0.76506	0.3997	L	0.39085	1.19	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	T	0.80013	-0.1560	10	0.66056	D	0.02	.	12.1537	0.54064	0.0:0.0:0.1433:0.8567	.	572;571	P33981;A8K8U5	TTK_HUMAN;.	K	571;571;572	ENSP00000422936:I571K;ENSP00000230510:I571K;ENSP00000358813:I572K	ENSP00000230510:I571K	I	+	2	0	TTK	80801521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	0.959000	0.37980	0.455000	0.32223	ATA	.	.	none		0.279	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
LYN	4067	hgsc.bcm.edu	37	8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:56910951G>A	ENST00000519728.1	+	11	1393	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	LYN_ENST00000420292.1_3'UTR|LYN_ENST00000520220.2_Missense_Mutation_p.R345Q	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	TACATTCACCGGGACCTGCGA	0.448																																					p.R366Q		Atlas-SNP	.											.	LYN	54	.	0			c.G1097A						PASS	.						115.0	110.0	112.0					8																	56910951		2203	4300	6503	SO:0001583	missense	4067	exon11			TTCACCGGGACCT	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"""SH2 domain containing"""	6735	protein-coding gene	gene with protein product		165120	"""v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"""			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1097G>A	8.37:g.56910951G>A	ENSP00000428924:p.Arg366Gln	194.0	0.0	0		187.0	65.0	0.347594	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851905	0.97023	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	D;D	0.88354	-2.37;-2.37	5.52	5.52	0.82312	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97099	0.9052	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.98468	1.0599	10	0.87932	D	0	.	19.4505	0.94865	0.0:0.0:1.0:0.0	.	436;366	Q6NUK7;P07948	.;LYN_HUMAN	Q	366;345	ENSP00000428924:R366Q;ENSP00000428424:R345Q	ENSP00000428924:R366Q	R	+	2	0	LYN	57073505	1.000000	0.71417	0.688000	0.30117	0.945000	0.59286	9.869000	0.99810	2.597000	0.87782	0.655000	0.94253	CGG	.	.	none		0.448	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350	
ADO	84890	hgsc.bcm.edu	37	10	64565347	64565347	+	Nonsense_Mutation	SNP	C	C	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:64565347C>G	ENST00000373783.1	+	1	832	c.528C>G	c.(526-528)taC>taG	p.Y176*	RP11-436D10.3_ENST00000425290.1_RNA	NM_032804.5	NP_116193.2	Q96SZ5	AEDO_HUMAN	2-aminoethanethiol (cysteamine) dioxygenase	176						mitochondrion (GO:0005739)	cysteamine dioxygenase activity (GO:0047800)|metal ion binding (GO:0046872)			lung(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					GGGCCGAGTACACCGAGGCCA	0.741																																					p.Y176X		Atlas-SNP	.											.	ADO	10	.	0			c.C528G						PASS	.						16.0	15.0	15.0					10																	64565347		2184	4278	6462	SO:0001587	stop_gained	84890	exon1			CGAGTACACCGAG	BC028589	CCDS7266.2	10q21.3	2007-08-28	2007-08-28	2007-08-28	ENSG00000181915	ENSG00000181915	1.13.11.19		23506	protein-coding gene	gene with protein product	"""cysteamine dioxygenase"""	611392	"""chromosome 10 open reading frame 22"""	C10orf22		17581819	Standard	NM_032804		Approved	FLJ14547	uc001jmg.3	Q96SZ5	OTTHUMG00000018306	ENST00000373783.1:c.528C>G	10.37:g.64565347C>G	ENSP00000362888:p.Tyr176*	26.0	0.0	0		22.0	4.0	0.181818	NM_032804	B1AL29	Nonsense_Mutation	SNP	ENST00000373783.1	37	CCDS7266.2	.	.	.	.	.	.	.	.	.	.	C	40	7.980773	0.98594	.	.	ENSG00000181915	ENST00000373783	.	.	.	4.93	4.0	0.46444	.	0.396168	0.26293	N	0.025215	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.37	12.6806	0.56920	0.0:0.6815:0.3185:0.0	.	.	.	.	X	176	.	ENSP00000362888:Y176X	Y	+	3	2	ADO	64235353	1.000000	0.71417	0.929000	0.37066	0.937000	0.57800	2.542000	0.45744	1.002000	0.39104	0.655000	0.94253	TAC	.	.	none		0.741	ADO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048243.2	NM_032804	
LLGL2	3993	hgsc.bcm.edu	37	17	73552167	73552167	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:73552167G>A	ENST00000392550.3	+	3	233	c.116G>A	c.(115-117)gGc>gAc	p.G39D	LLGL2_ENST00000375227.4_Missense_Mutation_p.G39D|LLGL2_ENST00000578363.1_Missense_Mutation_p.G39D|LLGL2_ENST00000577200.1_Missense_Mutation_p.G39D|LLGL2_ENST00000167462.5_Missense_Mutation_p.G39D	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	39					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			AGCGCCCTCGGCTACAGCCCG	0.687																																					p.G39D		Atlas-SNP	.											.	LLGL2	155	.	0			c.G116A						PASS	.						75.0	64.0	68.0					17																	73552167		2202	4300	6502	SO:0001583	missense	3993	exon3			CCCTCGGCTACAG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.116G>A	17.37:g.73552167G>A	ENSP00000376333:p.Gly39Asp	28.0	0.0	0		50.0	24.0	0.48	NM_001015002	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109326	0.37242	.	.	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000375227	T;T;T	0.61742	1.7;1.7;0.08	4.68	4.68	0.58851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.051374	0.85682	D	0.000000	T	0.53465	0.1798	L	0.36672	1.1	0.49687	D	0.999815	B;B;B	0.27971	0.169;0.124;0.196	B;B;B	0.33799	0.049;0.049;0.17	T	0.56649	-0.7944	10	0.56958	D	0.05	-7.1885	17.7752	0.88505	0.0:0.0:1.0:0.0	.	39;39;39	Q6P1M3-2;Q6P1M3;Q6P1M3-3	.;L2GL2_HUMAN;.	D	39	ENSP00000167462:G39D;ENSP00000376333:G39D;ENSP00000364375:G39D	ENSP00000167462:G39D	G	+	2	0	LLGL2	71063762	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	3.755000	0.55197	2.431000	0.82371	0.563000	0.77884	GGC	.	.	none		0.687	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
TET2	54790	hgsc.bcm.edu	37	4	106193850	106193850	+	Nonsense_Mutation	SNP	A	A	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:106193850A>T	ENST00000540549.1	+	10	5172	c.4312A>T	c.(4312-4314)Aaa>Taa	p.K1438*	TET2_ENST00000380013.4_Nonsense_Mutation_p.K1438*|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Nonsense_Mutation_p.K1459*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1438					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TCAGGAGGAGAAAAAACGGAG	0.473			"""Mis N, F"""		MDS																																p.K1438X		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.A4312T						PASS	.						161.0	152.0	155.0					4																	106193850		692	1591	2283	SO:0001587	stop_gained	54790	exon10			GAGGAGAAAAAAC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4312A>T	4.37:g.106193850A>T	ENSP00000442788:p.Lys1438*	106.0	0.0	0		130.0	108.0	0.830769	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	A	50	16.191500	0.99857	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9501	15.5771	0.76400	1.0:0.0:0.0:0.0	.	.	.	.	X	1438;1459;1438	.	ENSP00000369351:K1438X	K	+	1	0	TET2	106413299	1.000000	0.71417	0.996000	0.52242	0.835000	0.47333	6.960000	0.76036	2.324000	0.78689	0.533000	0.62120	AAA	.	.	none		0.473	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
RBM14	10432	hgsc.bcm.edu	37	11	66391989	66391989	+	Silent	SNP	C	C	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:66391989C>A	ENST00000310137.4	+	2	781	c.642C>A	c.(640-642)cgC>cgA	p.R214R	RBM4_ENST00000503028.2_Intron|RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM14_ENST00000409372.1_3'UTR|RBM4_ENST00000514361.3_Intron|RBM14-RBM4_ENST00000511114.1_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	214					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GTCGCGACCGCAGCCCTCTGC	0.642																																					p.R214R		Atlas-SNP	.											RBM14,rectum,carcinoma,+1,1	RBM14	59	1	0			c.C642A						scavenged	.						43.0	44.0	44.0					11																	66391989		2200	4295	6495	SO:0001819	synonymous_variant	10432	exon2			CGACCGCAGCCCT	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.642C>A	11.37:g.66391989C>A		42.0	1.0	0.0238095		50.0	2.0	0.04	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	37	CCDS8147.1																																																																																			.	.	none		0.642	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328	
C3	718	hgsc.bcm.edu	37	19	6714453	6714453	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:6714453G>A	ENST00000245907.6	-	5	601	c.509C>T	c.(508-510)cCg>cTg	p.P170L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	170					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GATGCCTTCCGGGTTCTGTGG	0.567																																					p.P170L		Atlas-SNP	.											.	C3	192	.	0			c.C509T						PASS	.						57.0	48.0	51.0					19																	6714453		2203	4299	6502	SO:0001583	missense	718	exon5			CCTTCCGGGTTCT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.509C>T	19.37:g.6714453G>A	ENSP00000245907:p.Pro170Leu	87.0	0.0	0		61.0	26.0	0.42623	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	g	16.30	3.085611	0.55861	.	.	ENSG00000125730	ENST00000245907	T	0.78481	-1.18	4.97	4.97	0.65823	Alpha-2-macroglobulin, N-terminal (1);	0.168178	0.53938	D	0.000053	D	0.91717	0.7381	H	0.96142	3.775	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94274	0.7513	10	0.87932	D	0	.	15.7294	0.77790	0.0:0.0:1.0:0.0	.	170	P01024	CO3_HUMAN	L	170	ENSP00000245907:P170L	ENSP00000245907:P170L	P	-	2	0	C3	6665453	1.000000	0.71417	0.904000	0.35570	0.061000	0.15899	6.362000	0.73077	2.297000	0.77311	0.509000	0.49947	CCG	.	.	none		0.567	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
RFX6	222546	hgsc.bcm.edu	37	6	117248414	117248414	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:117248414C>T	ENST00000332958.2	+	17	2126	c.2110C>T	c.(2110-2112)Cag>Tag	p.Q704*		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	704					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						CTCTAACTACCAGACTGTGTT	0.507																																					p.Q704X		Atlas-SNP	.											.	RFX6	141	.	0			c.C2110T						PASS	.						137.0	129.0	131.0					6																	117248414		2203	4300	6503	SO:0001587	stop_gained	222546	exon17			AACTACCAGACTG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.2110C>T	6.37:g.117248414C>T	ENSP00000332208:p.Gln704*	130.0	0.0	0		114.0	55.0	0.482456	NM_173560	Q5T6B3	Nonsense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	37	6.417248	0.97550	.	.	ENSG00000185002	ENST00000332958	.	.	.	5.15	5.15	0.70609	.	0.122893	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-14.9498	13.1466	0.59465	0.0:0.9235:0.0:0.0765	.	.	.	.	X	704	.	ENSP00000332208:Q704X	Q	+	1	0	RFX6	117355107	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.039000	0.64185	2.682000	0.91365	0.655000	0.94253	CAG	.	.	none		0.507	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
PITPNM3	83394	hgsc.bcm.edu	37	17	6358850	6358850	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:6358850G>A	ENST00000262483.8	-	20	2820	c.2733C>T	c.(2731-2733)caC>caT	p.H911H	PITPNM3_ENST00000576664.1_5'UTR|PITPNM3_ENST00000421306.3_Silent_p.H875H	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	911					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		CTGGCTGCGCGTGCAGCCCGA	0.697																																					p.H911H		Atlas-SNP	.											.	PITPNM3	91	.	0			c.C2733T						PASS	.						23.0	27.0	26.0					17																	6358850		2195	4299	6494	SO:0001819	synonymous_variant	83394	exon20			CTGCGCGTGCAGC	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.2733C>T	17.37:g.6358850G>A		42.0	0.0	0		42.0	16.0	0.380952	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	37	CCDS11076.1																																																																																			.	.	none		0.697	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
NUP210	23225	hgsc.bcm.edu	37	3	13379381	13379381	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:13379381C>T	ENST00000254508.5	-	26	3590	c.3508G>A	c.(3508-3510)Gtg>Atg	p.V1170M	NUP210_ENST00000485755.1_Intron	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1170					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CGGATCCTCACGGCCCTTAGC	0.642																																					p.V1170M		Atlas-SNP	.											.	NUP210	182	.	0			c.G3508A						PASS	.						53.0	46.0	49.0					3																	13379381		2203	4300	6503	SO:0001583	missense	23225	exon26			TCCTCACGGCCCT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3508G>A	3.37:g.13379381C>T	ENSP00000254508:p.Val1170Met	26.0	0.0	0		42.0	18.0	0.428571	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365480	0.41902	.	.	ENSG00000132182	ENST00000254508	T	0.09163	3.01	4.86	4.86	0.63082	.	0.073766	0.56097	D	0.000034	T	0.17874	0.0429	M	0.70595	2.14	0.50313	D	0.999868	D	0.60160	0.987	P	0.45881	0.496	T	0.03051	-1.1078	10	0.30078	T	0.28	-20.1592	15.1051	0.72315	0.0:1.0:0.0:0.0	.	1170	Q8TEM1	PO210_HUMAN	M	1170	ENSP00000254508:V1170M	ENSP00000254508:V1170M	V	-	1	0	NUP210	13354381	0.987000	0.35691	0.941000	0.38009	0.017000	0.09413	2.662000	0.46766	2.408000	0.81797	0.655000	0.94253	GTG	.	.	none		0.642	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
PLXNB3	5365	hgsc.bcm.edu	37	X	153035889	153035889	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:153035889A>G	ENST00000361971.5	+	9	1997	c.1883A>G	c.(1882-1884)gAg>gGg	p.E628G	PLXNB3_ENST00000538776.1_Missense_Mutation_p.E281G|PLXNB3_ENST00000538543.1_Missense_Mutation_p.E178G|PLXNB3_ENST00000538282.1_Missense_Mutation_p.E238G|PLXNB3_ENST00000538966.1_Missense_Mutation_p.E651G	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	628	PSI 2.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCCTTGGAGGCGGCTGCC	0.657																																					p.E651G		Atlas-SNP	.											.	PLXNB3	208	.	0			c.A1952G						PASS	.						57.0	43.0	47.0					X																	153035889		2193	4296	6489	SO:0001583	missense	5365	exon10			CCTTGGAGGCGGC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1883A>G	X.37:g.153035889A>G	ENSP00000355378:p.Glu628Gly	118.0	0.0	0		132.0	6.0	0.0454545	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	a	5.600	0.295469	0.10622	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.68624	5.21;5.17;4.6;1.91;-0.34	5.1	3.86	0.44501	.	0.274152	0.33591	N	0.004748	T	0.54631	0.1870	L	0.56769	1.78	0.23204	N	0.99813	B;B;B;B;B	0.28233	0.075;0.204;0.058;0.035;0.025	B;B;B;B;B	0.25614	0.021;0.055;0.04;0.062;0.045	T	0.39292	-0.9621	10	0.24483	T	0.36	.	4.6981	0.12813	0.6145:0.1945:0.0:0.191	.	281;310;178;651;628	B7Z3H9;B7Z9A5;F5GZZ4;F5H773;Q9ULL4	.;.;.;.;PLXB3_HUMAN	G	651;628;281;178;238	ENSP00000442736:E651G;ENSP00000355378:E628G;ENSP00000445569:E281G;ENSP00000444086:E178G;ENSP00000441919:E238G	ENSP00000355378:E628G	E	+	2	0	PLXNB3	152689083	0.004000	0.15560	0.572000	0.28498	0.065000	0.16274	0.309000	0.19332	1.683000	0.51011	0.427000	0.28365	GAG	.	.	none		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
B2M	567	hgsc.bcm.edu	37	15	45003779	45003779	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:45003779T>C	ENST00000558401.1	+	1	105	c.35T>C	c.(34-36)cTa>cCa	p.L12P	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Missense_Mutation_p.L12P|B2M_ENST00000544417.1_Missense_Mutation_p.L12P	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	12					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.A11fs*42(1)|p.L12Q(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GTGCTCGCGCTACTCTCTCTT	0.617																																					p.L12P		Atlas-SNP	.											B2M,colon,carcinoma,0,2	B2M	99	2	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	c.T35C						PASS	.						132.0	94.0	107.0					15																	45003779		2198	4298	6496	SO:0001583	missense	567	exon1			TCGCGCTACTCTC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.35T>C	15.37:g.45003779T>C	ENSP00000452780:p.Leu12Pro	104.0	0.0	0		99.0	76.0	0.767677	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.443926	0.63067	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01388	4.95	5.35	5.35	0.76521	.	9.011740	0.00721	U	0.000881	T	0.10809	0.0264	M	0.74647	2.275	0.29321	N	0.867335	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.17107	-1.0380	10	0.87932	D	0	.	11.9001	0.52678	0.0:0.0:0.0:1.0	.	12;12;12	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	P	12	ENSP00000437604:L12P	ENSP00000340858:L12P	L	+	2	0	B2M	42791071	0.253000	0.23982	0.051000	0.19133	0.007000	0.05969	3.556000	0.53734	2.371000	0.80710	0.533000	0.62120	CTA	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
ZNF337	26152	hgsc.bcm.edu	37	20	25656946	25656946	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr20:25656946C>T	ENST00000376436.1	-	4	1517	c.978G>A	c.(976-978)ggG>ggA	p.G326G	ZNF337_ENST00000252979.5_Silent_p.G326G|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000538750.1_Silent_p.G294G|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	326					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TATAGCCTCGCCCACACTCCT	0.483																																					p.G326G		Atlas-SNP	.											.	ZNF337	65	.	0			c.G978A						PASS	.						105.0	100.0	102.0					20																	25656946		2203	4300	6503	SO:0001819	synonymous_variant	26152	exon5			GCCTCGCCCACAC		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"""Zinc fingers, C2H2-type"", ""-"""	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.978G>A	20.37:g.25656946C>T		95.0	0.0	0		106.0	8.0	0.0754717	NM_015655	B4DSM2|Q9Y3Y5	Silent	SNP	ENST00000376436.1	37	CCDS13174.1																																																																																			.	.	none		0.483	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1		
ALOX15	246	hgsc.bcm.edu	37	17	4544856	4544856	+	Missense_Mutation	SNP	C	C	T	rs145573801	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:4544856C>T	ENST00000570836.1	-	2	187	c.91G>A	c.(91-93)Ggg>Agg	p.G31R	ALOX15_ENST00000545513.1_Missense_Mutation_p.G53R|ALOX15_ENST00000293761.3_Missense_Mutation_p.G31R|ALOX15_ENST00000574640.1_Missense_Mutation_p.G31R			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	31	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		GCCGCCTCCCCGTGCTGGCCG	0.687																																					p.G31R		Atlas-SNP	.											.	ALOX15	70	.	0			c.G91A						PASS	.						23.0	23.0	23.0					17																	4544856		2194	4291	6485	SO:0001583	missense	246	exon1			CCTCCCCGTGCTG	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.91G>A	17.37:g.4544856C>T	ENSP00000458832:p.Gly31Arg	60.0	0.0	0		95.0	5.0	0.0526316	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133041	0.77662	.	.	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.73047	-0.71;-0.71	5.33	2.14	0.27477	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.071907	0.53938	D	0.000048	T	0.69486	0.3116	L	0.60904	1.88	0.37169	D	0.902979	D;P;D	0.60160	0.987;0.792;0.972	B;B;P	0.47206	0.406;0.176;0.541	T	0.72858	-0.4165	10	0.42905	T	0.14	-18.9916	13.5218	0.61572	0.0:0.5739:0.4261:0.0	.	53;31;31	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	R	31;53	ENSP00000293761:G31R;ENSP00000439855:G53R	ENSP00000293761:G31R	G	-	1	0	ALOX15	4491605	0.682000	0.27624	0.783000	0.31826	0.940000	0.58332	0.928000	0.28831	0.218000	0.20820	0.655000	0.94253	GGG	C|1.000;G|0.000	.	alt		0.687	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
TLCD1	116238	hgsc.bcm.edu	37	17	27052991	27052991	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:27052991G>A	ENST00000292090.3	-	1	235	c.125C>T	c.(124-126)aCc>aTc	p.T42I	AC010761.14_ENST00000587898.1_RNA|NEK8_ENST00000268766.6_5'Flank|TLCD1_ENST00000394933.3_Intron|SNORD42A_ENST00000459584.1_RNA|SNORD4B_ENST00000459083.1_RNA	NM_138463.3	NP_612472.1	Q96CP7	TLCD1_HUMAN	TLC domain containing 1	42	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(2)|lung(2)	7	Lung NSC(42;0.00431)					CCAGCGCCAGGTGCGCAGGGG	0.697																																					p.T42I		Atlas-SNP	.											.	TLCD1	15	.	0			c.C125T						PASS	.						22.0	23.0	22.0					17																	27052991		2201	4298	6499	SO:0001583	missense	116238	exon1			CGCCAGGTGCGCA	BC014072	CCDS11242.1, CCDS54102.1	17q11.2	2007-03-23			ENSG00000160606	ENSG00000160606			25177	protein-coding gene	gene with protein product						12151215	Standard	NM_138463		Approved		uc002hco.3	Q96CP7	OTTHUMG00000132683	ENST00000292090.3:c.125C>T	17.37:g.27052991G>A	ENSP00000292090:p.Thr42Ile	60.0	0.0	0		63.0	4.0	0.0634921	NM_138463	A8MYP9	Missense_Mutation	SNP	ENST00000292090.3	37	CCDS11242.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480642	0.84747	.	.	ENSG00000160606	ENST00000292090	.	.	.	4.6	4.6	0.57074	TRAM/LAG1/CLN8 homology domain (2);	0.205916	0.42821	D	0.000648	T	0.41465	0.1160	N	0.19112	0.55	0.80722	D	1	B	0.26744	0.158	B	0.20767	0.031	T	0.39035	-0.9633	9	0.49607	T	0.09	-2.0919	12.7767	0.57453	0.0:0.0:1.0:0.0	.	42	Q96CP7	TLCD1_HUMAN	I	42	.	ENSP00000292090:T42I	T	-	2	0	TLCD1	24077118	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.514000	0.45503	2.385000	0.81259	0.555000	0.69702	ACC	.	.	none		0.697	TLCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255973.1	NM_138463	
COL21A1	81578	hgsc.bcm.edu	37	6	55922465	55922465	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:55922465G>A	ENST00000244728.5	-	30	3261	c.2864C>T	c.(2863-2865)cCa>cTa	p.P955L	COL21A1_ENST00000370819.1_Missense_Mutation_p.P952L|COL21A1_ENST00000370808.2_Missense_Mutation_p.P321L|COL21A1_ENST00000535941.1_Missense_Mutation_p.P955L|COL21A1_ENST00000467045.1_5'UTR	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	955					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CTAATAGTTTGGTCCTTTTCT	0.468																																					p.P955L		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2864T						PASS	.						84.0	79.0	81.0					6																	55922465		1908	4133	6041	SO:0001583	missense	81578	exon30			TAGTTTGGTCCTT	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2864C>T	6.37:g.55922465G>A	ENSP00000244728:p.Pro955Leu	102.0	0.0	0		106.0	15.0	0.141509	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604681	0.46423	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.91792	-2.52;-2.47;-2.51;-2.91	4.62	4.62	0.57501	.	0.000000	0.56097	D	0.000039	D	0.95736	0.8613	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.997;0.997	D	0.96364	0.9268	10	0.87932	D	0	.	17.8313	0.88683	0.0:0.0:1.0:0.0	.	321;955;955;312	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	L	955;952;955;952;321	ENSP00000244728:P955L;ENSP00000359855:P952L;ENSP00000444384:P955L;ENSP00000359844:P321L	ENSP00000244728:P955L	P	-	2	0	COL21A1	56030424	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.527000	0.90594	2.275000	0.75901	0.655000	0.94253	CCA	.	.	none		0.468	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
SLC17A9	63910	hgsc.bcm.edu	37	20	61594979	61594979	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr20:61594979A>G	ENST00000370351.4	+	7	900	c.769A>G	c.(769-771)Atc>Gtc	p.I257V	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Missense_Mutation_p.I251V	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	257					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						CTCCTTCTTCATCCTCCTCTC	0.677																																					p.I257V		Atlas-SNP	.											.	SLC17A9	54	.	0			c.A769G						PASS	.						54.0	59.0	58.0					20																	61594979		2148	4249	6397	SO:0001583	missense	63910	exon7			TTCTTCATCCTCC	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.769A>G	20.37:g.61594979A>G	ENSP00000359376:p.Ile257Val	110.0	0.0	0		131.0	63.0	0.480916	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	37	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	a	0.269	-0.994082	0.02145	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.59224	0.28;0.28	4.86	2.62	0.31277	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.162450	0.52532	N	0.000066	T	0.40247	0.1109	N	0.20574	0.59	0.28715	N	0.903358	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.006;0.005;0.005	T	0.22626	-1.0211	10	0.30078	T	0.28	.	11.9672	0.53042	0.9221:0.0:0.0779:0.0	.	277;257;251	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	V	257;251	ENSP00000359376:I257V;ENSP00000359374:I251V	ENSP00000359374:I251V	I	+	1	0	SLC17A9	61065424	1.000000	0.71417	0.996000	0.52242	0.054000	0.15201	2.976000	0.49289	0.231000	0.21079	-0.741000	0.03529	ATC	.	.	none		0.677	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53730084	53730084	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:53730084T>G	ENST00000379925.3	-	3	259	c.209A>C	c.(208-210)aAg>aCg	p.K70T	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000568653.3_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000566096.1_Missense_Mutation_p.K70T	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	70					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				ATCCTCCTGCTTGCGGGCATG	0.368																																					p.K70T		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.A209C						PASS	.						118.0	123.0	121.0					16																	53730084		2198	4300	6498	SO:0001583	missense	23322	exon3			TCCTGCTTGCGGG		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.209A>C	16.37:g.53730084T>G	ENSP00000369257:p.Lys70Thr	86.0	0.0	0		80.0	37.0	0.4625	NM_001127897	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.313073	0.81358	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.68765	-0.35;-0.35	5.73	5.73	0.89815	.	0.052346	0.64402	D	0.000001	T	0.78729	0.4329	L	0.58969	1.84	0.48236	D	0.999616	D;D;P;D	0.76494	0.991;0.991;0.5;0.999	P;P;B;D	0.70716	0.894;0.776;0.173;0.97	T	0.79308	-0.1857	10	0.51188	T	0.08	-19.9813	16.0142	0.80425	0.0:0.0:0.0:1.0	.	70;70;70;70	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	T	70	ENSP00000369257:K70T;ENSP00000262135:K70T	ENSP00000262135:K70T	K	-	2	0	RPGRIP1L	52287585	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.371000	0.73119	2.187000	0.69744	0.460000	0.39030	AAG	.	.	none		0.368	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
NBN	4683	hgsc.bcm.edu	37	8	90967770	90967770	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:90967770T>C	ENST00000265433.3	-	10	1292	c.1138A>G	c.(1138-1140)Agg>Ggg	p.R380G	NBN_ENST00000409330.1_Missense_Mutation_p.R298G	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	380	Interaction with MTOR, MAPKAP1 and RICTOR.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TCTTTTGGCCTTTCACTCAAA	0.338								Homologous recombination																													p.R380G		Atlas-SNP	.											.	NBN	86	.	0			c.A1138G						PASS	.						74.0	69.0	71.0					8																	90967770		2202	4298	6500	SO:0001583	missense	4683	exon10			TTGGCCTTTCACT	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1138A>G	8.37:g.90967770T>C	ENSP00000265433:p.Arg380Gly	71.0	0.0	0		78.0	4.0	0.0512821	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	T	8.917	0.960201	0.18507	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387	T;T	0.59083	1.95;0.29	5.45	5.45	0.79879	.	1.198520	0.05445	N	0.548399	T	0.54902	0.1887	L	0.51422	1.61	0.32695	N	0.513694	B;B	0.27450	0.179;0.179	B;B	0.24269	0.036;0.052	T	0.48080	-0.9066	10	0.24483	T	0.36	-0.1736	11.9007	0.52682	0.0:0.0:0.0:1.0	.	380;380	A6H8Y5;O60934	.;NBN_HUMAN	G	380;298;380	ENSP00000265433:R380G;ENSP00000386924:R298G	ENSP00000265433:R380G	R	-	1	2	NBN	91036946	0.946000	0.32159	0.941000	0.38009	0.575000	0.36095	1.542000	0.36137	2.063000	0.61619	0.528000	0.53228	AGG	.	.	none		0.338	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
STK11IP	114790	hgsc.bcm.edu	37	2	220474114	220474114	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:220474114C>T	ENST00000456909.1	+	17	2046	c.1956C>T	c.(1954-1956)acC>acT	p.T652T	STK11IP_ENST00000295641.10_Silent_p.T663T			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	663					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCCAGTCACCAATGTGGCTC	0.637																																					p.T663T		Atlas-SNP	.											.	STK11IP	152	.	0			c.C1989T						PASS	.						31.0	37.0	35.0					2																	220474114		2041	4196	6237	SO:0001819	synonymous_variant	114790	exon17			AGTCACCAATGTG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1956C>T	2.37:g.220474114C>T		72.0	0.0	0		77.0	4.0	0.0519481	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	37																																																																																				.	.	none		0.637	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
RNF219	79596	hgsc.bcm.edu	37	13	79219011	79219011	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:79219011C>G	ENST00000282003.6	-	2	252	c.194G>C	c.(193-195)tGc>tCc	p.C65S		NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	65							zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		AATTTCTTTGCAAGGATTTTC	0.353																																					p.C65S		Atlas-SNP	.											.	RNF219	94	.	0			c.G194C						PASS	.						109.0	111.0	110.0					13																	79219011		2203	4300	6503	SO:0001583	missense	79596	exon2			TCTTTGCAAGGAT	BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"""RING-type (C3HC4) zinc fingers"""	20308	protein-coding gene	gene with protein product		615906	"""chromosome 13 open reading frame 7"""	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.194G>C	13.37:g.79219011C>G	ENSP00000282003:p.Cys65Ser	63.0	0.0	0		66.0	19.0	0.287879	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477267	0.84640	.	.	ENSG00000152193	ENST00000282003	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70197	-0.4938	9	0.59425	D	0.04	-5.6669	19.0489	0.93034	0.0:1.0:0.0:0.0	.	65	Q5W0B1	RN219_HUMAN	S	65	.	ENSP00000282003:C65S	C	-	2	0	RNF219	78117012	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.294000	0.78760	2.489000	0.83994	0.655000	0.94253	TGC	.	.	none		0.353	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546	
CLPSL1	340204	hgsc.bcm.edu	37	6	35754842	35754842	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:35754842A>G	ENST00000373861.5	+	2	261	c.167A>G	c.(166-168)aAt>aGt	p.N56S	CLPSL1_ENST00000542261.1_Missense_Mutation_p.N55S			A2RUU4	COLL1_HUMAN	colipase-like 1	56					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										GCTCCAGACAATTGCGAGTCG	0.657																																					p.N56S		Atlas-SNP	.											.	.	.	.	0			c.A167G						PASS	.						23.0	31.0	28.0					6																	35754842		2159	4255	6414	SO:0001583	missense	340204	exon2			CAGACAATTGCGA		CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 127"""	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.167A>G	6.37:g.35754842A>G	ENSP00000362968:p.Asn56Ser	38.0	0.0	0		41.0	10.0	0.243902	NM_001010886	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Missense_Mutation	SNP	ENST00000373861.5	37	CCDS43456.1	.	.	.	.	.	.	.	.	.	.	A	0.108	-1.141934	0.01728	.	.	ENSG00000204140	ENST00000373861;ENST00000373860;ENST00000542261;ENST00000428710	T;T	0.31247	1.5;1.5	2.05	-4.09	0.03951	.	2.100700	0.03133	U	0.165408	T	0.03608	0.0103	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.12477	-1.0546	10	0.33940	T	0.23	.	0.212	0.00157	0.3332:0.2323:0.2143:0.2202	.	56	A2RUU4	CF127_HUMAN	S	56;56;55;9	ENSP00000362968:N56S;ENSP00000438478:N55S	ENSP00000362967:N56S	N	+	2	0	C6orf127	35862820	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.569000	0.00915	-3.437000	0.00163	-3.063000	0.00068	AAT	.	.	none		0.657	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886	
FSD1L	83856	hgsc.bcm.edu	37	9	108297595	108297595	+	Silent	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:108297595T>C	ENST00000481272.1	+	12	1493	c.1374T>C	c.(1372-1374)gaT>gaC	p.D458D	FSD1L_ENST00000484973.1_Silent_p.D425D|FSD1L_ENST00000394926.3_Silent_p.D437D|FSD1L_ENST00000374707.1_Silent_p.D239D|FSD1L_ENST00000374710.3_Silent_p.D426D|FSD1L_ENST00000539376.1_Silent_p.D311D	NM_001145313.1	NP_001138785.1	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing 1-like	458	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									NS(1)|endometrium(1)	2						GTGATTTTGATGGGGGTAAGT	0.333																																					p.D458D		Atlas-SNP	.											.	FSD1L	31	.	0			c.T1374C						PASS	.						46.0	40.0	42.0					9																	108297595		692	1590	2282	SO:0001819	synonymous_variant	83856	exon12			TTTTGATGGGGGT	AF316830	CCDS6765.2, CCDS47999.1, CCDS6765.3, CCDS75870.1	9q31	2013-02-11	2006-03-10	2006-03-10	ENSG00000106701	ENSG00000106701		"""Fibronectin type III domain containing"""	13753	protein-coding gene	gene with protein product		609829	"""cystatin and DUF19 domain containing 1"", ""coiled-coil domain containing 10"""	CSDUFD1, CCDC10, FSD1NL, FSD1CL		11267680	Standard	XM_005252254		Approved		uc004bcq.2	Q9BXM9	OTTHUMG00000020426	ENST00000481272.1:c.1374T>C	9.37:g.108297595T>C		61.0	0.0	0		58.0	14.0	0.241379	NM_001145313	A2A338|A6NKH7|B7Z5S6|B7Z5W3|Q5T879|Q5T880	Silent	SNP	ENST00000481272.1	37	CCDS47999.1																																																																																			.	.	none		0.333	FSD1L-007	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349935.1	NM_207647	
TLX3	30012	hgsc.bcm.edu	37	5	170736474	170736474	+	Silent	SNP	G	G	A	rs2303742	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:170736474G>A	ENST00000296921.5	+	1	187	c.105G>A	c.(103-105)ccG>ccA	p.P35P		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	35					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CACCCGCCCCGCGGGGCCCCG	0.766			T	BCL11B	T-ALL								G|||	14	0.00279553	0.0	0.0	5008	,	,		10162	0.0139		0.0	False		,,,				2504	0.0				p.P35P	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"""T-cell leukemia, homeobox 3 (HOX11L2)"""		L	TLX3_ENST00000296921,NS,carcinoma,+2,1	TLX3	23	1	0			c.G105A						scavenged	.						7.0	10.0	9.0					5																	170736474		2127	4181	6308	SO:0001819	synonymous_variant	30012	exon1			CGCCCCGCGGGGC	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"""Homeoboxes / ANTP class : NKL subclass"""	13532	protein-coding gene	gene with protein product		604640	"""homeo box 11-like 2"", ""T-cell leukemia, homeobox 3"""	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.105G>A	5.37:g.170736474G>A		4.0	2.0	0.5		14.0	12.0	0.857143	NM_021025	Q96AD3	Silent	SNP	ENST00000296921.5	37	CCDS34288.1																																																																																			G|0.995;A|0.005	0.005	strong		0.766	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3		
KIF17	57576	hgsc.bcm.edu	37	1	21031010	21031010	+	Silent	SNP	G	G	A	rs76507805		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:21031010G>A	ENST00000247986.2	-	5	1363	c.1053C>T	c.(1051-1053)cgC>cgT	p.R351R	KIF17_ENST00000375044.1_Silent_p.R251R|KIF17_ENST00000400463.3_Silent_p.R351R			Q9P2E2	KIF17_HUMAN	kinesin family member 17	351					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CCTGGTACTCGCGAAGCAGCG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		15725	0.001		0.0	False		,,,				2504	0.0				p.R351R		Atlas-SNP	.											KIF17,colon,carcinoma,0,1	KIF17	130	1	0			c.C1053T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	134.0	105.0	115.0		1053,1053	-4.3	1.0	1	dbSNP_131	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	351/1029,351/1030	21031010	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon5			GTACTCGCGAAGC	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1053C>T	1.37:g.21031010G>A		183.0	0.0	0		168.0	53.0	0.315476	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			G|1.000;A|0.000	0.000	strong		0.602	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
RIMBP2	23504	hgsc.bcm.edu	37	12	130892335	130892335	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:130892335G>A	ENST00000261655.4	-	16	3024	c.2861C>T	c.(2860-2862)aCg>aTg	p.T954M		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	954	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CATTCTCCGCGTCGATACCGA	0.512																																					p.T954M		Atlas-SNP	.											RIMBP2,NS,carcinoma,+1,1	RIMBP2	220	1	0			c.C2861T						PASS	.						290.0	222.0	245.0					12																	130892335		2203	4300	6503	SO:0001583	missense	23504	exon16			CTCCGCGTCGATA	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2861C>T	12.37:g.130892335G>A	ENSP00000261655:p.Thr954Met	128.0	0.0	0		121.0	42.0	0.347107	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189429	0.78789	.	.	ENSG00000060709	ENST00000261655;ENST00000536632	T;T	0.29397	1.57;1.57	4.61	4.61	0.57282	Src homology-3 domain (2);	0.054336	0.64402	D	0.000001	T	0.44201	0.1282	L	0.31371	0.925	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.36504	-0.9745	10	0.40728	T	0.16	-14.8894	17.447	0.87580	0.0:0.0:1.0:0.0	.	954	O15034	RIMB2_HUMAN	M	954;91	ENSP00000261655:T954M;ENSP00000439030:T91M	ENSP00000261655:T954M	T	-	2	0	RIMBP2	129458288	1.000000	0.71417	0.018000	0.16275	0.034000	0.12701	9.767000	0.98960	2.102000	0.63906	0.555000	0.69702	ACG	.	.	none		0.512	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
DUSP2	1844	hgsc.bcm.edu	37	2	96809900	96809900	+	Silent	SNP	G	G	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:96809900G>C	ENST00000288943.4	-	3	808	c.723C>G	c.(721-723)ggC>ggG	p.G241G	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	241	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				TACCAATGAAGCCTATGGCCT	0.592																																					p.G241G		Atlas-SNP	.											DUSP2,NS,lymphoid_neoplasm,-1,1	DUSP2	20	1	0			c.C723G						PASS	.						66.0	58.0	61.0					2																	96809900		2203	4300	6503	SO:0001819	synonymous_variant	1844	exon3			AATGAAGCCTATG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.723C>G	2.37:g.96809900G>C		60.0	0.0	0		60.0	25.0	0.416667	NM_004418	Q53T45	Silent	SNP	ENST00000288943.4	37	CCDS2016.1																																																																																			.	.	none		0.592	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
CDH13	1012	hgsc.bcm.edu	37	16	83813610	83813610	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:83813610A>G	ENST00000566620.1	+	12	2009	c.1719A>G	c.(1717-1719)atA>atG	p.I573M	CDH13_ENST00000268613.10_Missense_Mutation_p.I620M|CDH13_ENST00000428848.3_Missense_Mutation_p.I534M	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	573	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CTTTGCTGATAACCCTGGAGG	0.488																																					p.I620M		Atlas-SNP	.											.	CDH13	97	.	0			c.A1860G						PASS	.						92.0	86.0	88.0					16																	83813610		1936	4181	6117	SO:0001583	missense	1012	exon13			GCTGATAACCCTG	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1719A>G	16.37:g.83813610A>G	ENSP00000454435:p.Ile573Met	89.0	0.0	0		80.0	17.0	0.2125	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.681211	0.47886	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000539548;ENST00000540531	T	0.61040	0.14	5.52	-11.0	0.00169	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.73690	0.3619	M	0.92077	3.27	0.80722	D	1	D;D;D	0.58970	0.971;0.971;0.984	P;P;P	0.62435	0.868;0.902;0.813	D	0.88936	0.3376	9	0.87932	D	0	.	14.1687	0.65495	0.1048:0.6952:0.0618:0.1382	.	534;620;573	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	M	620;573;534;275;132;263	ENSP00000268613:I620M	ENSP00000268613:I620M	I	+	3	3	CDH13	82371111	0.000000	0.05858	0.159000	0.22649	0.522000	0.34438	-2.440000	0.01016	-3.003000	0.00275	-1.236000	0.01555	ATA	.	.	none		0.488	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
SNRPD2	6633	hgsc.bcm.edu	37	19	46191649	46191649	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:46191649C>T	ENST00000342669.3	-	2	622	c.178G>A	c.(178-180)Gat>Aat	p.D60N	SNRPD2_ENST00000391932.3_Missense_Mutation_p.D50N|SNRPD2_ENST00000587367.1_Missense_Mutation_p.D50N|SNRPD2_ENST00000588599.1_Missense_Mutation_p.D50N|SNRPD2_ENST00000590212.1_Missense_Mutation_p.D60N|SNRPD2_ENST00000585392.1_5'UTR|SNRPD2_ENST00000588301.1_Missense_Mutation_p.D60N	NM_004597.5	NP_004588.1	P62316	SMD2_HUMAN	small nuclear ribonucleoprotein D2 polypeptide 16.5kDa	60					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(1)|lung(2)	4		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00546)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.194)		ACTCACCTATCGAAGGCCTTC	0.562																																					p.D60N		Atlas-SNP	.											.	SNRPD2	7	.	0			c.G178A						PASS	.						100.0	87.0	92.0					19																	46191649		2203	4300	6503	SO:0001583	missense	6633	exon2			ACCTATCGAAGGC		CCDS33053.1, CCDS54281.1	19q13.2-q13.3	2011-10-11	2002-08-29		ENSG00000125743	ENSG00000125743			11159	protein-coding gene	gene with protein product	"""snRNP core protein D2"""	601061	"""small nuclear ribonucleoprotein D2 polypeptide (16.5kD)"""	SNRPD1		7527560, 1701240	Standard	NM_004597		Approved	Sm-D2	uc002pcw.3	P62316		ENST00000342669.3:c.178G>A	19.37:g.46191649C>T	ENSP00000342374:p.Asp60Asn	169.0	0.0	0		209.0	80.0	0.382775	NM_004597	A8K797|J3KPM5|P43330	Missense_Mutation	SNP	ENST00000342669.3	37	CCDS33053.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631630	0.87660	.	.	ENSG00000125743	ENST00000342669;ENST00000391932	T;T	0.80480	-1.38;-1.38	5.85	5.85	0.93711	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	D	0.85737	0.5766	H	0.95574	3.69	0.80722	D	1	P	0.41710	0.76	B	0.33799	0.17	D	0.89638	0.3860	10	0.87932	D	0	.	17.6515	0.88165	0.0:1.0:0.0:0.0	.	60	P62316	SMD2_HUMAN	N	60;50	ENSP00000342374:D60N;ENSP00000375798:D50N	ENSP00000342374:D60N	D	-	1	0	SNRPD2	50883489	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	5.436000	0.66538	2.767000	0.95098	0.655000	0.94253	GAT	.	.	none		0.562	SNRPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459648.1	NM_004597	
HTRA2	27429	hgsc.bcm.edu	37	2	74756500	74756500	+	5'Flank	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:74756500G>A	ENST00000258080.3	+	0	0				AUP1_ENST00000377526.3_Silent_p.S59S|HTRA2_ENST00000352222.3_5'Flank	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2						adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						TGCGAAGGACGCTGTCTGGCA	0.652																																					p.S59S		Atlas-SNP	.											.	AUP1	29	.	0			c.C177T						PASS	.						21.0	28.0	26.0					2																	74756500		2101	4228	6329	SO:0001631	upstream_gene_variant	550	exon2			AAGGACGCTGTCT		CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"""Serine peptidases / Serine peptidases"", ""Parkinson disease"""	14348	protein-coding gene	gene with protein product		606441	"""protease, serine, 25"""	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957		2.37:g.74756500G>A	Exception_encountered	117.0	0.0	0		77.0	57.0	0.74026	NM_181575	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	37	CCDS1951.1																																																																																			.	.	none		0.652	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247	
DMKN	93099	hgsc.bcm.edu	37	19	36002412	36002412	+	Silent	SNP	G	G	A	rs56743379|rs111543270		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:36002412G>A	ENST00000339686.3	-	5	995	c.819C>T	c.(817-819)agC>agT	p.S273S	DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.S273S|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.S273S|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000424570.2_Silent_p.S273S|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000440396.1_Silent_p.S273S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000451297.2_Silent_p.S273S|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000492341.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	273	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			tgctgccactgctgctgccac	0.657																																					p.S273S		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.C819T						PASS	.						29.0	22.0	24.0					19																	36002412		2184	4248	6432	SO:0001819	synonymous_variant	93099	exon5			GCCACTGCTGCTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.819C>T	19.37:g.36002412G>A		29.0	0.0	0		36.0	4.0	0.111111	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.657	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
NGFR	4804	hgsc.bcm.edu	37	17	47572823	47572823	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:47572823T>C	ENST00000172229.3	+	1	169	c.44T>C	c.(43-45)cTg>cCg	p.L15P	NGFR_ENST00000504201.1_5'Flank	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	15					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					GGGCCGCGCCTGCTGCTGTTG	0.711																																					p.L15P		Atlas-SNP	.											.	NGFR	46	.	0			c.T44C						PASS	.						4.0	7.0	6.0					17																	47572823		1842	3757	5599	SO:0001583	missense	4804	exon1			CGCGCCTGCTGCT	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.44T>C	17.37:g.47572823T>C	ENSP00000172229:p.Leu15Pro	7.0	0.0	0		13.0	5.0	0.384615	NM_002507	B2R961|B4E096	Missense_Mutation	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.463454	0.43736	.	.	ENSG00000064300	ENST00000172229	D	0.91631	-2.88	4.54	4.54	0.55810	.	1.870110	0.02589	N	0.099734	D	0.90652	0.7068	N	0.24115	0.695	0.80722	D	1	P	0.48834	0.916	P	0.49140	0.601	T	0.80696	-0.1267	10	0.45353	T	0.12	-3.3729	10.5353	0.45000	0.0:0.0:0.0:1.0	.	15	P08138	TNR16_HUMAN	P	15	ENSP00000172229:L15P	ENSP00000172229:L15P	L	+	2	0	NGFR	44927822	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	3.325000	0.52030	1.804000	0.52760	0.443000	0.29094	CTG	.	.	none		0.711	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		
ZFHX3	463	hgsc.bcm.edu	37	16	72830766	72830766	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:72830766C>T	ENST00000268489.5	-	9	6487	c.5815G>A	c.(5815-5817)Gat>Aat	p.D1939N	ZFHX3_ENST00000397992.5_Missense_Mutation_p.D1025N	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1939					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCTCTGGCATCTGAAGCAATG	0.517																																					p.D1939N		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,1	ZFHX3	404	1	0			c.G5815A						PASS	.						97.0	96.0	97.0					16																	72830766		2198	4300	6498	SO:0001583	missense	463	exon9			TGGCATCTGAAGC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5815G>A	16.37:g.72830766C>T	ENSP00000268489:p.Asp1939Asn	135.0	0.0	0		130.0	49.0	0.376923	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.416295	0.62511	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.74632	-0.86;-0.85	5.73	5.73	0.89815	.	0.000000	0.49916	D	0.000137	T	0.78323	0.4265	L	0.39898	1.24	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.72701	-0.4214	10	0.21014	T	0.42	.	19.9064	0.97008	0.0:1.0:0.0:0.0	.	1939	Q15911	ZFHX3_HUMAN	N	1939;1025	ENSP00000268489:D1939N;ENSP00000438926:D1025N	ENSP00000268489:D1939N	D	-	1	0	ZFHX3	71388267	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.810000	0.86072	2.693000	0.91896	0.655000	0.94253	GAT	.	.	none		0.517	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
NPAS4	266743	hgsc.bcm.edu	37	11	66191694	66191694	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:66191694C>T	ENST00000311034.2	+	7	1509	c.1333C>T	c.(1333-1335)Cag>Tag	p.Q445*		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	445					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						TGAGCCCTTCCAGACCCATTT	0.562																																					p.Q445X		Atlas-SNP	.											.	NPAS4	133	.	0			c.C1333T						PASS	.						187.0	184.0	185.0					11																	66191694		2200	4295	6495	SO:0001587	stop_gained	266743	exon7			CCCTTCCAGACCC	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.1333C>T	11.37:g.66191694C>T	ENSP00000311196:p.Gln445*	65.0	0.0	0		74.0	4.0	0.0540541	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Nonsense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	33	5.203210	0.95033	.	.	ENSG00000174576	ENST00000311034	.	.	.	4.71	4.71	0.59529	.	0.000000	0.47455	D	0.000227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-8.3061	13.0275	0.58823	0.0:1.0:0.0:0.0	.	.	.	.	X	445	.	ENSP00000311196:Q445X	Q	+	1	0	NPAS4	65948270	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.401000	0.34589	2.455000	0.83008	0.563000	0.77884	CAG	.	.	none		0.562	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552090	178552090	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:178552090C>T	ENST00000251582.7	-	19	2943	c.2842G>A	c.(2842-2844)Gac>Aac	p.D948N		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	948	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GTGGTGTTGTCGTGTAGCGGC	0.692																																					p.D948N		Atlas-SNP	.											ADAMTS2,caecum,carcinoma,0,2	ADAMTS2	190	2	0			c.G2842A						scavenged	.						112.0	113.0	113.0					5																	178552090		2203	4300	6503	SO:0001583	missense	9509	exon19			TGTTGTCGTGTAG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2842G>A	5.37:g.178552090C>T	ENSP00000251582:p.Asp948Asn	74.0	1.0	0.0135135		121.0	5.0	0.0413223	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	0.743	-0.775731	0.02951	.	.	ENSG00000087116	ENST00000251582	T	0.53857	0.6	5.31	2.0	0.26442	.	0.301971	0.27792	N	0.017833	T	0.26774	0.0655	N	0.12422	0.21	0.80722	D	1	B	0.24317	0.101	B	0.22601	0.04	T	0.10730	-1.0617	10	0.06757	T	0.87	.	8.4694	0.32975	0.0:0.7177:0.0:0.2823	.	948	O95450	ATS2_HUMAN	N	948	ENSP00000251582:D948N	ENSP00000251582:D948N	D	-	1	0	ADAMTS2	178484696	0.966000	0.33281	0.957000	0.39632	0.030000	0.12068	1.550000	0.36223	0.026000	0.15269	-1.140000	0.01884	GAC	.	.	none		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
PDS5B	23047	hgsc.bcm.edu	37	13	33316792	33316792	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:33316792G>A	ENST00000315596.10	+	23	2725	c.2539G>A	c.(2539-2541)Gga>Aga	p.G847R		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	847					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		CAGTAAATCAGGAACTTCTAC	0.338																																					p.G847R		Atlas-SNP	.											.	PDS5B	141	.	0			c.G2539A						PASS	.						136.0	127.0	129.0					13																	33316792		1863	4106	5969	SO:0001583	missense	23047	exon23			AAATCAGGAACTT	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2539G>A	13.37:g.33316792G>A	ENSP00000313851:p.Gly847Arg	115.0	0.0	0		123.0	38.0	0.308943	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	G	33	5.204381	0.95033	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.84	5.84	0.93424	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72614	0.3482	L	0.43152	1.355	0.80722	D	1	D	0.61697	0.99	P	0.60949	0.881	T	0.72283	-0.4339	9	0.56958	D	0.05	-8.6067	20.1294	0.97995	0.0:0.0:1.0:0.0	.	847	Q9NTI5	PDS5B_HUMAN	R	847	.	ENSP00000313851:G847R	G	+	1	0	PDS5B	32214792	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.756000	0.98918	2.758000	0.94735	0.591000	0.81541	GGA	.	.	none		0.338	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28327094	28327094	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:28327094C>T	ENST00000284987.5	-	2	1322	c.1201G>A	c.(1201-1203)Ggc>Agc	p.G401S	MIR4759_ENST00000584048.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	401	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GCGTGGAGGCCATCGTCTTCA	0.512																																					p.G401S	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G1201A						PASS	.						123.0	112.0	116.0					21																	28327094		2203	4300	6503	SO:0001583	missense	11096	exon2			GGAGGCCATCGTC	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1201G>A	21.37:g.28327094C>T	ENSP00000284987:p.Gly401Ser	73.0	0.0	0		58.0	14.0	0.241379	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	35	5.419488	0.96111	.	.	ENSG00000154736	ENST00000284987	D	0.86694	-2.16	5.05	5.05	0.67936	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.93119	0.7809	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93653	0.6975	10	0.87932	D	0	.	18.5978	0.91235	0.0:1.0:0.0:0.0	.	401	Q9UNA0	ATS5_HUMAN	S	401	ENSP00000284987:G401S	ENSP00000284987:G401S	G	-	1	0	ADAMTS5	27248965	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.651000	0.83577	2.641000	0.89580	0.557000	0.71058	GGC	.	.	none		0.512	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
CNPPD1	27013	hgsc.bcm.edu	37	2	220041491	220041491	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:220041491C>T	ENST00000409789.1	-	2	487	c.60G>A	c.(58-60)caG>caA	p.Q20Q	CNPPD1_ENST00000360507.5_Silent_p.Q20Q|FAM134A_ENST00000430297.2_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	20					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						CCGTGAAGTCCTGGAAGCCGG	0.726																																					p.Q20Q		Atlas-SNP	.											.	CNPPD1	22	.	0			c.G60A						PASS	.						18.0	19.0	18.0					2																	220041491		2167	4262	6429	SO:0001819	synonymous_variant	27013	exon1			GAAGTCCTGGAAG	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 24"""	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.60G>A	2.37:g.220041491C>T		46.0	0.0	0		75.0	4.0	0.0533333	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Silent	SNP	ENST00000409789.1	37	CCDS2433.1																																																																																			.	.	none		0.726	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680	
PLCH1	23007	hgsc.bcm.edu	37	3	155205862	155205862	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:155205862T>G	ENST00000340059.7	-	20	2537	c.2538A>C	c.(2536-2538)gaA>gaC	p.E846D	PLCH1_ENST00000494598.1_Missense_Mutation_p.E846D|PLCH1_ENST00000460012.1_Missense_Mutation_p.E828D|PLCH1_ENST00000447496.2_Missense_Mutation_p.E846D|PLCH1_ENST00000334686.6_Missense_Mutation_p.E828D|PLCH1-AS2_ENST00000472913.1_RNA|PLCH1_ENST00000414191.1_Missense_Mutation_p.E828D	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	846					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ATATGGATGCTTCTGTCAGTC	0.363																																					p.E846D		Atlas-SNP	.											.	PLCH1	406	.	0			c.A2538C						PASS	.						132.0	130.0	130.0					3																	155205862		2203	4300	6503	SO:0001583	missense	23007	exon20			GGATGCTTCTGTC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.2538A>C	3.37:g.155205862T>G	ENSP00000345988:p.Glu846Asp	80.0	0.0	0		84.0	7.0	0.0833333	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650690	0.67472	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63	5.18	1.45	0.22620	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.30448	0.0765	M	0.73962	2.25	0.54753	D	0.999989	D;D;D	0.71674	0.996;0.998;0.984	D;D;P	0.69824	0.966;0.926;0.888	T	0.00953	-1.1502	10	0.36615	T	0.2	.	8.9787	0.35953	0.0:0.2141:0.0:0.7859	.	828;846;846	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	D	846;828;846;846;828;828	ENSP00000419100:E846D;ENSP00000417502:E828D;ENSP00000402759:E846D;ENSP00000345988:E846D;ENSP00000335469:E828D;ENSP00000412977:E828D	ENSP00000335469:E828D	E	-	3	2	PLCH1	156688556	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	1.763000	0.38461	0.013000	0.14918	-0.250000	0.11733	GAA	.	.	none		0.363	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
AKAP9	10142	hgsc.bcm.edu	37	7	91625060	91625060	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:91625060A>C	ENST00000359028.2	+	8	1137	c.912A>C	c.(910-912)gaA>gaC	p.E304D	AKAP9_ENST00000394564.1_Missense_Mutation_p.E292D|AKAP9_ENST00000358100.2_Missense_Mutation_p.E304D|AKAP9_ENST00000356239.3_Missense_Mutation_p.E292D			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	304					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAAAGAAAGAAGACTTCACAA	0.343			T	BRAF	papillary thyroid																																p.E292D		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,carcinoma,+2,2	AKAP9	788	2	0			c.A876C						PASS	.						67.0	63.0	64.0					7																	91625060		2203	4300	6503	SO:0001583	missense	10142	exon7			GAAAGAAGACTTC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.912A>C	7.37:g.91625060A>C	ENSP00000351922:p.Glu304Asp	68.0	0.0	0		38.0	15.0	0.394737	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	13.26	2.183510	0.38609	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.1	2.75	0.32379	.	0.000000	0.42682	D	0.000674	T	0.50000	0.1590	L	0.59436	1.845	0.36863	D	0.888493	B;B;D;B	0.69078	0.42;0.42;0.997;0.011	B;B;D;B	0.69654	0.087;0.087;0.965;0.009	T	0.54268	-0.8319	10	0.56958	D	0.05	.	8.6538	0.34051	0.8413:0.0:0.1587:0.0	.	292;292;304;292	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	D	292;304;304;304;304;292	ENSP00000348573:E292D;ENSP00000351922:E304D;ENSP00000350813:E304D;ENSP00000378065:E292D	ENSP00000348573:E292D	E	+	3	2	AKAP9	91462996	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.124000	0.42006	0.384000	0.24942	0.533000	0.62120	GAA	.	.	none		0.343	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
GRID2	2895	hgsc.bcm.edu	37	4	94376883	94376883	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:94376883G>A	ENST00000282020.4	+	11	1874	c.1616G>A	c.(1615-1617)cGt>cAt	p.R539H	GRID2_ENST00000510992.1_Missense_Mutation_p.R444H	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	539					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		TTTACGACACGTTACATGGAC	0.443																																					p.R539H		Atlas-SNP	.											GRID2,NS,carcinoma,+1,1	GRID2	233	1	0			c.G1616A						PASS	.						160.0	144.0	149.0					4																	94376883		2203	4300	6503	SO:0001583	missense	2895	exon11			CGACACGTTACAT	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.1616G>A	4.37:g.94376883G>A	ENSP00000282020:p.Arg539His	147.0	0.0	0		180.0	62.0	0.344444	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086141	0.94100	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.27402	1.67;1.67	5.97	5.97	0.96955	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.59851	0.2224	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.59198	-0.7499	10	0.66056	D	0.02	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	444;539	E9PH24;O43424	.;GRID2_HUMAN	H	539;444	ENSP00000282020:R539H;ENSP00000421257:R444H	ENSP00000282020:R539H	R	+	2	0	GRID2	94595906	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.869000	0.99810	2.836000	0.97738	0.655000	0.94253	CGT	.	.	none		0.443	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
PRKCB	5579	hgsc.bcm.edu	37	16	24183630	24183630	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:24183630G>A	ENST00000321728.7	+	11	1454	c.1279G>A	c.(1279-1281)Gac>Aac	p.D427N	PRKCB_ENST00000303531.7_Missense_Mutation_p.D427N	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	427	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	GAATGGGGGCGACCTCATGTA	0.527																																					p.D427N		Atlas-SNP	.											PRKCB_ENST00000321728,caecum,carcinoma,0,3	PRKCB	383	3	0			c.G1279A						scavenged	.						125.0	103.0	110.0					16																	24183630		2197	4300	6497	SO:0001583	missense	5579	exon11			GGGGGCGACCTCA	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1279G>A	16.37:g.24183630G>A	ENSP00000318315:p.Asp427Asn	193.0	1.0	0.00518135		170.0	59.0	0.347059	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795660	0.90453	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.27402	1.67;1.67	5.25	5.25	0.73442	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56093	0.1962	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.58521	-0.7622	10	0.87932	D	0	.	18.1787	0.89769	0.0:0.0:1.0:0.0	.	427;427	P05771-2;P05771	.;KPCB_HUMAN	N	427	ENSP00000318315:D427N;ENSP00000305355:D427N	ENSP00000305355:D427N	D	+	1	0	PRKCB	24091131	1.000000	0.71417	0.958000	0.39756	0.462000	0.32619	9.768000	0.98965	2.606000	0.88127	0.557000	0.71058	GAC	.	.	none		0.527	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
NEB	4703	hgsc.bcm.edu	37	2	152470904	152470904	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:152470904C>T	ENST00000172853.10	-	73	10905	c.10758G>A	c.(10756-10758)aaG>aaA	p.K3586K	NEB_ENST00000427231.2_Silent_p.K3829K|NEB_ENST00000604864.1_Silent_p.K3829K|NEB_ENST00000409198.1_Silent_p.K3586K|NEB_ENST00000397345.3_Silent_p.K3829K|NEB_ENST00000603639.1_Silent_p.K3829K			P20929	NEBU_HUMAN	nebulin	3586					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GGATCTGACACTTCTTGGCCA	0.527																																					p.K3829K		Atlas-SNP	.											.	NEB	1697	.	0			c.G11487A						PASS	.						242.0	237.0	239.0					2																	152470904		2063	4213	6276	SO:0001819	synonymous_variant	4703	exon77			CTGACACTTCTTG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.10758G>A	2.37:g.152470904C>T		210.0	0.0	0		237.0	94.0	0.396624	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	none		0.527	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
SYCE2	256126	hgsc.bcm.edu	37	19	13010850	13010850	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:13010850A>G	ENST00000293695.7	-	5	598	c.580T>C	c.(580-582)Ttc>Ctc	p.F194L	GCDH_ENST00000588242.2_3'UTR	NM_001105578.1	NP_001099048.1	Q6PIF2	SYCE2_HUMAN	synaptonemal complex central element protein 2	194					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8						GAAGAAACGAACACGTCTGGG	0.532																																					p.F194L		Atlas-SNP	.											.	SYCE2	19	.	0			c.T580C						PASS	.						56.0	63.0	61.0					19																	13010850		1915	4123	6038	SO:0001583	missense	256126	exon5			AAACGAACACGTC	AK097443	CCDS42509.1	19p13.13	2008-02-05				ENSG00000161860			27411	protein-coding gene	gene with protein product	"""central element synaptonemal complex 1"""	611487				15944401	Standard	NM_001105578		Approved	CESC1	uc002mvr.2	Q6PIF2		ENST00000293695.7:c.580T>C	19.37:g.13010850A>G	ENSP00000293695:p.Phe194Leu	87.0	0.0	0		84.0	5.0	0.0595238	NM_001105578	B4DYD3	Missense_Mutation	SNP	ENST00000293695.7	37	CCDS42509.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.612603	0.28712	.	.	ENSG00000161860	ENST00000293695	D	0.85629	-2.01	3.46	-3.27	0.05048	.	.	.	.	.	T	0.71160	0.3307	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.56757	-0.7926	9	0.87932	D	0	.	5.1896	0.15203	0.2862:0.0:0.5364:0.1775	.	194	Q6PIF2	SYCE2_HUMAN	L	194	ENSP00000293695:F194L	ENSP00000293695:F194L	F	-	1	0	SYCE2	12871850	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.037000	0.03557	-0.830000	0.04262	-0.464000	0.05259	TTC	.	.	none		0.532	SYCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451913.1	XM_497609	
C2orf81	388963	hgsc.bcm.edu	37	2	74642265	74642265	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:74642265A>C	ENST00000517883.1	-	1	1445	c.754T>G	c.(754-756)Tcc>Gcc	p.S252A	C2orf81_ENST00000290390.5_Missense_Mutation_p.S320A			A6NN90	CB081_HUMAN	chromosome 2 open reading frame 81	313										endometrium(3)|kidney(1)	4						TGCTGGCAGGACGCGGAGGGG	0.721																																					p.S320A		Atlas-SNP	.											C2orf81,colon,carcinoma,0,1	C2orf81	23	1	0			c.T958G						scavenged	.						4.0	8.0	6.0					2																	74642265		638	1532	2170	SO:0001583	missense	388963	exon4			GGCAGGACGCGGA	AC005041, CH471053		2p13.1	2012-08-07			ENSG00000159239	ENSG00000159239			34350	protein-coding gene	gene with protein product						15815621	Standard	NM_001145054		Approved	LOC388963, hCG40743	uc010yrq.1	A6NN90	OTTHUMG00000164184	ENST00000517883.1:c.754T>G	2.37:g.74642265A>C	ENSP00000431103:p.Ser252Ala	7.0	0.0	0		5.0	3.0	0.6	NM_001145054		Missense_Mutation	SNP	ENST00000517883.1	37		.	.	.	.	.	.	.	.	.	.	a	12.67	2.008342	0.35415	.	.	ENSG00000159239	ENST00000517883;ENST00000290390	.	.	.	5.0	-4.83	0.03161	.	2.205130	0.02226	N	0.064447	T	0.21674	0.0522	L	0.36672	1.1	0.09310	N	1	B	0.28291	0.206	B	0.28011	0.085	T	0.07966	-1.0745	9	0.12430	T	0.62	0.3431	1.4608	0.02395	0.3364:0.2747:0.268:0.1209	.	320	G3XAA6	.	A	252;320	.	ENSP00000290390:S320A	S	-	1	0	C2orf81	74495773	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.495000	0.06443	-0.580000	0.05944	0.454000	0.30748	TCC	.	.	none		0.721	C2orf81-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000377683.1	NM_001145054	
OVGP1	5016	hgsc.bcm.edu	37	1	111957523	111957523	+	Missense_Mutation	SNP	G	G	T	rs3767608|rs201350653		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:111957523G>T	ENST00000369732.3	-	11	1655	c.1600C>A	c.(1600-1602)Cct>Act	p.P534T		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	534					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.T597_V604delTPVSHQSV(2)|p.T533_V540delTPVSHQSV(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TGACTCACAGGGGTCACAGAC	0.537																																					p.P534T		Atlas-SNP	.											OVGP1_ENST00000369728,NS,carcinoma,0,2	OVGP1	177	2	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.C1600A						PASS	.																																			SO:0001583	missense	5016	exon11			TCACAGGGGTCAC	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1600C>A	1.37:g.111957523G>T	ENSP00000358747:p.Pro534Thr	130.0	0.0	0		144.0	22.0	0.152778	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	G	9.491	1.100669	0.20552	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.19105	2.17	2.35	-0.421	0.12332	.	.	.	.	.	T	0.03608	0.0103	N	0.22421	0.69	0.09310	N	1	B;B	0.13145	0.007;0.0	B;B	0.06405	0.002;0.0	T	0.42999	-0.9418	9	0.36615	T	0.2	9.8099	5.0173	0.14343	0.4538:0.0:0.5462:0.0	.	534;598	Q12889;Q59HH5	OVGP1_HUMAN;.	T	534;598;342	ENSP00000358747:P534T	ENSP00000358743:P598T	P	-	1	0	OVGP1	111759046	0.000000	0.05858	0.001000	0.08648	0.112000	0.19704	-1.483000	0.02318	-0.296000	0.08947	0.460000	0.39030	CCT	G|1.000;A|0.000	.	alt		0.537	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
KANK1	23189	hgsc.bcm.edu	37	9	731215	731215	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:731215A>G	ENST00000382303.1	+	9	3606	c.2954A>G	c.(2953-2955)aAa>aGa	p.K985R	KANK1_ENST00000382297.2_Missense_Mutation_p.K985R|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Missense_Mutation_p.K827R	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	985	Nuclear localization signal 2 (NLS 2).				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GATGGTAACAAAGATTCAAAT	0.378																																					p.K985R		Atlas-SNP	.											.	KANK1	231	.	0			c.A2954G						PASS	.						142.0	127.0	132.0					9																	731215		2203	4300	6503	SO:0001583	missense	23189	exon9			GTAACAAAGATTC	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.2954A>G	9.37:g.731215A>G	ENSP00000371740:p.Lys985Arg	126.0	0.0	0		153.0	69.0	0.45098	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804544	0.31869	.	.	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293	T;T;T	0.17528	2.27;2.27;2.27	5.76	-2.74	0.05932	.	0.345964	0.24791	N	0.035577	T	0.12433	0.0302	L	0.57536	1.79	0.09310	N	0.999999	B	0.10296	0.003	B	0.09377	0.004	T	0.29731	-1.0002	10	0.21540	T	0.41	.	6.4346	0.21817	0.5965:0.0:0.2984:0.1051	.	985	Q14678	KANK1_HUMAN	R	985;8;985;827	ENSP00000371740:K985R;ENSP00000371734:K985R;ENSP00000371730:K827R	ENSP00000371730:K827R	K	+	2	0	KANK1	721215	0.072000	0.21174	0.004000	0.12327	0.888000	0.51559	1.007000	0.29860	-0.570000	0.06022	0.528000	0.53228	AAA	.	.	none		0.378	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
STPG2	285555	hgsc.bcm.edu	37	4	98893436	98893436	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:98893436A>C	ENST00000295268.3	-	7	1017	c.928T>G	c.(928-930)Tat>Gat	p.Y310D		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	310																	ATTACCTGATAATCAGCAGGT	0.353																																					p.Y310D		Atlas-SNP	.											.	.	.	.	0			c.T928G						PASS	.						72.0	74.0	73.0					4																	98893436		2203	4300	6503	SO:0001583	missense	285555	exon7			CCTGATAATCAGC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.928T>G	4.37:g.98893436A>C	ENSP00000295268:p.Tyr310Asp	162.0	0.0	0		175.0	66.0	0.377143	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.828153	0.50845	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.77877	-1.13;1.39	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000001	D	0.82879	0.5133	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84923	0.0855	10	0.87932	D	0	-16.3241	14.4978	0.67700	1.0:0.0:0.0:0.0	.	310	Q8N412	CD037_HUMAN	D	24;310	ENSP00000428346:Y24D;ENSP00000295268:Y310D	ENSP00000295268:Y310D	Y	-	1	0	C4orf37	99112459	1.000000	0.71417	0.985000	0.45067	0.357000	0.29423	5.252000	0.65445	2.066000	0.61787	0.455000	0.32223	TAT	.	.	none		0.353	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
NPY2R	4887	hgsc.bcm.edu	37	4	156135863	156135863	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:156135863C>T	ENST00000329476.3	+	2	1261	c.772C>T	c.(772-774)Cac>Tac	p.H258Y	NPY2R_ENST00000506608.1_Missense_Mutation_p.H258Y	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	258					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TGCAAATGACCACTACCATCA	0.483																																					p.H258Y		Atlas-SNP	.											.	NPY2R	87	.	0			c.C772T						PASS	.						105.0	106.0	106.0					4																	156135863		2203	4300	6503	SO:0001583	missense	4887	exon2			AATGACCACTACC	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.772C>T	4.37:g.156135863C>T	ENSP00000332591:p.His258Tyr	117.0	0.0	0		96.0	41.0	0.427083	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	37	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077872	0.36662	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.37058	1.22;1.22	5.8	5.8	0.92144	GPCR, rhodopsin-like superfamily (1);	0.295033	0.37577	N	0.002031	T	0.34571	0.0902	L	0.39085	1.19	0.42996	D	0.994507	B	0.32939	0.391	B	0.34590	0.186	T	0.06197	-1.0840	10	0.36615	T	0.2	.	19.0326	0.92963	0.0:1.0:0.0:0.0	.	258	P49146	NPY2R_HUMAN	Y	258	ENSP00000332591:H258Y;ENSP00000426366:H258Y	ENSP00000332591:H258Y	H	+	1	0	NPY2R	156355313	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	2.361000	0.44160	2.742000	0.94016	0.643000	0.83706	CAC	.	.	none		0.483	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230315	23230315	+	Silent	SNP	C	C	T	rs148489860	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230315C>T	ENST00000526893.1	+	1	356	c.82C>T	c.(82-84)Ctg>Ttg	p.L28L	IGLL5_ENST00000531372.1_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.L28L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCCCTGCTGCTGCTGGGTCT	0.662													C|||	11	0.00219649	0.0045	0.0	5008	,	,		12566	0.003		0.001	False		,,,				2504	0.001				p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C82T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CTGCTGCTGCTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.82C>T	22.37:g.23230315C>T		108.0	0.0	0		140.0	60.0	0.428571	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			C|1.000;T|0.000	0.000	strong		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
CLVS1	157807	hgsc.bcm.edu	37	8	62289218	62289218	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:62289218C>T	ENST00000519846.1	+	4	982	c.510C>T	c.(508-510)atC>atT	p.I170I	CLVS1_ENST00000518592.1_5'UTR|CLVS1_ENST00000325897.4_Silent_p.I170I			Q8IUQ0	CLVS1_HUMAN	clavesin 1	170	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						AAGTCCTAATCGAAGATCCGG	0.438																																					p.I170I		Atlas-SNP	.											CLVS1,NS,carcinoma,+2,1	CLVS1	74	1	0			c.C510T						PASS	.						112.0	106.0	108.0					8																	62289218		2203	4300	6503	SO:0001819	synonymous_variant	157807	exon3			CCTAATCGAAGAT	AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"""retinaldehyde binding protein 1-like 1"""	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.510C>T	8.37:g.62289218C>T		85.0	0.0	0		89.0	32.0	0.359551	NM_173519	B2R7M5|C8UZT3|Q8NB32	Silent	SNP	ENST00000519846.1	37	CCDS6176.1																																																																																			.	.	none		0.438	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
GPX5	2880	hgsc.bcm.edu	37	6	28500106	28500106	+	Missense_Mutation	SNP	G	G	A	rs138279209		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:28500106G>A	ENST00000412168.2	+	4	457	c.368G>A	c.(367-369)cGt>cAt	p.R123H	GPX5_ENST00000442674.2_3'UTR|GPX5_ENST00000469384.1_Missense_Mutation_p.V84I	NM_001509.2	NP_001500.1	O75715	GPX5_HUMAN	glutathione peroxidase 5 (epididymal androgen-related protein)	123					lipid metabolic process (GO:0006629)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)			endometrium(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16					Glutathione(DB00143)	AGGTATGTCCGTCCAGGGGGA	0.423																																					p.R123H		Atlas-SNP	.											.	GPX5	42	.	0			c.G368A						PASS	.	G	HIS/ARG,ILE/VAL	0,4406		0,0,2203	139.0	126.0	130.0		368,250	4.2	1.0	6	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPX5	NM_001509.2,NM_003996.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	123/222,84/101	28500106	1,13005	2203	4300	6503	SO:0001583	missense	2880	exon4			ATGTCCGTCCAGG	AJ005277	CCDS4652.1, CCDS4653.1	6p22.1	2008-02-05			ENSG00000224586	ENSG00000224586	1.11.1.9		4557	protein-coding gene	gene with protein product		603435				9639555	Standard	NM_001509		Approved		uc003nll.2	O75715	OTTHUMG00000016307	ENST00000412168.2:c.368G>A	6.37:g.28500106G>A	ENSP00000392398:p.Arg123His	125.0	0.0	0		121.0	95.0	0.785124	NM_001509	A1A4Y0	Missense_Mutation	SNP	ENST00000412168.2	37	CCDS4652.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.91|17.91	3.503579|3.503579	0.64298|0.64298	0.0|0.0	1.16E-4|1.16E-4	ENSG00000224586|ENSG00000224586	ENST00000412168|ENST00000469384	T|T	0.04156|0.10192	3.69|2.9	4.16|4.16	4.16|4.16	0.48862|0.48862	Thioredoxin-like fold (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.03564|0.03564	0.0102|0.0102	.|.	.|.	.|.	0.22581|0.22581	N|N	0.998967|0.998967	D|P	0.89917|0.39847	1.0|0.691	D|B	0.80764|0.28465	0.994|0.09	T|T	0.26744|0.26744	-1.0094|-1.0094	9|8	0.87932|0.66056	D|D	0|0.02	-14.4515|-14.4515	14.7712|14.7712	0.69679|0.69679	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	123|84	O75715|A1A4Y0	GPX5_HUMAN|.	H|I	123|84	ENSP00000392398:R123H|ENSP00000419935:V84I	ENSP00000392398:R123H|ENSP00000419935:V84I	R|V	+|+	2|1	0|0	GPX5|GPX5	28608085|28608085	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	8.310000|8.310000	0.89971|0.89971	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	CGT|GTC	G|1.000;A|0.000	0.000	weak		0.423	GPX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043672.2		
ZNF804A	91752	hgsc.bcm.edu	37	2	185463692	185463692	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:185463692G>A	ENST00000302277.6	+	1	600	c.6G>A	c.(4-6)gaG>gaA	p.E2E		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	2							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						gcCCCATGGAGTGTTACTACA	0.657																																					p.E2E		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G6A						PASS	.						61.0	60.0	60.0					2																	185463692		2203	4300	6503	SO:0001819	synonymous_variant	91752	exon1			CATGGAGTGTTAC	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.6G>A	2.37:g.185463692G>A		42.0	0.0	0		45.0	19.0	0.422222	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			.	.	none		0.657	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
BTG1	694	hgsc.bcm.edu	37	12	92539304	92539304	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:92539304G>C	ENST00000256015.3	-	1	369	c.8C>G	c.(7-9)cCc>cGc	p.P3R	RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	3					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GGTGTAGAAGGGATGCATggg	0.746			T	MYC	BCLL																																p.P3R		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	.	BTG1	30	.	0			c.C8G						PASS	.						25.0	29.0	28.0					12																	92539304		2199	4292	6491	SO:0001583	missense	694	exon1			TAGAAGGGATGCA		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.8C>G	12.37:g.92539304G>C	ENSP00000256015:p.Pro3Arg	57.0	0.0	0		83.0	39.0	0.46988	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.465474	0.63513	.	.	ENSG00000133639	ENST00000256015	T	0.21361	2.01	3.71	3.71	0.42584	.	0.119071	0.56097	D	0.000026	T	0.15219	0.0367	L	0.29908	0.895	0.45718	D	0.998629	B	0.33694	0.421	B	0.24541	0.054	T	0.09707	-1.0662	10	0.51188	T	0.08	-4.5437	15.638	0.76970	0.0:0.0:1.0:0.0	.	3	P62324	BTG1_HUMAN	R	3	ENSP00000256015:P3R	ENSP00000256015:P3R	P	-	2	0	BTG1	91063435	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.824000	0.86668	1.883000	0.54544	0.455000	0.32223	CCC	.	.	none		0.746	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
LPHN1	22859	hgsc.bcm.edu	37	19	14261777	14261777	+	Missense_Mutation	SNP	G	G	A	rs375528213		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:14261777G>A	ENST00000340736.6	-	24	4630	c.4333C>T	c.(4333-4335)Cgt>Tgt	p.R1445C	LPHN1_ENST00000361434.3_Missense_Mutation_p.R1440C|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1445					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGGCTAGGACGCCGCACCTGG	0.711																																					p.R1445C		Atlas-SNP	.											.	LPHN1	107	.	0			c.C4333T						PASS	.	G	CYS/ARG,CYS/ARG	0,4282		0,0,2141	9.0	10.0	10.0		4333,4318	0.2	1.0	19		10	1,8383		0,1,4191	no	missense,missense	LPHN1	NM_001008701.2,NM_014921.4	180,180	0,1,6332	AA,AG,GG		0.0119,0.0,0.0079	probably-damaging,probably-damaging	1445/1475,1440/1470	14261777	1,12665	2141	4192	6333	SO:0001583	missense	22859	exon24			TAGGACGCCGCAC	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4333C>T	19.37:g.14261777G>A	ENSP00000340688:p.Arg1445Cys	39.0	0.0	0		110.0	41.0	0.372727	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	37	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.806701	0.50421	0.0	1.19E-4	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.79454	-1.27;-1.27	3.94	0.249	0.15531	GPCR, family 2, latrophilin, C-terminal (1);	0.194324	0.31450	N	0.007633	D	0.82568	0.5065	M	0.65975	2.015	0.43913	D	0.996557	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.969	T	0.78700	-0.2102	10	0.87932	D	0	.	5.6925	0.17837	0.1007:0.0:0.5742:0.3251	.	1440;1445	O94910-2;O94910	.;LPHN1_HUMAN	C	1445;1440	ENSP00000340688:R1445C;ENSP00000355328:R1440C	ENSP00000340688:R1445C	R	-	1	0	LPHN1	14122777	0.997000	0.39634	0.996000	0.52242	0.857000	0.48899	0.527000	0.22987	-0.153000	0.11137	0.205000	0.17691	CGT	.	.	weak		0.711	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
ZNF223	7766	hgsc.bcm.edu	37	19	44571010	44571010	+	Silent	SNP	A	A	G	rs141349301		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:44571010A>G	ENST00000434772.3	+	5	1284	c.1029A>G	c.(1027-1029)ccA>ccG	p.P343P	ZNF223_ENST00000591793.1_Silent_p.P453P	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GAGAGAAACCATATAATTGTA	0.438																																					p.P343P		Atlas-SNP	.											.	ZNF223	61	.	0			c.A1029G						PASS	.						102.0	106.0	105.0					19																	44571010		2203	4300	6503	SO:0001819	synonymous_variant	7766	exon5			GAAACCATATAAT	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.1029A>G	19.37:g.44571010A>G		58.0	0.0	0		68.0	15.0	0.220588	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	37	CCDS12635.1																																																																																			A|1.000;T|0.000	.	alt		0.438	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
SGK1	6446	hgsc.bcm.edu	37	6	134494230	134494230	+	Silent	SNP	C	C	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:134494230C>A	ENST00000237305.7	-	6	568	c.480G>T	c.(478-480)gtG>gtT	p.V160V	SGK1_ENST00000413996.3_Silent_p.V174V|SGK1_ENST00000367857.5_Silent_p.V150V|SGK1_ENST00000528577.1_Silent_p.V188V|SGK1_ENST00000367858.5_Silent_p.V255V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000475719.2_Intron	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGTGAAGGCCCACCAGGAAAG	0.443																																					p.V255V		Atlas-SNP	.											.	SGK1	387	.	0			c.G765T						PASS	.						96.0	96.0	96.0					6																	134494230		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon8			AAGGCCCACCAGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.480G>T	6.37:g.134494230C>A		188.0	0.0	0		212.0	28.0	0.132075	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.443	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
FCAMR	83953	hgsc.bcm.edu	37	1	207140994	207140994	+	Silent	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:207140994T>C	ENST00000324852.4	-	2	516	c.42A>G	c.(40-42)gaA>gaG	p.E14E	FCAMR_ENST00000400962.3_Silent_p.E14E|FCAMR_ENST00000450945.2_Silent_p.E14E	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	315					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TCCTCACCACTTCCTGTTTGC	0.428																																					p.E14E	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.A42G						PASS	.						169.0	143.0	151.0					1																	207140994		1568	3582	5150	SO:0001819	synonymous_variant	83953	exon2			CACCACTTCCTGT	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.42A>G	1.37:g.207140994T>C		117.0	0.0	0		139.0	6.0	0.0431655	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Silent	SNP	ENST00000324852.4	37	CCDS53468.1																																																																																			.	.	none		0.428	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230333	23230333	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230333G>A	ENST00000526893.1	+	1	374	c.100G>A	c.(100-102)Gtc>Atc	p.V34I	IGLL5_ENST00000531372.1_Missense_Mutation_p.V34I|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.V34I	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	34						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TCTGGCCATGGTCGCCCATGG	0.667																																					p.V34I		Atlas-SNP	.											.	IGLL5	26	.	0			c.G100A						PASS	.																																			SO:0001583	missense	100423062	exon1			GCCATGGTCGCCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.100G>A	22.37:g.23230333G>A	ENSP00000431254:p.Val34Ile	108.0	0.0	0		126.0	50.0	0.396825	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252980	0.22965	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00581	6.42;6.42	3.55	1.39	0.22231	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.34061	0.436	B	0.21708	0.036	T	0.45160	-0.9280	9	0.28530	T	0.3	.	4.2734	0.10797	0.121:0.0:0.654:0.225	.	34	B9A064	IGLL5_HUMAN	I	34	ENSP00000436353:V34I;ENSP00000431254:V34I	ENSP00000431254:V34I	V	+	1	0	IGLL5	21560333	0.005000	0.15991	0.001000	0.08648	0.001000	0.01503	0.741000	0.26202	0.464000	0.27142	-0.196000	0.12772	GTC	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27834991	27834991	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:27834991C>G	ENST00000331442.3	-	1	368	c.317G>C	c.(316-318)gGc>gCc	p.G106A		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	106	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						TTTAAAGGAGCCAGAAGCACC	0.602																																					p.G106A		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.G317C						PASS	.						113.0	126.0	121.0					6																	27834991		2203	4300	6503	SO:0001583	missense	3009	exon1			AAGGAGCCAGAAG	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.317G>C	6.37:g.27834991C>G	ENSP00000330074:p.Gly106Ala	132.0	0.0	0		99.0	43.0	0.434343	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.578219	0.86645	.	.	ENSG00000184357	ENST00000331442	T	0.58060	0.36	5.3	4.42	0.53409	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.71576	0.3356	M	0.90977	3.165	0.80722	D	1	D	0.60575	0.988	D	0.67725	0.953	T	0.80647	-0.1289	10	0.87932	D	0	-16.951	15.3154	0.74074	0.0:0.8595:0.1405:0.0	.	106	P16401	H15_HUMAN	A	106	ENSP00000330074:G106A	ENSP00000330074:G106A	G	-	2	0	HIST1H1B	27942970	1.000000	0.71417	0.993000	0.49108	0.886000	0.51366	5.792000	0.69052	1.353000	0.45828	0.563000	0.77884	GGC	.	.	none		0.602	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067104	46067104	+	Silent	SNP	C	C	T	rs75548048	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:46067104C>T	ENST00000334670.8	+	1	774	c.729C>T	c.(727-729)ccC>ccT	p.P243P	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	243	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						TCTGCCACCCCGTGTGCAGGT	0.687													C|||	125	0.0249601	0.0915	0.0058	5008	,	,		20784	0.0		0.0	False		,,,				2504	0.0				p.P243P		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C729T						PASS	.	C	,	313,4093	167.3+/-198.3	16,281,1906	94.0	104.0	101.0		,729	-0.6	0.7	21	dbSNP_131	101	1,8599		0,1,4299	no	intron,coding-synonymous	TSPEAR,KRTAP10-11	NM_144991.2,NM_198692.2	,	16,282,6205	TT,TC,CC		0.0116,7.1039,2.4143	,	,243/299	46067104	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	386678	exon1			CCACCCCGTGTGC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.729C>T	21.37:g.46067104C>T		88.0	0.0	0		111.0	10.0	0.0900901	NM_198692	A2RRF9	Silent	SNP	ENST00000334670.8	37	CCDS42962.1																																																																																			C|0.980;T|0.020	0.020	strong		0.687	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
LRRC32	2615	hgsc.bcm.edu	37	11	76371849	76371849	+	Missense_Mutation	SNP	G	G	A	rs201402758		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:76371849G>A	ENST00000407242.2	-	3	1030	c.788C>T	c.(787-789)gCg>gTg	p.A263V	LRRC32_ENST00000260061.5_Missense_Mutation_p.A263V|LRRC32_ENST00000464145.1_Intron|LRRC32_ENST00000404995.1_Missense_Mutation_p.A263V|AP001189.4_ENST00000447519.1_RNA	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	263					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						TCTCGGGAGCGCGGCCAGGTC	0.632																																					p.A263V		Atlas-SNP	.											.	LRRC32	74	.	0			c.C788T						PASS	.						59.0	59.0	59.0					11																	76371849		2200	4292	6492	SO:0001583	missense	2615	exon3			GGGAGCGCGGCCA	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"""glycoprotein A repetitions predominant"""	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.788C>T	11.37:g.76371849G>A	ENSP00000384126:p.Ala263Val	121.0	0.0	0		174.0	59.0	0.33908	NM_005512	Q86V06	Missense_Mutation	SNP	ENST00000407242.2	37	CCDS8245.1	.	.	.	.	.	.	.	.	.	.	G	1.050	-0.676017	0.03378	.	.	ENSG00000137507	ENST00000260061;ENST00000407242;ENST00000404995	T;T;T	0.79653	-1.29;-1.29;-1.29	4.55	1.48	0.22813	.	0.688404	0.14657	N	0.306188	T	0.60792	0.2296	L	0.28274	0.84	0.09310	N	1	B	0.15719	0.014	B	0.04013	0.001	T	0.34129	-0.9841	10	0.16420	T	0.52	.	2.0366	0.03541	0.102:0.2514:0.3483:0.2982	.	263	Q14392	LRC32_HUMAN	V	263	ENSP00000260061:A263V;ENSP00000384126:A263V;ENSP00000385766:A263V	ENSP00000260061:A263V	A	-	2	0	LRRC32	76049497	0.000000	0.05858	0.133000	0.22050	0.150000	0.21749	0.012000	0.13287	1.116000	0.41820	0.555000	0.69702	GCG	.	.	weak		0.632	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512	
SYNE1	23345	hgsc.bcm.edu	37	6	152679666	152679666	+	Missense_Mutation	SNP	C	C	T	rs550088683		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:152679666C>T	ENST00000367255.5	-	66	11051	c.10450G>A	c.(10450-10452)Gta>Ata	p.V3484I	SYNE1_ENST00000423061.1_Missense_Mutation_p.V3491I|SYNE1_ENST00000265368.4_Missense_Mutation_p.V3484I|SYNE1_ENST00000341594.5_Missense_Mutation_p.V3455I|SYNE1_ENST00000448038.1_Missense_Mutation_p.V3491I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3484					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)		GACTTGGTTACGGCTTCCTAT	0.363										HNSCC(10;0.0054)			C|||	1	0.000199681	0.0	0.0	5008	,	,		16527	0.0		0.0	False		,,,				2504	0.001				p.V3491I		Atlas-SNP	.											SYNE1_ENST00000423061,NS,carcinoma,0,3	SYNE1	3227	3	0			c.G10471A						scavenged	.						95.0	88.0	90.0					6																	152679666		2203	4300	6503	SO:0001583	missense	23345	exon66			TGGTTACGGCTTC	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.10450G>A	6.37:g.152679666C>T	ENSP00000356224:p.Val3484Ile	135.0	1.0	0.00740741		127.0	39.0	0.307087	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624999	0.28889	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.53423	0.72;1.37;0.62;1.37;0.64	5.35	3.57	0.40892	.	0.254853	0.27544	N	0.018893	T	0.20536	0.0494	L	0.52364	1.645	0.80722	D	1	B;B;B;B	0.26577	0.04;0.04;0.04;0.153	B;B;B;B	0.22152	0.017;0.017;0.017;0.038	T	0.04216	-1.0968	10	0.28530	T	0.3	.	7.9553	0.30038	0.0:0.6903:0.0:0.3097	.	3484;3484;3484;3491	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	I	3484;3491;3484;3491;3455	ENSP00000356224:V3484I;ENSP00000396024:V3491I;ENSP00000265368:V3484I;ENSP00000390975:V3491I;ENSP00000341887:V3455I	ENSP00000265368:V3484I	V	-	1	0	SYNE1	152721359	1.000000	0.71417	0.457000	0.27056	0.881000	0.50899	2.800000	0.47900	0.647000	0.30713	0.561000	0.74099	GTA	.	.	none		0.363	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
C21orf2	755	hgsc.bcm.edu	37	21	45753031	45753031	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:45753031C>T	ENST00000339818.4	-	4	465	c.258G>A	c.(256-258)ctG>ctA	p.L86L	AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Silent_p.L86L|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Silent_p.L86L	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	86					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		GCAGACGCGGCAGCCCCTTCA	0.697																																					p.L86L		Atlas-SNP	.											.	C21orf2	10	.	0			c.G258A						PASS	.						18.0	20.0	20.0					21																	45753031		2201	4295	6496	SO:0001819	synonymous_variant	755	exon4			ACGCGGCAGCCCC	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.258G>A	21.37:g.45753031C>T		63.0	0.0	0		100.0	4.0	0.04	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			.	.	none		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
MYO1D	4642	hgsc.bcm.edu	37	17	30932257	30932257	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:30932257C>A	ENST00000318217.5	-	21	3016	c.2712G>T	c.(2710-2712)ttG>ttT	p.L904F	MYO1D_ENST00000579584.1_Missense_Mutation_p.L904F|MYO1D_ENST00000394649.4_Missense_Mutation_p.L816F	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	904	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			TCAGACCAGTCAACTGCAAAG	0.418																																					p.L904F		Atlas-SNP	.											.	MYO1D	93	.	0			c.G2712T						PASS	.						92.0	81.0	85.0					17																	30932257		2203	4300	6503	SO:0001583	missense	4642	exon21			ACCAGTCAACTGC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2712G>T	17.37:g.30932257C>A	ENSP00000324527:p.Leu904Phe	119.0	0.0	0		103.0	43.0	0.417476	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903118	0.33628	.	.	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.41400	1.0	4.94	3.92	0.45320	Myosin tail 2 (1);	0.000000	0.32503	U	0.006009	T	0.35537	0.0935	L	0.43923	1.385	0.80722	D	1	B;B	0.17852	0.014;0.024	B;B	0.19666	0.026;0.026	T	0.23511	-1.0186	10	0.87932	D	0	.	10.4809	0.44693	0.0:0.8966:0.0:0.1034	.	815;904	Q7Z3N6;O94832	.;MYO1D_HUMAN	F	904;96	ENSP00000324527:L904F	ENSP00000324527:L904F	L	-	3	2	MYO1D	27956370	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	1.952000	0.40343	1.124000	0.41980	-0.345000	0.07892	TTG	.	.	none		0.418	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
PRKACA	5566	hgsc.bcm.edu	37	19	14204559	14204559	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:14204559G>A	ENST00000308677.4	-	9	1007	c.811C>T	c.(811-813)Cgg>Tgg	p.R271W	SAMD1_ENST00000541938.1_5'Flank|PRKACA_ENST00000350356.3_5'UTR|PRKACA_ENST00000589994.1_Missense_Mutation_p.R263W|PRKACA_ENST00000590853.1_Intron	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	271	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						AGGAGGTTCCGCAGCAGGTCC	0.547																																					p.R271W		Atlas-SNP	.											.	PRKACA	65	.	0			c.C811T						PASS	.						97.0	88.0	91.0					19																	14204559		2203	4300	6503	SO:0001583	missense	5566	exon9			GGTTCCGCAGCAG		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.811C>T	19.37:g.14204559G>A	ENSP00000309591:p.Arg271Trp	152.0	0.0	0		162.0	67.0	0.41358	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Missense_Mutation	SNP	ENST00000308677.4	37	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850706	0.71719	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695	T	0.66815	-0.23	4.89	4.89	0.63831	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48286	D	0.000193	T	0.82190	0.4983	M	0.88906	2.99	0.42130	D	0.991466	D;D	0.67145	0.995;0.996	D;D	0.69307	0.963;0.918	D	0.85403	0.1132	10	0.87932	D	0	.	10.785	0.46401	0.0:0.0:0.8106:0.1894	.	271;263	P17612;P17612-2	KAPCA_HUMAN;.	W	271;263;271	ENSP00000309591:R271W	ENSP00000309591:R271W	R	-	1	2	PRKACA	14065559	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	2.068000	0.41471	2.271000	0.75665	0.491000	0.48974	CGG	.	.	none		0.547	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
WSCD2	9671	hgsc.bcm.edu	37	12	108620920	108620920	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:108620920G>A	ENST00000332082.4	+	7	1776	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	WSCD2_ENST00000547525.1_Missense_Mutation_p.V320M|WSCD2_ENST00000261400.3_Missense_Mutation_p.V320M|WSCD2_ENST00000549903.1_Missense_Mutation_p.V320M			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	320	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						TTACTTCATTGTGTACCAGAC	0.587																																					p.V320M		Atlas-SNP	.											.	WSCD2	125	.	0			c.G958A						PASS	.						59.0	63.0	61.0					12																	108620920		2041	4193	6234	SO:0001583	missense	9671	exon6			TTCATTGTGTACC		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.958G>A	12.37:g.108620920G>A	ENSP00000331933:p.Val320Met	106.0	0.0	0		102.0	17.0	0.166667	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.899521	0.72754	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.38401	1.14;4.62;1.14;4.62	5.22	5.22	0.72569	Carbohydrate-binding WSC (1);Carbohydrate-binding WSC, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	M	0.72894	2.215	0.80722	D	1	P;D	0.71674	0.587;0.998	B;D	0.78314	0.146;0.991	T	0.60692	-0.7213	10	0.52906	T	0.07	-25.5959	17.9638	0.89093	0.0:0.0:1.0:0.0	.	320;320	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	M	320	ENSP00000448047:V320M;ENSP00000261400:V320M;ENSP00000331933:V320M;ENSP00000447272:V320M	ENSP00000261400:V320M	V	+	1	0	WSCD2	107145050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.078000	0.71282	2.725000	0.93324	0.655000	0.94253	GTG	.	.	none		0.587	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230364	23230364	+	Missense_Mutation	SNP	C	C	A	rs538723125	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230364C>A	ENST00000526893.1	+	1	405	c.131C>A	c.(130-132)gCa>gAa	p.A44E	IGLL5_ENST00000531372.1_Missense_Mutation_p.A44E|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.A44E	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	44						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCAATGGTTGCACCGCAAAGC	0.682																																					p.A44E		Atlas-SNP	.											.	IGLL5	26	.	0			c.C131A						PASS	.																																			SO:0001583	missense	100423062	exon1			TGGTTGCACCGCA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.131C>A	22.37:g.23230364C>A	ENSP00000431254:p.Ala44Glu	109.0	0.0	0		142.0	58.0	0.408451	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.592719	0.46214	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00686	5.85;5.86	3.92	-0.956	0.10353	.	.	.	.	.	T	0.00580	0.0019	L	0.29908	0.895	0.09310	N	1	P	0.44877	0.845	B	0.38655	0.278	T	0.48091	-0.9065	9	0.15952	T	0.53	.	4.4817	0.11771	0.0:0.4301:0.3576:0.2123	.	44	B9A064	IGLL5_HUMAN	E	44	ENSP00000436353:A44E;ENSP00000431254:A44E	ENSP00000431254:A44E	A	+	2	0	IGLL5	21560364	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.266000	0.18534	-0.052000	0.13311	0.643000	0.83706	GCA	.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
DEK	7913	hgsc.bcm.edu	37	6	18249894	18249894	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:18249894T>G	ENST00000397239.3	-	7	1197	c.750A>C	c.(748-750)gaA>gaC	p.E250D	DEK_ENST00000244776.7_Missense_Mutation_p.E216D	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	250	Asp/Glu-rich (acidic).				chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CCTCTTCACTTTCTTTATCTT	0.328			T	NUP214	AML																																p.E250D		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	DEK,NS,carcinoma,0,1	DEK	31	1	0			c.A750C						PASS	.						67.0	63.0	64.0					6																	18249894		2201	4298	6499	SO:0001583	missense	7913	exon7			TTCACTTTCTTTA	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.750A>C	6.37:g.18249894T>G	ENSP00000380414:p.Glu250Asp	124.0	0.0	0		89.0	33.0	0.370787	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Missense_Mutation	SNP	ENST00000397239.3	37	CCDS34344.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.745676	0.49151	.	.	ENSG00000124795	ENST00000397239;ENST00000244776;ENST00000507591	T;T	0.52754	0.68;0.65	6.17	3.8	0.43715	.	0.698644	0.14633	N	0.307696	T	0.21307	0.0513	L	0.44542	1.39	0.37002	D	0.895305	P;P	0.50443	0.935;0.935	B;B	0.42462	0.388;0.388	T	0.03945	-1.0990	10	0.14252	T	0.57	-0.8892	10.6274	0.45516	0.0:0.1285:0.0:0.8715	.	216;250	B4DN37;P35659	.;DEK_HUMAN	D	250;216;26	ENSP00000380414:E250D;ENSP00000244776:E216D	ENSP00000244776:E216D	E	-	3	2	DEK	18357873	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.118000	0.31246	0.572000	0.29383	-0.256000	0.11100	GAA	.	.	none		0.328	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
RNF133	168433	hgsc.bcm.edu	37	7	122338692	122338692	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:122338692C>T	ENST00000340112.2	-	1	518	c.281G>A	c.(280-282)cGa>cAa	p.R94Q	CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	94	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						GTACTTTGATCGGCTGAAAAT	0.458																																					p.R94Q	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.G281A						PASS	.						157.0	168.0	164.0					7																	122338692		2203	4299	6502	SO:0001583	missense	168433	exon1			TTTGATCGGCTGA	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"""RING-type (C3HC4) zinc fingers"""	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.281G>A	7.37:g.122338692C>T	ENSP00000344489:p.Arg94Gln	112.0	0.0	0		73.0	26.0	0.356164	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656505	0.29425	.	.	ENSG00000188050	ENST00000340112	T	0.14516	2.5	5.79	-5.14	0.02875	.	1.811660	0.03352	N	0.196336	T	0.13200	0.0320	M	0.66939	2.045	0.09310	N	1	P	0.50943	0.94	B	0.43867	0.434	T	0.39820	-0.9595	10	0.14252	T	0.57	.	2.5082	0.04650	0.1832:0.2353:0.0878:0.4937	.	94	Q8WVZ7	RN133_HUMAN	Q	94	ENSP00000344489:R94Q	ENSP00000344489:R94Q	R	-	2	0	RNF133	122125928	0.000000	0.05858	0.000000	0.03702	0.956000	0.61745	-0.849000	0.04322	-1.082000	0.03101	0.655000	0.94253	CGA	.	.	none		0.458	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175	
TECRL	253017	hgsc.bcm.edu	37	4	65188493	65188493	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:65188493C>T	ENST00000381210.3	-	4	459	c.349G>A	c.(349-351)Gac>Aac	p.D117N	TECRL_ENST00000507440.1_Missense_Mutation_p.D117N|TECRL_ENST00000513125.1_5'Flank	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	117					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						GTAATGTAGTCCTTCAAAAAA	0.323																																					p.D117N		Atlas-SNP	.											.	TECRL	106	.	0			c.G349A						PASS	.						58.0	58.0	58.0					4																	65188493		2203	4300	6503	SO:0001583	missense	253017	exon4			TGTAGTCCTTCAA	AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"""glycoprotein, synaptic 2-like"""					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.349G>A	4.37:g.65188493C>T	ENSP00000370607:p.Asp117Asn	128.0	0.0	0		98.0	4.0	0.0408163	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	37	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005165	0.35415	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.48522	0.81;0.81;0.81	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.68100	0.2964	M	0.73962	2.25	0.53005	D	0.999963	D;D	0.89917	1.0;0.993	D;D	0.87578	0.998;0.984	T	0.65861	-0.6065	10	0.37606	T	0.19	0.1933	15.4919	0.75611	0.0:1.0:0.0:0.0	.	117;117	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	N	117	ENSP00000426043:D117N;ENSP00000370607:D117N;ENSP00000422497:D117N	ENSP00000370607:D117N	D	-	1	0	TECRL	64871088	1.000000	0.71417	0.996000	0.52242	0.018000	0.09664	4.729000	0.62008	2.728000	0.93425	0.585000	0.79938	GAC	.	.	none		0.323	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	
CADM2	253559	hgsc.bcm.edu	37	3	85932591	85932591	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:85932591T>G	ENST00000407528.2	+	3	424	c.362T>G	c.(361-363)cTg>cGg	p.L121R	CADM2_ENST00000383699.3_Missense_Mutation_p.L130R|CADM2_ENST00000405615.2_Missense_Mutation_p.L123R	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	121					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTCACCGTTCTGGGTAAGTGC	0.353																																					p.L130R		Atlas-SNP	.											.	CADM2	195	.	0			c.T389G						PASS	.						78.0	66.0	70.0					3																	85932591		2203	4300	6503	SO:0001583	missense	253559	exon4			CCGTTCTGGGTAA	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.362T>G	3.37:g.85932591T>G	ENSP00000384575:p.Leu121Arg	79.0	0.0	0		59.0	22.0	0.372881	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.262776	0.59431	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.29142	1.58;1.58;1.58	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.62889	0.2465	M	0.89414	3.03	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.995;0.997;0.998	T	0.70684	-0.4804	10	0.72032	D	0.01	.	15.9801	0.80102	0.0:0.0:0.0:1.0	.	123;130;121	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	R	130;121;123	ENSP00000373200:L130R;ENSP00000384575:L121R;ENSP00000384193:L123R	ENSP00000373200:L130R	L	+	2	0	CADM2	86015281	1.000000	0.71417	1.000000	0.80357	0.251000	0.25915	7.655000	0.83696	2.230000	0.72887	0.528000	0.53228	CTG	.	.	none		0.353	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
HTR7	3363	hgsc.bcm.edu	37	10	92509323	92509323	+	Missense_Mutation	SNP	A	A	G	rs560218001		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:92509323A>G	ENST00000336152.3	-	2	594	c.568T>C	c.(568-570)Tac>Cac	p.Y190H	HTR7_ENST00000371719.2_Missense_Mutation_p.Y190H|HTR7_ENST00000371721.3_Missense_Mutation_p.Y190H|HTR7_ENST00000277874.6_Missense_Mutation_p.Y190H	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	190					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	CTCACAGGGTATGTGAGGGGC	0.517																																					p.Y190H		Atlas-SNP	.											.	HTR7	122	.	0			c.T568C						PASS	.						104.0	106.0	106.0					10																	92509323		2203	4300	6503	SO:0001583	missense	3363	exon2			CAGGGTATGTGAG	BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5302	protein-coding gene	gene with protein product		182137	"""5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"""			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.568T>C	10.37:g.92509323A>G	ENSP00000337949:p.Tyr190His	83.0	0.0	0		87.0	4.0	0.045977	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	37	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	A	18.25	3.581537	0.65992	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61540	0.2355	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68119	-0.5493	10	0.62326	D	0.03	.	15.6519	0.77104	1.0:0.0:0.0:0.0	.	190;190	P34969;P34969-2	5HT7R_HUMAN;.	H	190	ENSP00000337949:Y190H;ENSP00000277874:Y190H;ENSP00000360784:Y190H;ENSP00000360786:Y190H	ENSP00000277874:Y190H	Y	-	1	0	HTR7	92499303	1.000000	0.71417	0.969000	0.41365	0.409000	0.31022	9.139000	0.94554	2.285000	0.76669	0.528000	0.53228	TAC	.	.	none		0.517	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872	
ITSN1	6453	hgsc.bcm.edu	37	21	35190669	35190669	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:35190669C>T	ENST00000381318.3	+	23	3114	c.2826C>T	c.(2824-2826)gtC>gtT	p.V942V	ITSN1_ENST00000399352.1_Silent_p.V937V|ITSN1_ENST00000399353.1_Silent_p.V900V|ITSN1_ENST00000399326.3_Silent_p.V937V|ITSN1_ENST00000399349.1_Silent_p.V937V|ITSN1_ENST00000381285.4_Silent_p.V942V|ITSN1_ENST00000399355.2_Silent_p.V942V|ITSN1_ENST00000399367.3_Silent_p.V937V|ITSN1_ENST00000437442.2_Silent_p.V937V|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Silent_p.V942V|ITSN1_ENST00000379960.5_Intron	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	942	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						TCATCACCGTCCTGGAACAGC	0.453																																					p.V942V		Atlas-SNP	.											.	ITSN1	166	.	0			c.C2826T						PASS	.						176.0	169.0	171.0					21																	35190669		2203	4300	6503	SO:0001819	synonymous_variant	6453	exon23			CACCGTCCTGGAA	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.2826C>T	21.37:g.35190669C>T		155.0	0.0	0		142.0	60.0	0.422535	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Silent	SNP	ENST00000381318.3	37	CCDS33545.1																																																																																			.	.	none		0.453	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
MYOF	26509	hgsc.bcm.edu	37	10	95089487	95089487	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:95089487A>G	ENST00000359263.4	-	44	4915	c.4916T>C	c.(4915-4917)aTt>aCt	p.I1639T	MYOF_ENST00000358334.5_Missense_Mutation_p.I1626T|MYOF_ENST00000371502.4_Missense_Mutation_p.I1658T|MYOF_ENST00000371501.4_Missense_Mutation_p.I1639T|MYOF_ENST00000485212.1_5'UTR	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1639					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTCCAGATCAATAATTGTTTC	0.433																																					p.I1639T		Atlas-SNP	.											.	MYOF	177	.	0			c.T4916C						PASS	.						127.0	123.0	124.0					10																	95089487		1858	4102	5960	SO:0001583	missense	26509	exon44			AGATCAATAATTG	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4916T>C	10.37:g.95089487A>G	ENSP00000352208:p.Ile1639Thr	131.0	0.0	0		143.0	63.0	0.440559	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166718	0.78339	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.3	5.3	0.74995	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.097327	0.64402	D	0.000002	T	0.74183	0.3683	M	0.92923	3.36	0.80722	D	1	D;P	0.57571	0.98;0.954	D;P	0.63957	0.92;0.701	T	0.81597	-0.0860	10	0.87932	D	0	-7.8203	15.4031	0.74858	1.0:0.0:0.0:0.0	.	1626;1639	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	T	1626;1639;1639;1658	ENSP00000351094:I1626T;ENSP00000352208:I1639T;ENSP00000360556:I1639T;ENSP00000360557:I1658T	ENSP00000351094:I1626T	I	-	2	0	MYOF	95079477	1.000000	0.71417	0.794000	0.32065	0.854000	0.48673	8.723000	0.91458	2.232000	0.73038	0.454000	0.30748	ATT	.	.	none		0.433	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
PARD6G	84552	hgsc.bcm.edu	37	18	77960661	77960661	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr18:77960661T>C	ENST00000353265.3	-	2	424	c.227A>G	c.(226-228)aAt>aGt	p.N76S	PARD6G_ENST00000470488.2_Missense_Mutation_p.N76S|AC139100.3_ENST00000588950.1_RNA	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma	76	OPR.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		GTTGTCATCATTGTTGATGGG	0.498																																					p.N76S		Atlas-SNP	.											.	PARD6G	20	.	0			c.A227G						PASS	.						108.0	100.0	103.0					18																	77960661		2203	4300	6503	SO:0001583	missense	84552	exon2			TCATCATTGTTGA		CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"""par-6 (partitioning defective 6, C.elegans) homolog gamma"", ""par-6 partitioning defective 6 homolog gamma (C. elegans)"""			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.227A>G	18.37:g.77960661T>C	ENSP00000343144:p.Asn76Ser	136.0	0.0	0		91.0	42.0	0.461538	NM_032510	A8QM57	Missense_Mutation	SNP	ENST00000353265.3	37	CCDS12022.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311065	0.81358	.	.	ENSG00000178184	ENST00000353265	T	0.16324	2.35	5.43	5.43	0.79202	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	0.992;1.0	P;D	0.91635	0.829;0.999	T	0.50355	-0.8838	9	.	.	.	-32.4304	14.5927	0.68378	0.0:0.0:0.0:1.0	.	76;76	A8QM57;Q9BYG4	.;PAR6G_HUMAN	S	76	ENSP00000343144:N76S	.	N	-	2	0	PARD6G	76061652	1.000000	0.71417	0.931000	0.37212	0.850000	0.48378	6.824000	0.75288	2.282000	0.76494	0.533000	0.62120	AAT	.	.	none		0.498	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510	
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:195506555C>T	ENST00000463781.3	-	2	12355	c.11896G>A	c.(11896-11898)Gcc>Acc	p.A3966T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3966T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3966T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.592													.|||	176	0.0351438	0.0083	0.0677	5008	,	,		7977	0.0119		0.0915	False		,,,				2504	0.0143				p.A3966T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.G11896A						scavenged	.						15.0	10.0	11.0					3																	195506555		666	1488	2154	SO:0001583	missense	4585	exon2			AGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11896G>A	3.37:g.195506555C>T	ENSP00000417498:p.Ala3966Thr	31.0	1.0	0.0322581		33.0	6.0	0.181818	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.905	-0.721125	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.48522	1.23;0.81	.	.	.	.	.	.	.	.	T	0.22551	0.0544	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.12915	-1.0529	7	.	.	.	-3.1782	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	.	3838	E7ESK3	.	T	3966	ENSP00000417498:A3966T;ENSP00000420243:A3966T	.	A	-	1	0	MUC4	196991334	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.202000	0.09451	-2.037000	0.00920	-2.088000	0.00374	GCC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950587	59950587	+	Missense_Mutation	SNP	C	C	T	rs548137663		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:59950587C>T	ENST00000247194.4	-	1	561	c.448G>A	c.(448-450)Gac>Aac	p.D150N	JKAMP_ENST00000425728.2_5'Flank|JKAMP_ENST00000554271.1_5'Flank|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000556985.1_5'Flank|L3HYPDH_ENST00000487285.1_5'Flank|JKAMP_ENST00000261247.9_5'Flank|JKAMP_ENST00000356057.5_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	150					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	CTGCGGCCGTCCTCGCATGCC	0.711											OREG0022712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		14809	0.001		0.0	False		,,,				2504	0.0				p.D150N		Atlas-SNP	.											.	.	.	.	0			c.G448A						PASS	.						6.0	7.0	7.0					14																	59950587		2110	4104	6214	SO:0001583	missense	112849	exon1			GGCCGTCCTCGCA	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"""trans-L-3-hydroxyproline dehydratase"""	614811	"""chromosome 14 open reading frame 149"""	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.448G>A	14.37:g.59950587C>T	ENSP00000247194:p.Asp150Asn	9.0	0.0	0	1042	16.0	8.0	0.5	NM_144581	Q96LJ5	Missense_Mutation	SNP	ENST00000247194.4	37	CCDS9739.1	.	.	.	.	.	.	.	.	.	.	C	13.37	2.216802	0.39201	.	.	ENSG00000126790	ENST00000247194	T	0.17370	2.28	5.58	3.77	0.43336	.	0.421261	0.27227	N	0.020326	T	0.12178	0.0296	L	0.28458	0.855	0.58432	D	0.999993	B;B	0.16166	0.016;0.001	B;B	0.18263	0.021;0.003	T	0.09443	-1.0674	10	0.15952	T	0.53	.	11.8035	0.52141	0.0:0.8581:0.0:0.1419	.	150;150	B4DGY8;Q96EM0	.;PRCM_HUMAN	N	150	ENSP00000247194:D150N	ENSP00000247194:D150N	D	-	1	0	C14orf149	59020340	0.816000	0.29132	0.851000	0.33527	0.692000	0.40212	1.630000	0.37081	0.726000	0.32339	0.561000	0.74099	GAC	.	.	none		0.711	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581	
BAI1	575	hgsc.bcm.edu	37	8	143625724	143625724	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:143625724C>T	ENST00000517894.1	+	31	5595	c.4701C>T	c.(4699-4701)ggC>ggT	p.G1567G	BAI1_ENST00000323289.5_Silent_p.G1567G			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1567	Necessary for interaction with MAGI1.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AGAGGTCGGGCGCCACGATCC	0.706																																					p.G1567G		Atlas-SNP	.											.	BAI1	146	.	0			c.C4701T						PASS	.						13.0	23.0	19.0					8																	143625724		1749	3389	5138	SO:0001819	synonymous_variant	575	exon30			GTCGGGCGCCACG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"""-"", ""GPCR / Class B : Orphans"""	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.4701C>T	8.37:g.143625724C>T		12.0	0.0	0		43.0	20.0	0.465116	NM_001702		Silent	SNP	ENST00000517894.1	37																																																																																				.	.	none		0.706	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	
KIAA1377	57562	hgsc.bcm.edu	37	11	101834043	101834043	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:101834043A>C	ENST00000263468.8	+	6	2547	c.2277A>C	c.(2275-2277)aaA>aaC	p.K759N	KIAA1377_ENST00000537689.1_Missense_Mutation_p.K560N	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	759										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		TAATTAGAAAACCAGGATCTG	0.378																																					p.K759N		Atlas-SNP	.											.	KIAA1377	111	.	0			c.A2277C						PASS	.						65.0	72.0	70.0					11																	101834043		2203	4299	6502	SO:0001583	missense	57562	exon6			TAGAAAACCAGGA	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2277A>C	11.37:g.101834043A>C	ENSP00000263468:p.Lys759Asn	69.0	0.0	0		80.0	9.0	0.1125	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	A	8.638	0.895225	0.17613	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07327	3.2;3.2	5.23	5.23	0.72850	.	0.157535	0.45867	D	0.000338	T	0.06645	0.0170	N	0.22421	0.69	0.27731	N	0.944796	B	0.32467	0.372	B	0.29077	0.098	T	0.18903	-1.0322	10	0.72032	D	0.01	-14.8212	11.7668	0.51935	0.8685:0.0:0.0:0.1315	.	759	Q9P2H0	K1377_HUMAN	N	759;560	ENSP00000263468:K759N;ENSP00000443184:K560N	ENSP00000263468:K759N	K	+	3	2	KIAA1377	101339253	0.995000	0.38212	0.714000	0.30535	0.134000	0.20937	3.343000	0.52167	2.093000	0.63338	0.533000	0.62120	AAA	.	.	none		0.378	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
COL16A1	1307	hgsc.bcm.edu	37	1	32164126	32164126	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:32164126C>T	ENST00000373672.3	-	5	864	c.348G>A	c.(346-348)acG>acA	p.T116T	COL16A1_ENST00000271069.6_Silent_p.T116T|COL16A1_ENST00000373668.3_Silent_p.T116T	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	116	Laminin G-like.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		ACAGATACCACGTCTTCTGGT	0.557																																					p.T116T	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G348A						PASS	.						122.0	128.0	126.0					1																	32164126		2023	4176	6199	SO:0001819	synonymous_variant	1307	exon5			ATACCACGTCTTC	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.348G>A	1.37:g.32164126C>T		58.0	0.0	0		83.0	7.0	0.0843373	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			.	.	none		0.557	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857830	149857830	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:149857830T>C	ENST00000369155.2	-	1	402	c.361A>G	c.(361-363)Aag>Gag	p.K121E	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	121					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CTGGTGTACTTGGTGACCGCC	0.667																																					p.K121E		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.A361G						PASS	.						30.0	35.0	33.0					1																	149857830		2202	4299	6501	SO:0001583	missense	8349	exon1			TGTACTTGGTGAC	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"""Histones / Replication-dependent"""	4760	protein-coding gene	gene with protein product		601831	"""H2B histone family, member Q"", ""histone 2, H2be"""	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.361A>G	1.37:g.149857830T>C	ENSP00000358151:p.Lys121Glu	80.0	0.0	0		117.0	38.0	0.324786	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	37	CCDS936.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.909008	0.92107	.	.	ENSG00000184678	ENST00000369155	T	0.46063	0.88	6.07	6.07	0.98685	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.54078	0.1836	H	0.98664	4.295	0.38928	D	0.957879	P	0.52842	0.956	B	0.40329	0.326	T	0.76302	-0.3009	10	0.87932	D	0	.	15.47	0.75434	0.0:0.0:0.0:1.0	.	121	Q16778	H2B2E_HUMAN	E	121	ENSP00000358151:K121E	ENSP00000358151:K121E	K	-	1	0	HIST2H2BE	148124454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.924000	0.87555	2.330000	0.79161	0.477000	0.44152	AAG	.	.	none		0.667	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528	
PCDHA10	56139	hgsc.bcm.edu	37	5	140236835	140236835	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:140236835A>G	ENST00000307360.5	+	1	1202	c.1202A>G	c.(1201-1203)aAg>aGg	p.K401R	PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.K401R|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	401	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCACCTACAAGAATTACTAC	0.597																																					p.K401R		Atlas-SNP	.											.	PCDHA10	358	.	0			c.A1202G						PASS	.						144.0	129.0	134.0					5																	140236835		2197	4275	6472	SO:0001583	missense	56139	exon1			CCTACAAGAATTA	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1202A>G	5.37:g.140236835A>G	ENSP00000304234:p.Lys401Arg	130.0	0.0	0		189.0	77.0	0.407407	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	A	9.832	1.188630	0.21954	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.51817	4.64;0.69	4.0	1.57	0.23409	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.39036	0.1063	L	0.46819	1.47	0.21325	N	0.999726	B;B;B	0.26809	0.086;0.029;0.16	B;B;B	0.32928	0.085;0.03;0.155	T	0.34976	-0.9807	9	0.39692	T	0.17	.	5.0725	0.14613	0.6033:0.1492:0.2475:0.0	.	401;401;401	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	R	401	ENSP00000421030:K401R;ENSP00000304234:K401R	ENSP00000304234:K401R	K	+	2	0	PCDHA10	140217019	0.000000	0.05858	0.999000	0.59377	0.741000	0.42261	0.427000	0.21379	0.653000	0.30826	0.459000	0.35465	AAG	.	.	none		0.597	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
P2RY8	286530	hgsc.bcm.edu	37	X	1585217	1585217	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:1585217G>T	ENST00000381297.4	-	2	445	c.235C>A	c.(235-237)Caa>Aaa	p.Q79K	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TAGTAGATTTGGAAAGGCAAC	0.572			T	CRLF2	"""B-ALL, Downs associated ALL"""																																p.Q79K		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	.	P2RY8	53	.	0			c.C235A						PASS	.						141.0	127.0	132.0					X																	1585217		2203	4296	6499	SO:0001583	missense	286530	exon2			AGATTTGGAAAGG	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.235C>A	X.37:g.1585217G>T	ENSP00000370697:p.Gln79Lys	218.0	0.0	0		260.0	105.0	0.403846	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	g	3.768	-0.048128	0.07407	.	.	ENSG00000182162	ENST00000381297	T	0.71461	-0.57	2.1	2.1	0.27182	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000002	T	0.65015	0.2651	N	0.16066	0.365	0.09310	N	0.999999	D	0.76494	0.999	D	0.87578	0.998	T	0.58244	-0.7670	10	0.02654	T	1	.	12.2776	0.54744	0.0:0.0:1.0:0.0	.	79	Q86VZ1	P2RY8_HUMAN	K	79	ENSP00000370697:Q79K	ENSP00000370697:Q79K	Q	-	1	0	P2RY8	1545217	1.000000	0.71417	0.577000	0.28562	0.017000	0.09413	5.642000	0.67888	0.637000	0.30526	0.279000	0.19357	CAA	.	.	none		0.572	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230312C>G	ENST00000526893.1	+	1	353	c.79C>G	c.(79-81)Ctg>Gtg	p.L27V	IGLL5_ENST00000531372.1_Missense_Mutation_p.L27V|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.L27V	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27V		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79G						PASS	.																																			SO:0001583	missense	100423062	exon1			CCCCTGCTGCTGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.79C>G	22.37:g.23230312C>G	ENSP00000431254:p.Leu27Val	108.0	0.0	0		142.0	61.0	0.429577	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.278851	0.23307	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00626	6.13;6.14	3.81	-2.69	0.06022	.	.	.	.	.	T	0.00524	0.0017	L	0.29908	0.895	0.09310	N	1	P	0.37061	0.58	B	0.28232	0.087	T	0.47032	-0.9148	9	0.72032	D	0.01	.	7.0435	0.25033	0.3778:0.5232:0.0:0.099	.	27	B9A064	IGLL5_HUMAN	V	27	ENSP00000436353:L27V;ENSP00000431254:L27V	ENSP00000431254:L27V	L	+	1	2	IGLL5	21560312	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.733000	0.01850	-0.440000	0.07211	-0.165000	0.13383	CTG	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
OR5B3	441608	hgsc.bcm.edu	37	11	58170412	58170412	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:58170412G>A	ENST00000309403.2	-	1	470	c.471C>T	c.(469-471)caC>caT	p.H157H		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGTCCCCAGTGTGGATGGAGG	0.468																																					p.H157H		Atlas-SNP	.											OR5B3,right_upper_lobe,carcinoma,-2,1	OR5B3	65	1	0			c.C471T						PASS	.						114.0	106.0	109.0					11																	58170412		2201	4295	6496	SO:0001819	synonymous_variant	441608	exon1			CCCAGTGTGGATG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.471C>T	11.37:g.58170412G>A		89.0	0.0	0		100.0	4.0	0.04	NM_001005469	Q6IEV6	Silent	SNP	ENST00000309403.2	37	CCDS31549.1																																																																																			.	.	none		0.468	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
PGM3	5238	hgsc.bcm.edu	37	6	83898451	83898451	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:83898451C>T	ENST00000283977.4	-	2	154	c.28G>A	c.(28-30)Gcc>Acc	p.A10T	PGM3_ENST00000506587.1_Missense_Mutation_p.A119T|PGM3_ENST00000512866.1_Missense_Mutation_p.A91T|PGM3_ENST00000513973.1_Missense_Mutation_p.A91T					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		AAACAGGTGGCATGTTCCTCC	0.413																																					p.A119T		Atlas-SNP	.											.	PGM3	39	.	0			c.G355A						PASS	.						148.0	120.0	129.0					6																	83898451		2203	4300	6503	SO:0001583	missense	5238	exon4			AGGTGGCATGTTC	BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"""acetylglucosamine phosphomutase"""	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.28G>A	6.37:g.83898451C>T	ENSP00000283977:p.Ala10Thr	108.0	0.0	0		90.0	34.0	0.377778	NM_001199917		Missense_Mutation	SNP	ENST00000283977.4	37		.	.	.	.	.	.	.	.	.	.	C	32	5.185099	0.94885	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587;ENST00000510258;ENST00000507554;ENST00000508748	T;T;T;T;T;T	0.63096	-0.02;-0.02;0.59;-0.02;-0.02;-0.02	5.82	5.82	0.92795	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (1);Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.000000	0.85682	D	0.000000	D	0.84083	0.5394	H	0.94582	3.555	0.80722	D	1	D;D;D	0.76494	0.999;0.99;0.999	D;D;D	0.74348	0.983;0.955;0.974	D	0.87601	0.2497	10	0.87932	D	0	-9.7285	20.0851	0.97797	0.0:1.0:0.0:0.0	.	119;119;91	E9PF86;B4DX94;O95394	.;.;AGM1_HUMAN	T	91;91;10;119;10;91;119	ENSP00000424874:A91T;ENSP00000421565:A91T;ENSP00000283977:A10T;ENSP00000425809:A119T;ENSP00000425558:A91T;ENSP00000424865:A119T	ENSP00000283977:A10T	A	-	1	0	PGM3	83955170	1.000000	0.71417	0.811000	0.32455	0.624000	0.37722	7.487000	0.81328	2.758000	0.94735	0.650000	0.86243	GCC	.	.	none		0.413	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599	
RIMS2	9699	hgsc.bcm.edu	37	8	104513174	104513174	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:104513174G>A	ENST00000406091.3	+	1	60	c.60G>A	c.(58-60)ccG>ccA	p.P20P	RP11-1C8.4_ENST00000523422.1_RNA|RP11-1C8.4_ENST00000517376.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	20					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CCTCTCAGCCGCCTCTGCAGC	0.647										HNSCC(12;0.0054)																											p.P20P		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G60A						PASS	.						22.0	25.0	24.0					8																	104513174		1877	4089	5966	SO:0001819	synonymous_variant	9699	exon1			TCAGCCGCCTCTG	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.60G>A	8.37:g.104513174G>A		71.0	0.0	0		93.0	6.0	0.0645161	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	37	CCDS55269.1																																																																																			.	.	none		0.647	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117	
PPP2R5B	5526	hgsc.bcm.edu	37	11	64700699	64700699	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:64700699T>C	ENST00000164133.2	+	13	1949	c.1327T>C	c.(1327-1329)Tac>Cac	p.Y443H		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	443					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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						CACAGCCTCCTACAAGCTGGA	0.552																																					p.Y443H		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.T1327C						PASS	.						96.0	81.0	87.0					11																	64700699		2201	4297	6498	SO:0001583	missense	5526	exon13			GCCTCCTACAAGC	L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9310	protein-coding gene	gene with protein product	"""PP2A, B subunit, B' beta isoform"", ""PP2A, B subunit, B56 beta isoform"", ""PP2A, B subunit, PR61 beta isoform"", ""PP2A, B subunit, R5 beta isoform"", ""serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"""	601644	"""protein phosphatase 2, regulatory subunit B (B56), beta isoform"", ""protein phosphatase 2, regulatory subunit B', beta isoform"""			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.1327T>C	11.37:g.64700699T>C	ENSP00000164133:p.Tyr443His	54.0	0.0	0		64.0	4.0	0.0625	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717126	0.68844	.	.	ENSG00000068971	ENST00000164133;ENST00000527441	.	.	.	4.04	4.04	0.47022	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.71316	0.3325	M	0.70108	2.13	0.58432	D	0.999999	P	0.44195	0.828	P	0.53912	0.737	T	0.74878	-0.3514	9	0.66056	D	0.02	-16.1599	11.5916	0.50949	0.0:0.0:0.0:1.0	.	443	Q15173	2A5B_HUMAN	H	443	.	ENSP00000164133:Y443H	Y	+	1	0	PPP2R5B	64457275	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.508000	0.81686	2.054000	0.61138	0.459000	0.35465	TAC	.	.	none		0.552	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230402	23230402	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230402G>A	ENST00000526893.1	+	1	443	c.169G>A	c.(169-171)Gga>Aga	p.G57R	IGLL5_ENST00000531372.1_Missense_Mutation_p.G57R|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.G57R	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGCCTCAGTTGGAAGCAGCCG	0.662																																					p.G57R		Atlas-SNP	.											.	IGLL5	26	.	0			c.G169A						PASS	.																																			SO:0001583	missense	100423062	exon1			TCAGTTGGAAGCA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.169G>A	22.37:g.23230402G>A	ENSP00000431254:p.Gly57Arg	101.0	0.0	0		146.0	61.0	0.417808	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.690900	0.48097	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00587	6.39;6.38	3.92	-1.17	0.09648	.	.	.	.	.	T	0.00496	0.0016	L	0.32530	0.975	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.40079	-0.9582	9	0.37606	T	0.19	.	5.1199	0.14854	0.2033:0.4108:0.3859:0.0	.	57	B9A064	IGLL5_HUMAN	R	57	ENSP00000436353:G57R;ENSP00000431254:G57R	ENSP00000431254:G57R	G	+	1	0	IGLL5	21560402	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.250000	0.08830	-0.072000	0.12864	-0.189000	0.12847	GGA	.	.	none		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
CARD11	84433	hgsc.bcm.edu	37	7	2977605	2977605	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:2977605A>G	ENST00000396946.4	-	8	1482	c.1079T>C	c.(1078-1080)aTg>aCg	p.M360T		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	360					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.M353T(1)|p.M353K(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GTGCTTGTACATTTCACAGTC	0.592			Mis		DLBCL																																p.M360T		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,colon,carcinoma,-1,4	CARD11	339	4	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1079C						PASS	.						143.0	116.0	125.0					7																	2977605		2203	4300	6503	SO:0001583	missense	84433	exon8			TTGTACATTTCAC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1079T>C	7.37:g.2977605A>G	ENSP00000380150:p.Met360Thr	52.0	0.0	0		69.0	33.0	0.478261	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	18.62	3.663818	0.67700	.	.	ENSG00000198286	ENST00000396946	T	0.32988	1.43	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.32406	0.0828	L	0.54323	1.7	0.58432	D	0.999999	B	0.24823	0.112	B	0.27715	0.082	T	0.12578	-1.0542	10	0.54805	T	0.06	-50.9525	13.8813	0.63684	1.0:0.0:0.0:0.0	.	360	Q9BXL7	CAR11_HUMAN	T	360	ENSP00000380150:M360T	ENSP00000380150:M360T	M	-	2	0	CARD11	2944131	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	9.048000	0.93830	1.878000	0.54408	0.482000	0.46254	ATG	.	.	none		0.592	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
GDPD4	220032	hgsc.bcm.edu	37	11	76996151	76996151	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:76996151C>T	ENST00000376217.2	-	2	282	c.32G>A	c.(31-33)aGt>aAt	p.S11N	GDPD4_ENST00000527489.1_5'UTR|GDPD4_ENST00000315938.4_Missense_Mutation_p.S11N			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	11					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						AAAGTATTCACTGGATGTTTC	0.383																																					p.S11N		Atlas-SNP	.											.	GDPD4	49	.	0			c.G32A						PASS	.						76.0	67.0	70.0					11																	76996151		2200	4292	6492	SO:0001583	missense	220032	exon2			TATTCACTGGATG	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.32G>A	11.37:g.76996151C>T	ENSP00000365390:p.Ser11Asn	67.0	0.0	0		88.0	26.0	0.295455	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		.	.	.	.	.	.	.	.	.	.	c	0.018	-1.481167	0.01027	.	.	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.19669	2.13;2.13	3.94	2.82	0.32997	.	0.095444	0.64402	N	0.000002	T	0.02727	0.0082	N	0.00056	-2.365	0.19775	N	0.99995	B	0.02656	0.0	B	0.01281	0.0	T	0.42085	-0.9472	10	0.02654	T	1	-15.0283	6.3686	0.21469	0.0:0.111:0.0:0.889	.	11	Q6W3E5-2	.	N	11	ENSP00000365390:S11N;ENSP00000320815:S11N	ENSP00000320815:S11N	S	-	2	0	GDPD4	76673799	0.998000	0.40836	1.000000	0.80357	0.434000	0.31775	1.836000	0.39191	0.855000	0.35359	-0.374000	0.07098	AGT	.	.	none		0.383	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
PDGFC	56034	hgsc.bcm.edu	37	4	157689051	157689051	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:157689051T>A	ENST00000502773.1	-	5	1285	c.795A>T	c.(793-795)agA>agT	p.R265S	PDGFC_ENST00000542208.1_Missense_Mutation_p.R110S|PDGFC_ENST00000541126.1_Missense_Mutation_p.R102S|PDGFC_ENST00000422544.2_Intron|PDGFC_ENST00000504672.1_Intron	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	265					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		TGGTATCGGTTCTCTTTAGTT	0.453																																					p.R265S		Atlas-SNP	.											.	PDGFC	46	.	0			c.A795T						PASS	.						187.0	171.0	176.0					4																	157689051		2203	4299	6502	SO:0001583	missense	56034	exon5			ATCGGTTCTCTTT	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.795A>T	4.37:g.157689051T>A	ENSP00000422464:p.Arg265Ser	110.0	0.0	0		94.0	38.0	0.404255	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Missense_Mutation	SNP	ENST00000502773.1	37	CCDS3795.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.076337	0.76415	.	.	ENSG00000145431	ENST00000502773;ENST00000541126;ENST00000542208	T;T;T	0.42131	2.56;1.0;0.98	5.35	1.63	0.23807	Platelet-derived growth factor (PDGF) (3);	0.098787	0.64402	D	0.000003	T	0.51398	0.1672	M	0.63428	1.95	0.48087	D	0.999582	D;B	0.57571	0.98;0.124	P;B	0.57846	0.828;0.247	T	0.50154	-0.8861	10	0.56958	D	0.05	-15.9159	9.5005	0.39015	0.0:0.4019:0.0:0.5981	.	110;265	B4E3A5;Q9NRA1	.;PDGFC_HUMAN	S	265;102;110	ENSP00000422464:R265S;ENSP00000442943:R102S;ENSP00000439728:R110S	ENSP00000422464:R265S	R	-	3	2	PDGFC	157908501	0.987000	0.35691	1.000000	0.80357	0.999000	0.98932	0.193000	0.17116	0.369000	0.24510	0.533000	0.62120	AGA	.	.	none		0.453	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1		
USH2A	7399	hgsc.bcm.edu	37	1	216495278	216495278	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:216495278T>G	ENST00000307340.3	-	9	1977	c.1591A>C	c.(1591-1593)Agc>Cgc	p.S531R	USH2A_ENST00000366943.2_Missense_Mutation_p.S531R|USH2A_ENST00000366942.3_Missense_Mutation_p.S531R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	531	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TATGGCTGGCTTGTTGTGTCG	0.413										HNSCC(13;0.011)																											p.S531R		Atlas-SNP	.											.	USH2A	1168	.	0			c.A1591C						PASS	.						145.0	133.0	137.0					1																	216495278		2203	4300	6503	SO:0001583	missense	7399	exon9			GCTGGCTTGTTGT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1591A>C	1.37:g.216495278T>G	ENSP00000305941:p.Ser531Arg	172.0	0.0	0		151.0	9.0	0.0596026	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	6.897	0.535088	0.13188	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.63913	-0.07;-0.07;-0.07	5.65	2.07	0.26955	EGF-like, laminin (3);	0.596017	0.14863	N	0.293961	T	0.45994	0.1370	L	0.33189	0.99	0.09310	N	1	B;B	0.15473	0.012;0.013	B;B	0.17433	0.005;0.018	T	0.27872	-1.0061	10	0.15952	T	0.53	.	8.4255	0.32727	0.0:0.2872:0.0:0.7128	.	531;531	O75445-2;O75445	.;USH2A_HUMAN	R	531	ENSP00000305941:S531R;ENSP00000355910:S531R;ENSP00000355909:S531R	ENSP00000305941:S531R	S	-	1	0	USH2A	214561901	0.000000	0.05858	0.024000	0.17045	0.041000	0.13682	0.201000	0.17276	0.097000	0.17492	0.455000	0.32223	AGC	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
MUC4	4585	hgsc.bcm.edu	37	3	195518110	195518110	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:195518110G>A	ENST00000463781.3	-	2	800	c.341C>T	c.(340-342)gCt>gTt	p.A114V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A114V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	119					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATCTGGAGGAGCTGTCTCCAT	0.468																																					p.A114V		Atlas-SNP	.											MUC4_ENST00000463781,caecum,adenoma,0,1	MUC4	1505	1	0			c.C341T						PASS	.						169.0	145.0	153.0					3																	195518110		1992	4142	6134	SO:0001583	missense	4585	exon2			GGAGGAGCTGTCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.341C>T	3.37:g.195518110G>A	ENSP00000417498:p.Ala114Val	121.0	0.0	0		156.0	11.0	0.0705128	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.679	0.493843	0.12702	.	.	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.32272	1.46;1.47	3.46	1.61	0.23674	.	4.057260	0.00950	N	0.002944	T	0.20007	0.0481	N	0.19112	0.55	0.09310	N	1	B	0.34015	0.435	B	0.29353	0.101	T	0.16041	-1.0416	10	0.35671	T	0.21	-0.1442	5.2629	0.15584	0.277:0.0:0.723:0.0	.	114	E7ESK3	.	V	114;114;88	ENSP00000417498:A114V;ENSP00000420243:A114V	ENSP00000376209:A88V	A	-	2	0	MUC4	197002505	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.806000	0.00758	0.455000	0.26910	-0.302000	0.09304	GCT	.	.	none		0.468	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GUCY1A3	2982	hgsc.bcm.edu	37	4	156634257	156634257	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:156634257A>G	ENST00000296518.7	+	7	1303	c.1094A>G	c.(1093-1095)gAc>gGc	p.D365G	GUCY1A3_ENST00000506455.1_Missense_Mutation_p.D365G|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.D365G|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.D365G|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.D365G|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.D107G|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.D365G			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	365					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TAGGTTATGGACCTCAAAGGC	0.408																																					p.D365G		Atlas-SNP	.											.	GUCY1A3	133	.	0			c.A1094G						PASS	.						63.0	61.0	61.0					4																	156634257		2203	4300	6503	SO:0001583	missense	2982	exon7			TTATGGACCTCAA		CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1094A>G	4.37:g.156634257A>G	ENSP00000296518:p.Asp365Gly	119.0	0.0	0		113.0	39.0	0.345133	NM_001130687	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.681155	0.88542	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	6.03	6.03	0.97812	Haem NO binding associated (1);	0.000000	0.64402	D	0.000003	D	0.90546	0.7037	L	0.40543	1.245	0.80722	D	1	P;P	0.46142	0.873;0.873	P;P	0.56088	0.791;0.791	D	0.90068	0.4161	10	0.42905	T	0.14	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	365;365	B3KU69;Q02108	.;GCYA3_HUMAN	G	365;365;365;365;107;365;365	ENSP00000424361:D365G;ENSP00000421493:D365G;ENSP00000426968:D365G;ENSP00000412201:D365G;ENSP00000377418:D107G;ENSP00000296518:D365G;ENSP00000426040:D365G	ENSP00000296518:D365G	D	+	2	0	GUCY1A3	156853707	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.930000	0.92872	2.308000	0.77769	0.533000	0.62120	GAC	.	.	none		0.408	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2		
PIM1	5292	hgsc.bcm.edu	37	6	37138355	37138355	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:37138355C>T	ENST00000373509.5	+	1	377	c.4C>T	c.(4-6)Ctc>Ttc	p.L2F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	93					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)	p.L2V(1)|p.L2F(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	GGTTGGGATGCTCTTGTCCAA	0.701			T	BCL6	NHL																																p.L93F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C277T						PASS	.						30.0	30.0	30.0					6																	37138355		2201	4298	6499	SO:0001583	missense	5292	exon1			GGGATGCTCTTGT		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.4C>T	6.37:g.37138355C>T	ENSP00000362608:p.Leu2Phe	29.0	0.0	0		33.0	10.0	0.30303	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693535	0.88735	.	.	ENSG00000137193	ENST00000373509	T	0.71222	-0.55	4.05	4.05	0.47172	.	0.000000	0.32147	N	0.006517	T	0.61899	0.2384	N	0.08118	0	0.48830	D	0.999711	D	0.76494	0.999	D	0.66196	0.942	T	0.73933	-0.3826	10	0.72032	D	0.01	.	16.7252	0.85419	0.0:1.0:0.0:0.0	.	93	P11309	PIM1_HUMAN	F	2	ENSP00000362608:L2F	ENSP00000362608:L2F	L	+	1	0	PIM1	37246333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.672000	0.61597	2.211000	0.71520	0.542000	0.68232	CTC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
OR5C1	392391	hgsc.bcm.edu	37	9	125551542	125551542	+	Silent	SNP	C	C	T	rs201755571		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:125551542C>T	ENST00000373680.2	+	1	393	c.331C>T	c.(331-333)Ctg>Ttg	p.L111L		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						CTTTGCAGGTCTGGCTGATAC	0.567																																					p.L111L		Atlas-SNP	.											.	OR5C1	45	.	0			c.C331T						PASS	.						136.0	121.0	126.0					9																	125551542		2203	4300	6503	SO:0001819	synonymous_variant	392391	exon1			GCAGGTCTGGCTG	AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"""GPCR / Class A : Olfactory receptors"""	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.331C>T	9.37:g.125551542C>T		91.0	0.0	0		81.0	4.0	0.0493827	NM_001001923	B2RN54|B9EGT0|Q96RC4	Silent	SNP	ENST00000373680.2	37	CCDS35131.1																																																																																			C|1.000;A|0.000	.	alt		0.567	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1		
DUSP2	1844	hgsc.bcm.edu	37	2	96810590	96810590	+	Silent	SNP	G	G	C	rs187607778		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:96810590G>C	ENST00000288943.4	-	2	505	c.420C>G	c.(418-420)ccC>ccG	p.P140P	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	140	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				AGCACAGATCGGGACAGCAGC	0.672													G|||	1	0.000199681	0.0	0.0014	5008	,	,		10971	0.0		0.0	False		,,,				2504	0.0				p.P140P		Atlas-SNP	.											DUSP2,NS,carcinoma,0,1	DUSP2	20	1	0			c.C420G						PASS	.						15.0	20.0	18.0					2																	96810590		2129	4223	6352	SO:0001819	synonymous_variant	1844	exon2			CAGATCGGGACAG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.420C>G	2.37:g.96810590G>C		84.0	0.0	0		97.0	48.0	0.494845	NM_004418	Q53T45	Silent	SNP	ENST00000288943.4	37	CCDS2016.1																																																																																			C|0.000;G|1.000	0.000	strong		0.672	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:26245986A>T	ENST00000337620.4	+	3	452		c.e3-1		CBX3_ENST00000396386.2_Splice_Site|CBX3_ENST00000409747.1_Splice_Site|CBX3_ENST00000497498.1_Splice_Site	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						GTTTTATTTTAGCAAAAAATG	0.308																																					.		Atlas-SNP	.											CBX3,colon,adenoma,0,1	CBX3	25	1	0			c.25-2A>T						scavenged	.						32.0	33.0	32.0					7																	26245986		2200	4300	6500	SO:0001630	splice_region_variant	11335	exon3			TATTTTAGCAAAA	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"""HP1 gamma homolog (Drosophila)"""	604477	"""chromobox homolog 3 (Drosophila HP1 gamma)"""			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.25-1A>T	7.37:g.26245986A>T		20.0	1.0	0.05		40.0	5.0	0.125	NM_007276	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Splice_Site	SNP	ENST00000337620.4	37	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999549	0.54147	.	.	ENSG00000122565	ENST00000337620;ENST00000396386;ENST00000456948;ENST00000409747	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2344	0.54508	0.8582:0.1418:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBX3	26212511	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.092000	0.50207	2.323000	0.78572	0.533000	0.62120	.	.	.	none		0.308	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	Intron
NPAS4	266743	hgsc.bcm.edu	37	11	66191437	66191437	+	Missense_Mutation	SNP	C	C	A	rs145746289		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:66191437C>A	ENST00000311034.2	+	7	1252	c.1076C>A	c.(1075-1077)aCt>aAt	p.T359N		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	359					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						TGCTCCAGCACTAACCCACTC	0.557																																					p.T359N		Atlas-SNP	.											.	NPAS4	133	.	0			c.C1076A						PASS	.						148.0	153.0	152.0					11																	66191437		2200	4295	6495	SO:0001583	missense	266743	exon7			CCAGCACTAACCC	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.1076C>A	11.37:g.66191437C>A	ENSP00000311196:p.Thr359Asn	48.0	0.0	0		49.0	17.0	0.346939	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720846	0.30503	.	.	ENSG00000174576	ENST00000311034	T	0.43688	0.94	4.81	3.88	0.44766	.	0.870088	0.09718	N	0.764833	T	0.25494	0.0620	N	0.08118	0	0.22468	N	0.999071	B	0.14438	0.01	B	0.13407	0.009	T	0.16482	-1.0401	10	0.23302	T	0.38	0.8502	12.7895	0.57526	0.0:0.8339:0.1661:0.0	.	359	Q8IUM7	NPAS4_HUMAN	N	359	ENSP00000311196:T359N	ENSP00000311196:T359N	T	+	2	0	NPAS4	65948013	0.994000	0.37717	0.903000	0.35520	0.977000	0.68977	3.604000	0.54081	1.219000	0.43474	0.563000	0.77884	ACT	C|1.000;T|0.000	.	alt		0.557	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864	
DNAH6	1768	hgsc.bcm.edu	37	2	84785000	84785000	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:84785000A>G	ENST00000237449.6	+	10	1752	c.1744A>G	c.(1744-1746)Agt>Ggt	p.S582G	DNAH6_ENST00000389394.3_Missense_Mutation_p.S582G|DNAH6_ENST00000398278.2_Missense_Mutation_p.S582G			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	582	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AACTGGGCCAAGTTTAGCAGC	0.338																																					p.S582G		Atlas-SNP	.											.	DNAH6	194	.	0			c.A1744G						PASS	.						90.0	89.0	89.0					2																	84785000		2203	4300	6503	SO:0001583	missense	1768	exon11			GGGCCAAGTTTAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1744A>G	2.37:g.84785000A>G	ENSP00000237449:p.Ser582Gly	70.0	0.0	0		51.0	18.0	0.352941	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.675857	0.29783	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.25749	1.78;1.91;1.78	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000007	T	0.30479	0.0766	M	0.61703	1.905	0.23920	N	0.996469	B;P	0.38827	0.0;0.649	B;B	0.41510	0.0;0.359	T	0.16837	-1.0389	10	0.25106	T	0.35	.	13.8456	0.63466	1.0:0.0:0.0:0.0	.	582;161	Q9C0G6;Q9C0G6-3	DYH6_HUMAN;.	G	582	ENSP00000374045:S582G;ENSP00000381326:S582G;ENSP00000237449:S582G	ENSP00000237449:S582G	S	+	1	0	DNAH6	84638511	1.000000	0.71417	0.627000	0.29227	0.457000	0.32468	5.904000	0.69886	1.914000	0.55421	0.459000	0.35465	AGT	.	.	none		0.338	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
BOD1L1	259282	hgsc.bcm.edu	37	4	13602085	13602085	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:13602085T>C	ENST00000040738.5	-	10	6574	c.6439A>G	c.(6439-6441)Agc>Ggc	p.S2147G		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2147						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S2147G(1)									TCCCCTATGCTTGTGGAAATC	0.502																																					p.S2147G		Atlas-SNP	.											BOD1L,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	kidney(1)	c.A6439G						scavenged	.						83.0	73.0	77.0					4																	13602085		2203	4300	6503	SO:0001583	missense	259282	exon10			CTATGCTTGTGGA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.6439A>G	4.37:g.13602085T>C	ENSP00000040738:p.Ser2147Gly	65.0	0.0	0		65.0	3.0	0.0461538	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	20.9	4.072314	0.76415	.	.	ENSG00000038219	ENST00000040738	T	0.16457	2.34	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.43411	0.1246	M	0.78456	2.415	0.40176	D	0.977236	D	0.76494	0.999	D	0.78314	0.991	T	0.47368	-0.9123	10	0.87932	D	0	-5.3309	14.1665	0.65480	0.0:0.0:0.0:1.0	.	2147	Q8NFC6	BOD1L_HUMAN	G	2147	ENSP00000040738:S2147G	ENSP00000040738:S2147G	S	-	1	0	BOD1L	13211183	1.000000	0.71417	0.997000	0.53966	0.856000	0.48823	4.896000	0.63222	2.083000	0.62718	0.454000	0.30748	AGC	.	.	none		0.502	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
RNF123	63891	hgsc.bcm.edu	37	3	49757994	49757994	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:49757994G>A	ENST00000327697.6	+	36	3695	c.3551G>A	c.(3550-3552)cGc>cAc	p.R1184H	RNF123_ENST00000433785.1_Missense_Mutation_p.R296H|AMIGO3_ENST00000535833.1_5'UTR|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308375.6_3'UTR|GMPPB_ENST00000480687.1_3'UTR|RNF123_ENST00000497099.1_3'UTR	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	1184					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TTCCAGCTACGCTCAATATGC	0.617																																					p.R1184H		Atlas-SNP	.											.	RNF123	100	.	0			c.G3551A						PASS	.						56.0	50.0	52.0					3																	49757994		2203	4300	6503	SO:0001583	missense	63891	exon36			AGCTACGCTCAAT	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.3551G>A	3.37:g.49757994G>A	ENSP00000328287:p.Arg1184His	78.0	0.0	0		105.0	42.0	0.4	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877886	0.51801	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000433785	T	0.72725	-0.68	5.29	5.29	0.74685	.	0.059077	0.64402	D	0.000001	T	0.65207	0.2669	L	0.40543	1.245	0.53688	D	0.999979	B	0.15473	0.013	B	0.08055	0.003	T	0.61734	-0.7002	10	0.59425	D	0.04	-23.7591	18.1046	0.89516	0.0:0.0:1.0:0.0	.	1184	Q5XPI4	RN123_HUMAN	H	1184;1184;296	ENSP00000328287:R1184H	ENSP00000328287:R1184H	R	+	2	0	RNF123	49732998	0.990000	0.36364	0.988000	0.46212	0.910000	0.53928	3.769000	0.55303	2.756000	0.94617	0.561000	0.74099	CGC	.	.	none		0.617	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84.0	83.0	83.0					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	34.0	1.0	0.0294118		37.0	3.0	0.0810811	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
NFKBIE	4794	hgsc.bcm.edu	37	6	44229533	44229533	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:44229533A>T	ENST00000275015.5	-	3	937	c.938T>A	c.(937-939)cTg>cAg	p.L313Q		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	313					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTTCAGCACCAGTGCCCGAAC	0.647																																					p.L313Q		Atlas-SNP	.											.	NFKBIE	31	.	0			c.T938A						PASS	.						30.0	30.0	30.0					6																	44229533		2203	4300	6503	SO:0001583	missense	4794	exon3			AGCACCAGTGCCC	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.938T>A	6.37:g.44229533A>T	ENSP00000275015:p.Leu313Gln	50.0	0.0	0		56.0	24.0	0.428571	NM_004556	Q5T9V9	Missense_Mutation	SNP	ENST00000275015.5	37	CCDS34463.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589276	0.46214	.	.	ENSG00000146232	ENST00000275015	T	0.71579	-0.58	5.28	5.28	0.74379	Ankyrin repeat-containing domain (3);	0.083592	0.49916	D	0.000132	D	0.88934	0.6572	H	0.98629	4.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93185	0.6578	10	0.87932	D	0	-19.4802	14.894	0.70630	1.0:0.0:0.0:0.0	.	313	O00221	IKBE_HUMAN	Q	313	ENSP00000275015:L313Q	ENSP00000275015:L313Q	L	-	2	0	NFKBIE	44337511	1.000000	0.71417	0.985000	0.45067	0.980000	0.70556	9.339000	0.96797	2.000000	0.58554	0.533000	0.62120	CTG	.	.	none		0.647	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
GFM2	84340	hgsc.bcm.edu	37	5	74021852	74021852	+	Missense_Mutation	SNP	A	A	T	rs5868753|rs76339998	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:74021852A>T	ENST00000296805.3	-	18	2283	c.1826T>A	c.(1825-1827)tTt>tAt	p.F609Y	GFM2_ENST00000345239.2_Missense_Mutation_p.F562Y|GFM2_ENST00000509430.1_Missense_Mutation_p.F609Y|GFM2_ENST00000515125.1_5'UTR|RNU6-658P_ENST00000384606.1_RNA	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2									p.F609Y(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		AGCATACTCAAACTCAATCAC	0.413																																					p.F609Y		Atlas-SNP	.											GFM2,NS,carcinoma,0,1	GFM2	38	1	1	Substitution - Missense(1)	lung(1)	c.T1826A						PASS	.						58.0	107.0	90.0					5																	74021852		2163	4289	6452	SO:0001583	missense	84340	exon18			TACTCAAACTCAA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1826T>A	5.37:g.74021852A>T	ENSP00000296805:p.Phe609Tyr	44.0	0.0	0		66.0	6.0	0.0909091	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	63	0.028846153846153848	54	0.10975609756097561	4	0.011049723756906077	1	0.0017482517482517483	4	0.005277044854881266	-	1.721	-0.496544	0.04291	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.29142	1.58;1.58;1.58	5.7	3.31	0.37934	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	.	.	.	.	T	0.00271	0.0008	N	0.19112	0.55	0.21984	N	0.999437	.;P	0.46457	.;0.878	.;B	0.33690	.;0.168	T	0.07809	-1.0753	9	0.02654	T	1	.	9.8843	0.41253	0.8619:0.0:0.1381:0.0	.	562;609	Q969S9-2;Q969S9	.;RRF2M_HUMAN	Y	609;562;609	ENSP00000296805:F609Y;ENSP00000296804:F562Y;ENSP00000427004:F609Y	ENSP00000296805:F609Y	F	-	2	0	GFM2	74057608	0.863000	0.29885	0.002000	0.10522	0.043000	0.13939	3.787000	0.55439	0.442000	0.26555	0.460000	0.39030	TTT	A|0.971;T|0.029	0.029	strong		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
LAMA2	3908	hgsc.bcm.edu	37	6	129636794	129636794	+	Silent	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:129636794A>G	ENST00000421865.2	+	25	3778	c.3729A>G	c.(3727-3729)ggA>ggG	p.G1243G		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1243	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AATTTGAAGGAAAGAAGGTAA	0.348																																					p.G1243G		Atlas-SNP	.											.	LAMA2	481	.	0			c.A3729G						PASS	.						97.0	94.0	95.0					6																	129636794		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon25			TGAAGGAAAGAAG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3729A>G	6.37:g.129636794A>G		78.0	0.0	0		95.0	4.0	0.0421053	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			.	.	none		0.348	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
DHRS12	79758	hgsc.bcm.edu	37	13	52345982	52345982	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:52345982C>T	ENST00000444610.2	-	8	694	c.681G>A	c.(679-681)atG>atA	p.M227I	DHRS12_ENST00000218981.1_Missense_Mutation_p.M178I|DHRS12_ENST00000280056.2_Missense_Mutation_p.M178I|DHRS12_ENST00000490949.1_5'UTR	NM_001270424.1	NP_001257353.1	A0PJE2	DHR12_HUMAN	dehydrogenase/reductase (SDR family) member 12	227							oxidoreductase activity (GO:0016491)			cervix(1)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	7		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)		AGCCAGGATGCATGGAAGAAA	0.557																																					p.M227I		Atlas-SNP	.											.	DHRS12	28	.	0			c.G681A						PASS	.						93.0	101.0	99.0					13																	52345982		2203	4300	6503	SO:0001583	missense	79758	exon8			AGGATGCATGGAA	AK023701	CCDS9430.1, CCDS31976.1, CCDS58292.1	13q14.3	2013-10-11			ENSG00000102796	ENSG00000102796		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	25832	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 40C, member 1"""					19027726	Standard	NM_001031719		Approved	FLJ13639, SDR40C1	uc001vfq.4	A0PJE2	OTTHUMG00000016952	ENST00000444610.2:c.681G>A	13.37:g.52345982C>T	ENSP00000411565:p.Met227Ile	125.0	0.0	0		142.0	34.0	0.239437	NM_001270424	Q96GB2|Q9H8H1	Missense_Mutation	SNP	ENST00000444610.2	37	CCDS58292.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.286334	0.59867	.	.	ENSG00000102796	ENST00000444610;ENST00000218981;ENST00000280056	T;T;T	0.17054	2.3;2.3;3.33	4.57	0.634	0.17718	NAD(P)-binding domain (1);	0.046421	0.85682	D	0.000000	T	0.26810	0.0656	L	0.55213	1.73	0.30247	N	0.794416	B;D;D	0.69078	0.34;0.997;0.997	B;D;D	0.66847	0.171;0.947;0.932	T	0.07404	-1.0774	10	0.62326	D	0.03	.	4.3567	0.11181	0.1627:0.541:0.0:0.2963	.	178;178;227	A0PJE2-3;A0PJE2-2;A0PJE2	.;.;DHR12_HUMAN	I	227;178;178	ENSP00000411565:M227I;ENSP00000218981:M178I;ENSP00000280056:M178I	ENSP00000218981:M178I	M	-	3	0	DHRS12	51243983	1.000000	0.71417	0.007000	0.13788	0.080000	0.17528	1.538000	0.36094	0.539000	0.28788	-0.262000	0.10625	ATG	.	.	none		0.557	DHRS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045036.3	NM_024705	
TMTC4	84899	hgsc.bcm.edu	37	13	101287349	101287349	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:101287349G>A	ENST00000376234.3	-	10	1435	c.1246C>T	c.(1246-1248)Ctc>Ttc	p.L416F	TMTC4_ENST00000342624.5_Missense_Mutation_p.L435F|TMTC4_ENST00000328767.5_Missense_Mutation_p.L305F|TMTC4_ENST00000462211.1_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	416						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACGCTGGGGAGGTAGAGGACA	0.537																																					p.L435F		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1303T						PASS	.						77.0	71.0	73.0					13																	101287349		2203	4300	6503	SO:0001583	missense	84899	exon11			TGGGGAGGTAGAG		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1246C>T	13.37:g.101287349G>A	ENSP00000365408:p.Leu416Phe	117.0	0.0	0		108.0	37.0	0.342593	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015661	0.54468	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.69175	-0.38;-0.38;-0.38	5.5	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.81403	0.4815	M	0.83692	2.655	0.58432	D	0.999998	P;D;D;D	0.89917	0.908;0.999;0.999;1.0	P;D;D;D	0.78314	0.692;0.991;0.98;0.991	D	0.83482	0.0065	10	0.72032	D	0.01	.	11.3755	0.49726	0.1445:0.0:0.8555:0.0	.	305;416;416;435	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	F	416;435;305	ENSP00000365408:L416F;ENSP00000343871:L435F;ENSP00000365409:L305F	ENSP00000365409:L305F	L	-	1	0	TMTC4	100085350	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	3.246000	0.51414	1.332000	0.45431	-0.251000	0.11542	CTC	.	.	none		0.537	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
DROSHA	29102	hgsc.bcm.edu	37	5	31521306	31521306	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:31521306T>C	ENST00000511367.2	-	5	1115	c.871A>G	c.(871-873)Aga>Gga	p.R291G	DROSHA_ENST00000442743.1_Missense_Mutation_p.R291G|DROSHA_ENST00000513349.1_Missense_Mutation_p.R291G|DROSHA_ENST00000344624.3_Missense_Mutation_p.R291G	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	291	Arg-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TGCCTGTGTCTCTCCCGTTCT	0.398																																					p.R291G		Atlas-SNP	.											.	DROSHA	130	.	0			c.A871G						PASS	.						256.0	236.0	242.0					5																	31521306		1899	4117	6016	SO:0001583	missense	29102	exon5			TGTGTCTCTCCCG	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.871A>G	5.37:g.31521306T>C	ENSP00000425979:p.Arg291Gly	144.0	0.0	0		107.0	5.0	0.046729	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.179709	0.57800	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000382188	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.95	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.55513	0.1925	N	0.24115	0.695	0.58432	D	0.999999	D;D	0.54601	0.967;0.967	D;D	0.63597	0.916;0.916	T	0.56117	-0.8032	10	0.44086	T	0.13	-20.9464	12.9148	0.58200	0.0:0.0:0.1352:0.8648	.	291;291	E7EMP9;Q9NRR4	.;RNC_HUMAN	G	291;291;291;291;284	ENSP00000425979:R291G;ENSP00000339845:R291G;ENSP00000409335:R291G;ENSP00000424161:R291G	ENSP00000339845:R291G	R	-	1	2	DROSHA	31557063	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.481000	0.53179	2.279000	0.76181	0.533000	0.62120	AGA	.	.	none		0.398	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
SERPINB10	5273	hgsc.bcm.edu	37	18	61600364	61600364	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr18:61600364T>G	ENST00000238508.3	+	7	775	c.716T>G	c.(715-717)cTt>cGt	p.L239R		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	239					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				GCAGTGGGCCTTCAACTCTAC	0.383																																					p.L239R		Atlas-SNP	.											.	SERPINB10	53	.	0			c.T716G						PASS	.						118.0	130.0	126.0					18																	61600364		2203	4300	6503	SO:0001583	missense	5273	exon6			TGGGCCTTCAACT	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.716T>G	18.37:g.61600364T>G	ENSP00000238508:p.Leu239Arg	81.0	0.0	0		61.0	12.0	0.196721	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.116431	0.56505	.	.	ENSG00000242550	ENST00000238508	D	0.86694	-2.16	5.95	5.95	0.96441	Serpin domain (3);	0.219993	0.40385	N	0.001119	D	0.96175	0.8753	H	0.98646	4.29	0.47153	D	0.999333	D	0.89917	1.0	D	0.69824	0.966	D	0.97755	1.0217	10	0.87932	D	0	.	15.61	0.76707	0.0:0.0:0.0:1.0	.	239	P48595	SPB10_HUMAN	R	239	ENSP00000238508:L239R	ENSP00000238508:L239R	L	+	2	0	SERPINB10	59751344	0.981000	0.34729	0.564000	0.28396	0.115000	0.19883	5.005000	0.63972	2.282000	0.76494	0.533000	0.62120	CTT	.	.	none		0.383	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
PFDN2	5202	hgsc.bcm.edu	37	1	161071920	161071920	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:161071920T>G	ENST00000368010.3	-	3	290	c.206A>C	c.(205-207)aAg>aCg	p.K69T	PFDN2_ENST00000468311.1_Intron	NM_012394.3	NP_036526.2	Q9UHV9	PFD2_HUMAN	prefoldin subunit 2	69					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	unfolded protein binding (GO:0051082)			lung(1)|skin(1)	2	all_cancers(52;1.84e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			GCGGTAGCACTTACGAGTTTC	0.517																																					p.K69T		Atlas-SNP	.											.	PFDN2	10	.	0			c.A206C						PASS	.						134.0	116.0	122.0					1																	161071920		2203	4300	6503	SO:0001583	missense	5202	exon3			TAGCACTTACGAG	AF165883	CCDS1217.1	1q23.3	2008-02-05	2006-02-24		ENSG00000143256	ENSG00000143256			8867	protein-coding gene	gene with protein product		613466	"""prefoldin 2"""			10051400	Standard	NM_012394		Approved		uc001fxu.3	Q9UHV9	OTTHUMG00000031481	ENST00000368010.3:c.206A>C	1.37:g.161071920T>G	ENSP00000356989:p.Lys69Thr	144.0	0.0	0		123.0	9.0	0.0731707	NM_012394	Q9P0P7|Q9UN05	Missense_Mutation	SNP	ENST00000368010.3	37	CCDS1217.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.994360	0.74703	.	.	ENSG00000143256	ENST00000368010	T	0.48522	0.81	5.15	2.82	0.32997	Prefoldin beta-like (1);Prefoldin (1);	0.088219	0.85682	D	0.000000	T	0.53190	0.1781	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.56571	-0.7957	10	0.59425	D	0.04	-14.807	8.0692	0.30678	0.0:0.1676:0.0:0.8324	.	69	Q9UHV9	PFD2_HUMAN	T	69	ENSP00000356989:K69T	ENSP00000356989:K69T	K	-	2	0	PFDN2	159338544	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.467000	0.35321	0.423000	0.26033	0.459000	0.35465	AAG	.	.	none		0.517	PFDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077100.1	NM_012394	
ATP10A	57194	hgsc.bcm.edu	37	15	25969147	25969147	+	Missense_Mutation	SNP	C	C	T	rs144743073	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:25969147C>T	ENST00000356865.6	-	6	1112	c.1001G>A	c.(1000-1002)cGg>cAg	p.R334Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	334					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CTCTTGATACCGCCATATCCA	0.358													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19965	0.0		0.0	False		,,,				2504	0.0				p.R334Q		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1001A						PASS	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	136.0	136.0	136.0		1001	2.4	0.0	15	dbSNP_134	136	0,8600		0,0,4300	no	missense	ATP10A	NM_024490.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	334/1500	25969147	1,13005	2203	4300	6503	SO:0001583	missense	57194	exon6			TGATACCGCCATA	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1001G>A	15.37:g.25969147C>T	ENSP00000349325:p.Arg334Gln	124.0	0.0	0		83.0	31.0	0.373494	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	4.862	0.160142	0.09287	2.27E-4	0.0	ENSG00000206190	ENST00000356865	T	0.45668	0.89	5.3	2.36	0.29203	ATPase, P-type, ATPase-associated domain (1);	0.118743	0.56097	D	0.000021	T	0.20129	0.0484	N	0.12637	0.245	0.35235	D	0.777281	B	0.21520	0.057	B	0.18561	0.022	T	0.14755	-1.0461	10	0.18710	T	0.47	-27.5818	7.1544	0.25628	0.0:0.5527:0.0:0.4473	.	334	O60312	AT10A_HUMAN	Q	334	ENSP00000349325:R334Q	ENSP00000349325:R334Q	R	-	2	0	ATP10A	23520240	1.000000	0.71417	0.035000	0.18076	0.036000	0.12997	4.520000	0.60524	0.748000	0.32831	-0.251000	0.11542	CGG	C|1.000;T|0.000	0.000	weak		0.358	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
CFH	3075	hgsc.bcm.edu	37	1	196648799	196648799	+	Silent	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:196648799T>C	ENST00000359637.2	+	5	536	c.474T>C	c.(472-474)tcT>tcC	p.S158S	CFH_ENST00000367429.4_Silent_p.S222S|CFH_ENST00000439155.2_Silent_p.S222S			P08603	CFAH_HUMAN	complement factor H	222	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						CTCCTATATCTCAGAAGATTA	0.308																																					p.S222S		Atlas-SNP	.											.	CFH	251	.	0			c.T666C						PASS	.						54.0	58.0	57.0					1																	196648799		2203	4297	6500	SO:0001819	synonymous_variant	3075	exon6			TATATCTCAGAAG	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.474T>C	1.37:g.196648799T>C		118.0	0.0	0		88.0	29.0	0.329545	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000359637.2	37																																																																																				.	.	none		0.308	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186	
ZAP70	7535	hgsc.bcm.edu	37	2	98340878	98340878	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:98340878G>A	ENST00000264972.5	+	3	594	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	ZAP70_ENST00000442208.1_5'Flank	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	127	Interdomain A.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						GCGTGACTACGTGCGCCAGAC	0.706																																					p.V127M		Atlas-SNP	.											.	ZAP70	77	.	0			c.G379A						PASS	.						5.0	6.0	6.0					2																	98340878		2020	4011	6031	SO:0001583	missense	7535	exon3			GACTACGTGCGCC	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.379G>A	2.37:g.98340878G>A	ENSP00000264972:p.Val127Met	11.0	0.0	0		30.0	16.0	0.533333	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	37	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687188	0.88639	.	.	ENSG00000115085	ENST00000264972	T	0.26660	1.72	4.9	4.9	0.64082	Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain (1);	0.308316	0.22701	N	0.056684	T	0.43765	0.1262	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.58928	0.848;0.836	T	0.38178	-0.9673	10	0.72032	D	0.01	.	15.9444	0.79782	0.0:0.0:1.0:0.0	.	127;127	B4E0E2;P43403	.;ZAP70_HUMAN	M	127	ENSP00000264972:V127M	ENSP00000264972:V127M	V	+	1	0	ZAP70	97707310	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.289000	0.72696	2.449000	0.82847	0.467000	0.42956	GTG	.	.	none		0.706	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1		
CPLX3	594855	hgsc.bcm.edu	37	15	75119053	75119053	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:75119053C>A	ENST00000395018.4	+	1	166	c.9C>A	c.(7-9)ttC>ttA	p.F3L	RP11-414J4.2_ENST00000564823.1_RNA	NM_001030005.2	NP_001025176.1	Q8WVH0	CPLX3_HUMAN	complexin 3	3					insulin secretion (GO:0030073)|regulation of neurotransmitter secretion (GO:0046928)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)	neurotransmitter transporter activity (GO:0005326)			large_intestine(2)|lung(2)	4						CCATGGCGTTCATGGTGAAGA	0.672																																					p.F3L		Atlas-SNP	.											.	CPLX3	12	.	0			c.C9A						PASS	.						36.0	40.0	39.0					15																	75119053		2197	4295	6492	SO:0001583	missense	594855	exon1			GGCGTTCATGGTG	BC018026	CCDS32294.1	15q24.1	2005-08-09			ENSG00000213578	ENSG00000213578			27652	protein-coding gene	gene with protein product		609585				15911881	Standard	NM_001030005		Approved	CPX-III	uc002ayu.1	Q8WVH0	OTTHUMG00000142816	ENST00000395018.4:c.9C>A	15.37:g.75119053C>A	ENSP00000378464:p.Phe3Leu	26.0	0.0	0		55.0	45.0	0.818182	NM_001030005	D3DW66|Q8TEM6|Q9H818	Missense_Mutation	SNP	ENST00000395018.4	37	CCDS32294.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.225855	0.79576	.	.	ENSG00000213578	ENST00000395018	.	.	.	4.3	3.38	0.38709	.	0.000000	0.64402	U	0.000001	T	0.75057	0.3798	M	0.71036	2.16	0.41174	D	0.986185	D	0.57257	0.979	D	0.71414	0.973	T	0.75227	-0.3392	9	0.66056	D	0.02	-10.3249	10.8632	0.46839	0.0:0.8306:0.0:0.1694	.	3	Q8WVH0	CPLX3_HUMAN	L	3	.	ENSP00000378464:F3L	F	+	3	2	CPLX3	72906106	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.306000	0.33505	0.461000	0.27071	-1.164000	0.01763	TTC	.	.	none		0.672	CPLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286402.2	NM_001030005	
TSPYL2	64061	hgsc.bcm.edu	37	X	53112146	53112146	+	Missense_Mutation	SNP	C	C	T	rs144264921	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:53112146C>T	ENST00000375442.4	+	1	598	c.466C>T	c.(466-468)Ccc>Tcc	p.P156S		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	156					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						GGGGTGGGCGCCCCAGAGGTT	0.587													C|||	3	0.000794702	0.0015	0.0	3775	,	,		10753	0.0		0.001	False		,,,				2504	0.0				p.P156S		Atlas-SNP	.											.	TSPYL2	53	.	0			c.C466T						PASS	.		SER/PRO	6,3828		0,6,0,1626,570	25.0	24.0	24.0		466	-0.7	0.4	X	dbSNP_134	24	3,6724		0,1,2,2427,1869	yes	missense	TSPYL2	NM_022117.3	74	0,7,2,4053,2439	TT,TC,T,CC,C		0.0446,0.1565,0.0852	benign	156/694	53112146	9,10552	2202	4299	6501	SO:0001583	missense	64061	exon1			TGGGCGCCCCAGA	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.466C>T	X.37:g.53112146C>T	ENSP00000364591:p.Pro156Ser	66.0	0.0	0		85.0	4.0	0.0470588	NM_022117	O94799|Q96DG7|Q9BZW6	Missense_Mutation	SNP	ENST00000375442.4	37	CCDS14350.1	.	.	.	.	.	.	.	.	.	.	C	1.215	-0.628646	0.03610	0.001565	4.46E-4	ENSG00000184205	ENST00000375442	T	0.19532	2.14	3.48	-0.742	0.11108	.	1.020780	0.07854	N	0.965098	T	0.07234	0.0183	N	0.02916	-0.46	0.20821	N	0.999844	B;B	0.14438	0.01;0.01	B;B	0.08055	0.003;0.003	T	0.40251	-0.9573	10	0.09590	T	0.72	-10.5495	6.56	0.22481	0.0:0.5958:0.0:0.4042	.	156;156	Q9H2G4;A8K8U7	TSYL2_HUMAN;.	S	156	ENSP00000364591:P156S	ENSP00000364591:P156S	P	+	1	0	TSPYL2	53128871	0.006000	0.16342	0.447000	0.26932	0.809000	0.45718	-0.888000	0.04148	-0.236000	0.09753	0.519000	0.50382	CCC	C|0.998;T|0.002	0.002	strong		0.587	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117	
BTG2	7832	hgsc.bcm.edu	37	1	203276256	203276256	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:203276256C>T	ENST00000290551.4	+	2	238	c.167C>T	c.(166-168)cCc>cTc	p.P56L	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	56					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CACTGGTTTCCCGAAAAGCCG	0.592																																					p.P56L		Atlas-SNP	.											.	BTG2	16	.	0			c.C167T						PASS	.						41.0	43.0	43.0					1																	203276256		2203	4300	6503	SO:0001583	missense	7832	exon2			GGTTTCCCGAAAA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.167C>T	1.37:g.203276256C>T	ENSP00000290551:p.Pro56Leu	84.0	0.0	0		106.0	40.0	0.377358	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836232	0.71373	.	.	ENSG00000159388	ENST00000290551	T	0.31510	1.49	4.53	2.64	0.31445	Anti-proliferative protein (4);	0.073067	0.53938	D	0.000041	T	0.58047	0.2095	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61004	-0.7150	10	0.87932	D	0	-46.4298	8.7979	0.34890	0.0:0.7636:0.1512:0.0852	.	56	P78543	BTG2_HUMAN	L	56	ENSP00000290551:P56L	ENSP00000290551:P56L	P	+	2	0	BTG2	201542879	1.000000	0.71417	0.819000	0.32651	0.843000	0.47879	5.614000	0.67695	0.527000	0.28560	0.313000	0.20887	CCC	.	.	none		0.592	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
CRMP1	1400	hgsc.bcm.edu	37	4	5868477	5868477	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:5868477G>A	ENST00000397890.2	-	2	260	c.46C>T	c.(46-48)Cga>Tga	p.R16*	CRMP1_ENST00000324989.7_Nonsense_Mutation_p.R130*|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Nonsense_Mutation_p.R14*	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	16					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		ATGAGGAGTCGGTCACTCTGC	0.383																																					p.R130X		Atlas-SNP	.											CRMP1,NS,carcinoma,+1,1	CRMP1	118	1	0			c.C388T						scavenged	.						102.0	88.0	93.0					4																	5868477		2203	4300	6503	SO:0001587	stop_gained	1400	exon2			GGAGTCGGTCACT	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.46C>T	4.37:g.5868477G>A	ENSP00000380987:p.Arg16*	100.0	1.0	0.01		83.0	24.0	0.289157	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Nonsense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	G	41	8.922703	0.99004	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	.	.	.	4.26	4.26	0.50523	.	0.237948	0.33772	N	0.004567	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.8303	15.8244	0.78686	0.0:0.0:1.0:0.0	.	.	.	.	X	130;16;16;14	.	ENSP00000321606:R130X	R	-	1	2	CRMP1	5919378	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.469000	0.60169	2.194000	0.70268	0.563000	0.77884	CGA	.	.	none		0.383	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
CIT	11113	hgsc.bcm.edu	37	12	120295436	120295436	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:120295436A>G	ENST00000261833.7	-	4	357	c.305T>C	c.(304-306)cTt>cCt	p.L102P	CIT_ENST00000392521.2_Missense_Mutation_p.L102P	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	102	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		ACAACCTACAAGACTTCTGAC	0.473																																					p.L102P		Atlas-SNP	.											.	CIT	535	.	0			c.T305C						PASS	.						190.0	190.0	190.0					12																	120295436		2203	4300	6503	SO:0001583	missense	11113	exon4			CCTACAAGACTTC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.305T>C	12.37:g.120295436A>G	ENSP00000261833:p.Leu102Pro	104.0	0.0	0		110.0	33.0	0.3	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.231625	0.58777	.	.	ENSG00000122966	ENST00000392521;ENST00000261833;ENST00000536325	T;T;T	0.42513	0.97;0.97;3.04	5.4	5.4	0.78164	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.089941	0.42294	D	0.000735	T	0.38772	0.1053	L	0.44542	1.39	0.80722	D	1	P;B	0.40107	0.703;0.0	B;B	0.37650	0.255;0.014	T	0.39663	-0.9603	10	0.87932	D	0	.	15.7159	0.77667	1.0:0.0:0.0:0.0	.	102;102	Q2M5E1;O14578	.;CTRO_HUMAN	P	102;102;19	ENSP00000376306:L102P;ENSP00000261833:L102P;ENSP00000443199:L19P	ENSP00000261833:L102P	L	-	2	0	CIT	118779819	1.000000	0.71417	0.975000	0.42487	0.992000	0.81027	9.027000	0.93706	2.170000	0.68504	0.482000	0.46254	CTT	.	.	none		0.473	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
HRCT1	646962	hgsc.bcm.edu	37	9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	rs112821450|rs143611048|rs79156963	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:35906583T>A	ENST00000354323.2	+	1	395	c.299T>A	c.(298-300)cTc>cAc	p.L100H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	100	His-rich.					integral component of membrane (GO:0016021)		p.L100H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						cctcaccacctccaccaccac	0.667																																					p.L100H		Atlas-SNP	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	1	Substitution - Missense(1)	NS(1)	c.T299A						scavenged	.						13.0	10.0	11.0					9																	35906583		1961	3863	5824	SO:0001583	missense	646962	exon1			ACCACCTCCACCA		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.299T>A	9.37:g.35906583T>A	ENSP00000346283:p.Leu100His	25.0	1.0	0.04		31.0	3.0	0.0967742	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	T	9.866	1.197686	0.22037	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.43	-0.386	0.12466	.	.	.	.	.	T	0.09730	0.0239	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25117	-1.0141	8	0.87932	D	0	-5.7925	0.5802	0.00711	0.4571:0.1878:0.1238:0.2312	.	100	Q6UXD1	HRCT1_HUMAN	H	100	.	ENSP00000346283:L100H	L	+	2	0	HRCT1	35896583	0.000000	0.05858	0.107000	0.21349	0.466000	0.32739	-0.309000	0.08145	-0.078000	0.12730	-0.376000	0.06991	CTC	T|0.500;A|0.500	0.500	weak		0.667	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
CDRT1	374286	hgsc.bcm.edu	37	17	15519066	15519066	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:15519066T>G	ENST00000395906.3	-	2	562	c.563A>C	c.(562-564)aAg>aCg	p.K188T	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.K498T	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	188										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GGTCGCAGACTTGGAGCTGTG	0.483																																					p.K188T		Atlas-SNP	.											.	CDRT1	83	.	0			c.A563C						PASS	.						55.0	56.0	56.0					17																	15519066		2200	4278	6478	SO:0001583	missense	374286	exon2			GCAGACTTGGAGC	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.563A>C	17.37:g.15519066T>G	ENSP00000379242:p.Lys188Thr	208.0	0.0	0		231.0	18.0	0.0779221	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.808|4.808	0.150194|0.150194	0.09185|0.09185	.|.	.|.	ENSG00000251537|ENSG00000251537	ENST00000261644;ENST00000395906|ENST00000455584	T|.	0.23950|.	1.88|.	3.68|3.68	-5.28|-5.28	0.02755|0.02755	.|.	0.556354|.	0.17795|.	N|.	0.161741|.	T|T	0.12008|0.12008	0.0292|0.0292	N|N	0.03115|0.03115	-0.41|-0.41	0.09310|0.09310	N|N	1|1	B;B|.	0.12013|.	0.005;0.002|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.30679|0.30679	-0.9970|-0.9970	10|5	0.27082|.	T|.	0.32|.	.|.	7.1977|7.1977	0.25862|0.25862	0.2497:0.0:0.5367:0.2136|0.2497:0.0:0.5367:0.2136	.|.	188;512|.	O95170;Q59EB2|.	CDRT1_HUMAN;.|.	T|R	188|513	ENSP00000379242:K188T|.	ENSP00000261644:K188T|.	K|S	-|-	2|1	0|0	RP11-385D13.1|RP11-385D13.1	15459791|15459791	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	0.192000|0.192000	0.17096|0.17096	-1.167000|-1.167000	0.02779|0.02779	-0.501000|-0.501000	0.04562|0.04562	AAG|AGT	.	.	none		0.483	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
TLN2	83660	hgsc.bcm.edu	37	15	63017221	63017221	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:63017221C>T	ENST00000561311.1	+	26	3403	c.3173C>T	c.(3172-3174)aCg>aTg	p.T1058M	TLN2_ENST00000306829.6_Missense_Mutation_p.T1058M			Q9Y4G6	TLN2_HUMAN	talin 2	1058	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GCTCTGAATACGGTGCAGACG	0.527																																					p.T1058M		Atlas-SNP	.											.	TLN2	253	.	0			c.C3173T						PASS	.						72.0	68.0	69.0					15																	63017221		2203	4300	6503	SO:0001583	missense	83660	exon24			TGAATACGGTGCA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.3173C>T	15.37:g.63017221C>T	ENSP00000453508:p.Thr1058Met	36.0	0.0	0		37.0	31.0	0.837838	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501273	0.26861	.	.	ENSG00000171914	ENST00000306829	T	0.67865	-0.29	5.54	5.54	0.83059	.	0.136037	0.64402	D	0.000002	T	0.54208	0.1844	N	0.17082	0.46	0.39663	D	0.970632	B	0.22746	0.074	B	0.14578	0.011	T	0.50285	-0.8846	10	0.40728	T	0.16	-16.3734	19.8379	0.96666	0.0:1.0:0.0:0.0	.	1058	Q9Y4G6	TLN2_HUMAN	M	1058	ENSP00000303476:T1058M	ENSP00000303476:T1058M	T	+	2	0	TLN2	60804513	0.998000	0.40836	0.927000	0.36925	0.015000	0.08874	4.850000	0.62889	2.765000	0.95021	0.655000	0.94253	ACG	.	.	none		0.527	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230412	23230412	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230412G>C	ENST00000526893.1	+	1	453	c.179G>C	c.(178-180)cGa>cCa	p.R60P	IGLL5_ENST00000531372.1_Missense_Mutation_p.R60P|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.R60P	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	60						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GGAAGCAGCCGATCCAGCCTG	0.652																																					p.R60P		Atlas-SNP	.											.	IGLL5	26	.	0			c.G179C						PASS	.																																			SO:0001583	missense	100423062	exon1			GCAGCCGATCCAG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.179G>C	22.37:g.23230412G>C	ENSP00000431254:p.Arg60Pro	94.0	0.0	0		148.0	64.0	0.432432	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919402	0.33908	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00622	6.17;6.16	3.92	-7.84	0.01196	.	.	.	.	.	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47341	-0.9125	9	0.62326	D	0.03	.	2.9625	0.05897	0.0917:0.3589:0.1664:0.3831	.	60	B9A064	IGLL5_HUMAN	P	60	ENSP00000436353:R60P;ENSP00000431254:R60P	ENSP00000431254:R60P	R	+	2	0	IGLL5	21560412	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.219000	0.00553	-1.485000	0.01854	0.643000	0.83706	CGA	.	.	none		0.652	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
PLEKHM2	23207	hgsc.bcm.edu	37	1	16051840	16051840	+	Silent	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:16051840T>C	ENST00000375799.3	+	8	968	c.741T>C	c.(739-741)ggT>ggC	p.G247G	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Silent_p.G227G	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	247	Interaction with KIF5B.				Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CGGTCAGTGGTCCCCGCTCCA	0.662																																					p.G247G		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.T741C						PASS	.						23.0	31.0	28.0					1																	16051840		1874	3784	5658	SO:0001819	synonymous_variant	23207	exon8			CAGTGGTCCCCGC	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.741T>C	1.37:g.16051840T>C		85.0	0.0	0		95.0	4.0	0.0421053	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			.	.	none		0.662	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
MKNK2	2872	hgsc.bcm.edu	37	19	2041911	2041911	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:2041911G>A	ENST00000591601.1	-	10	908	c.873C>T	c.(871-873)ggC>ggT	p.G291G	MKNK2_ENST00000591142.1_Silent_p.G35G|MKNK2_ENST00000591588.1_Silent_p.G35G|MKNK2_ENST00000250896.3_Silent_p.G291G|MKNK2_ENST00000309340.7_Silent_p.G291G|MKNK2_ENST00000588014.1_Silent_p.G35G|MKNK2_ENST00000541165.1_Silent_p.G160G			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	291	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGCGGGTAGCCGCTGAGTA	0.697																																					p.G291G		Atlas-SNP	.											.	MKNK2	56	.	0			c.C873T						PASS	.						24.0	20.0	22.0					19																	2041911		2102	4136	6238	SO:0001819	synonymous_variant	2872	exon11			CGGGTAGCCGCTG	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.873C>T	19.37:g.2041911G>A		35.0	0.0	0		38.0	5.0	0.131579	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Silent	SNP	ENST00000591601.1	37	CCDS12080.1																																																																																			.	.	none		0.697	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054	
NOSIP	51070	hgsc.bcm.edu	37	19	50063941	50063941	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:50063941C>T	ENST00000596358.1	-	2	66	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	NOSIP_ENST00000339093.3_Missense_Mutation_p.R3Q|NOSIP_ENST00000391853.3_Missense_Mutation_p.R3Q	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	3					negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		CTTGCCATGCCGCGTCATCCT	0.632																																					p.R3Q		Atlas-SNP	.											.	NOSIP	28	.	0			c.G8A						PASS	.						85.0	60.0	68.0					19																	50063941		2203	4299	6502	SO:0001583	missense	51070	exon3			CCATGCCGCGTCA	AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.8G>A	19.37:g.50063941C>T	ENSP00000470034:p.Arg3Gln	45.0	0.0	0		59.0	18.0	0.305085	NM_015953	Q96FD2	Missense_Mutation	SNP	ENST00000596358.1	37	CCDS12772.1	.	.	.	.	.	.	.	.	.	.	C	34	5.315578	0.95655	.	.	ENSG00000142546	ENST00000339093;ENST00000391853	T;T	0.78595	-1.19;-1.19	5.41	2.1	0.27182	.	0.000000	0.85682	D	0.000000	D	0.87006	0.6070	M	0.86805	2.84	0.45718	D	0.998623	D	0.89917	1.0	D	0.85130	0.997	D	0.85312	0.1079	10	0.87932	D	0	-23.987	7.983	0.30194	0.0:0.7195:0.1321:0.1484	.	3	Q9Y314	NOSIP_HUMAN	Q	3	ENSP00000343497:R3Q;ENSP00000375726:R3Q	ENSP00000343497:R3Q	R	-	2	0	NOSIP	54755753	1.000000	0.71417	0.003000	0.11579	0.601000	0.36947	6.534000	0.73833	0.268000	0.21939	0.655000	0.94253	CGG	.	.	none		0.632	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1		
TPM3P9	147804	hgsc.bcm.edu	37	19	53950528	53950528	+	RNA	SNP	T	T	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:53950528T>G	ENST00000424846.3	+	0	2920				ZNF761_ENST00000454407.1_RNA	NR_003148.3				tropomyosin 3 pseudogene 9																		AGGGATGGCTTTTTCTCAGGT	0.443																																					p.F3V		Atlas-SNP	.											.	ZNF761	104	.	0			c.T7G						PASS	.						131.0	125.0	127.0					19																	53950528		876	1991	2867			388561	exon4			ATGGCTTTTTCTC			19q13.42	2012-07-04			ENSG00000241015	ENSG00000241015			44142	pseudogene	pseudogene							Standard	NR_003148		Approved				OTTHUMG00000157312		19.37:g.53950528T>G		21.0	0.0	0		34.0	12.0	0.352941	NM_001008401		Missense_Mutation	SNP	ENST00000424846.3	37																																																																																				.	.	none		0.443	TPM3P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347070.1	NR_003148	
UHRF2	115426	hgsc.bcm.edu	37	9	6413558	6413558	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:6413558C>G	ENST00000276893.5	+	1	236	c.68C>G	c.(67-69)gCc>gGc	p.A23G	UHRF2_ENST00000381373.3_Missense_Mutation_p.A23G|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	23	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		TCTCGCAAAGCCACGATTGAG	0.632																																					p.A23G		Atlas-SNP	.											.	UHRF2	50	.	0			c.C68G						PASS	.						52.0	52.0	52.0					9																	6413558		2203	4300	6503	SO:0001583	missense	115426	exon1			GCAAAGCCACGAT	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.68C>G	9.37:g.6413558C>G	ENSP00000276893:p.Ala23Gly	82.0	0.0	0		108.0	28.0	0.259259	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045016	0.75846	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.73575	-0.76;-0.76	4.83	3.0	0.34707	Ubiquitin supergroup (1);Ubiquitin (2);	0.198751	0.42964	D	0.000626	T	0.67683	0.2919	L	0.31476	0.935	0.36395	D	0.86274	B	0.32893	0.389	B	0.41894	0.369	T	0.72520	-0.4268	10	0.87932	D	0	-7.1406	10.6553	0.45671	0.0:0.8436:0.0:0.1564	.	23	Q96PU4	UHRF2_HUMAN	G	23	ENSP00000276893:A23G;ENSP00000370778:A23G	ENSP00000276893:A23G	A	+	2	0	UHRF2	6403558	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.968000	0.76086	0.645000	0.30675	-0.258000	0.10820	GCC	.	.	none		0.632	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
PPP1R36	145376	hgsc.bcm.edu	37	14	65053990	65053990	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:65053990G>A	ENST00000298705.1	+	10	886	c.790G>A	c.(790-792)Ggg>Agg	p.G264R	RP11-973N13.3_ENST00000556634.1_RNA|RP11-973N13.3_ENST00000554454.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	264					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AGAAGAAGTAGGGAGACTCTT	0.413																																					p.G264R		Atlas-SNP	.											.	.	.	.	0			c.G790A						PASS	.						153.0	144.0	147.0					14																	65053990		2203	4300	6503	SO:0001583	missense	145376	exon10			GAAGTAGGGAGAC		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.790G>A	14.37:g.65053990G>A	ENSP00000298705:p.Gly264Arg	197.0	0.0	0		154.0	72.0	0.467532	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.356036	0.82243	.	.	ENSG00000165807	ENST00000298705	T	0.30981	1.51	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000005	T	0.57359	0.2048	M	0.79475	2.455	0.43708	D	0.996177	D	0.89917	1.0	D	0.97110	1.0	T	0.61083	-0.7134	10	0.87932	D	0	-21.7724	15.0284	0.71687	0.0:0.0:1.0:0.0	.	264	Q96LQ0	PPR36_HUMAN	R	264	ENSP00000298705:G264R	ENSP00000298705:G264R	G	+	1	0	C14orf50	64123743	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.068000	0.64364	2.596000	0.87737	0.655000	0.94253	GGG	.	.	none		0.413	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
SLITRK3	22865	hgsc.bcm.edu	37	3	164907346	164907346	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:164907346G>T	ENST00000475390.1	-	2	1716	c.1273C>A	c.(1273-1275)Cgt>Agt	p.R425S	SLITRK3_ENST00000241274.3_Missense_Mutation_p.R425S			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	425					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AAATCAGAACGGTATATTTTC	0.398										HNSCC(40;0.11)																											p.R425S		Atlas-SNP	.											SLITRK3,NS,carcinoma,+1,1	SLITRK3	263	1	0			c.C1273A						scavenged	.						54.0	56.0	55.0					3																	164907346		2203	4300	6503	SO:0001583	missense	22865	exon2			CAGAACGGTATAT	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1273C>A	3.37:g.164907346G>T	ENSP00000420091:p.Arg425Ser	65.0	0.0	0		49.0	3.0	0.0612245	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429477	0.43122	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.53206	0.63;0.63	5.58	5.58	0.84498	.	0.000000	0.38436	N	0.001696	T	0.42517	0.1206	L	0.44542	1.39	0.51012	D	0.999905	P	0.48998	0.918	P	0.44477	0.451	T	0.10660	-1.0620	10	0.17369	T	0.5	-15.343	14.2462	0.65990	0.0:0.0:0.851:0.149	.	425	O94933	SLIK3_HUMAN	S	425	ENSP00000420091:R425S;ENSP00000241274:R425S	ENSP00000241274:R425S	R	-	1	0	SLITRK3	166390040	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.906000	0.69900	2.906000	0.99361	0.655000	0.94253	CGT	.	.	none		0.398	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
ADAMTSL5	339366	hgsc.bcm.edu	37	19	1510692	1510692	+	Missense_Mutation	SNP	C	C	T	rs550092054		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:1510692C>T	ENST00000413997.2	-	3	166	c.167G>A	c.(166-168)cGc>cAc	p.R56H	ADAMTSL5_ENST00000330475.4_Missense_Mutation_p.R46H|ADAMTSL5_ENST00000590562.1_5'UTR|CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000395467.2_5'UTR			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	56	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGGAGCAGCGGGTCCAGGA	0.741																																					p.R46H		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.G137A						PASS	.						4.0	4.0	4.0					19																	1510692		1835	3619	5454	SO:0001583	missense	339366	exon3			GAGCAGCGGGTCC	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain containing 6"""	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.167G>A	19.37:g.1510692C>T	ENSP00000399364:p.Arg56His	27.0	0.0	0		43.0	16.0	0.372093	NM_213604	B4DXK7|Q8IW95	Missense_Mutation	SNP	ENST00000413997.2	37		.	.	.	.	.	.	.	.	.	.	C	16.83	3.230248	0.58777	.	.	ENSG00000185761	ENST00000413997;ENST00000330475	T;T	0.53206	0.63;0.63	3.43	1.08	0.20341	.	0.329393	0.27206	N	0.020425	T	0.30916	0.0780	N	0.11698	0.16	0.80722	D	1	D;D	0.63046	0.992;0.992	P;P	0.51918	0.684;0.594	T	0.14980	-1.0453	10	0.44086	T	0.13	.	2.1487	0.03794	0.1977:0.4922:0.1932:0.1169	.	56;46	B4DXK7;Q6ZMM2	.;ATL5_HUMAN	H	56;46	ENSP00000399364:R56H;ENSP00000327608:R46H	ENSP00000327608:R46H	R	-	2	0	ADAMTSL5	1461692	0.015000	0.18098	0.987000	0.45799	0.871000	0.50021	0.129000	0.15830	0.129000	0.18514	0.456000	0.33151	CGC	.	.	none		0.741	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056233	26056233	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:26056233C>T	ENST00000343677.2	-	1	466	c.424G>A	c.(424-426)Gct>Act	p.A142T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	142					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						GCGCCGCCAGCCGCCTTCTTG	0.577																																					p.A142T		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G424A						PASS	.						61.0	74.0	69.0					6																	26056233		2197	4295	6492	SO:0001583	missense	3006	exon1			CGCCAGCCGCCTT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.424G>A	6.37:g.26056233C>T	ENSP00000339566:p.Ala142Thr	179.0	0.0	0		152.0	9.0	0.0592105	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	0.704	-0.789557	0.02884	.	.	ENSG00000187837	ENST00000343677	T	0.14022	2.54	5.54	-9.61	0.00550	.	0.479745	0.21639	N	0.071371	T	0.00936	0.0031	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34725	-0.9817	10	0.02654	T	1	-4.9914	14.0678	0.64841	0.2008:0.6751:0.0:0.1241	.	142	P16403	H12_HUMAN	T	142	ENSP00000339566:A142T	ENSP00000339566:A142T	A	-	1	0	HIST1H1C	26164212	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.462000	0.02364	-1.623000	0.01558	-0.238000	0.12139	GCT	.	.	none		0.577	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
ZCCHC12	170261	hgsc.bcm.edu	37	X	117959875	117959875	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:117959875A>G	ENST00000310164.2	+	4	1175	c.668A>G	c.(667-669)gAt>gGt	p.D223G		NM_173798.2	NP_776159.1	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	223					BMP signaling pathway (GO:0030509)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	22						GAGGATTGGGATGATGCTTTT	0.483																																					p.D223G		Atlas-SNP	.											.	ZCCHC12	60	.	0			c.A668G						PASS	.						59.0	52.0	55.0					X																	117959875		2203	4300	6503	SO:0001583	missense	170261	exon4			ATTGGGATGATGC	AK122676	CCDS14574.1	Xq24	2013-10-11			ENSG00000174460	ENSG00000174460		"""Zinc fingers, CCHC domain containing"", ""Paraneoplastic Ma antigens"""	27273	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 7A"""	300701				21739307, 19578717	Standard	NM_173798		Approved	FLJ16123, SIZN, SIZN1, PNMA7A	uc004equ.3	Q6PEW1	OTTHUMG00000022261	ENST00000310164.2:c.668A>G	X.37:g.117959875A>G	ENSP00000308921:p.Asp223Gly	66.0	0.0	0		77.0	4.0	0.0519481	NM_173798	B3KV48|Q6PID5|Q8N1C1	Missense_Mutation	SNP	ENST00000310164.2	37	CCDS14574.1	.	.	.	.	.	.	.	.	.	.	A	7.022	0.558807	0.13436	.	.	ENSG00000174460	ENST00000310164	T	0.34472	1.36	3.0	3.0	0.34707	.	.	.	.	.	T	0.36908	0.0984	M	0.72479	2.2	0.26670	N	0.971746	B	0.33612	0.419	B	0.35413	0.202	T	0.36187	-0.9758	9	0.59425	D	0.04	-9.0207	6.8214	0.23859	1.0:0.0:0.0:0.0	.	223	Q6PEW1	ZCH12_HUMAN	G	223	ENSP00000308921:D223G	ENSP00000308921:D223G	D	+	2	0	ZCCHC12	117843903	1.000000	0.71417	0.968000	0.41197	0.127000	0.20565	3.563000	0.53784	1.412000	0.46977	0.486000	0.48141	GAT	.	.	none		0.483	ZCCHC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058014.1	NM_173798	
COL3A1	1281	hgsc.bcm.edu	37	2	189849577	189849577	+	Silent	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:189849577A>G	ENST00000304636.3	+	2	341	c.171A>G	c.(169-171)tcA>tcG	p.S57S	COL3A1_ENST00000317840.5_Silent_p.S57S	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	57	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TCTGTGACTCAGGATCCGTTC	0.463																																					p.S57S		Atlas-SNP	.											.	COL3A1	292	.	0			c.A171G						PASS	.						168.0	145.0	153.0					2																	189849577		2203	4299	6502	SO:0001819	synonymous_variant	1281	exon2			TGACTCAGGATCC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.171A>G	2.37:g.189849577A>G		124.0	0.0	0		122.0	42.0	0.344262	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																			.	.	none		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32926229	32926229	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:32926229A>T	ENST00000361627.3	+	10	2053	c.1331A>T	c.(1330-1332)aAt>aTt	p.N444I	ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.N255I|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.N444I|ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.N255I|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.N416I	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	444					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CTAGGGAAAAATGGCAGAGAA	0.353																																					p.N444I	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A1331T						PASS	.						36.0	35.0	35.0					15																	32926229		2201	4300	6501	SO:0001583	missense	9824	exon10			GGAAAAATGGCAG	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1331A>T	15.37:g.32926229A>T	ENSP00000355090:p.Asn444Ile	282.0	0.0	0		237.0	48.0	0.202532	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	17.09	3.300482	0.60195	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.10288	2.89	5.51	-3.26	0.05064	.	0.454459	0.22141	N	0.064049	T	0.15478	0.0373	L	0.44542	1.39	0.32060	N	0.595807	P;D	0.57571	0.901;0.98	B;P	0.54312	0.296;0.748	T	0.06844	-1.0804	10	0.87932	D	0	.	13.7577	0.62946	0.3388:0.0:0.6612:0.0	.	444;255	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	I	444;255	ENSP00000355090:N444I	ENSP00000355090:N444I	N	+	2	0	ARHGAP11A	30713521	1.000000	0.71417	0.899000	0.35326	0.825000	0.46686	1.904000	0.39868	-0.528000	0.06366	-0.290000	0.09829	AAT	.	.	none		0.353	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
TLL1	7092	hgsc.bcm.edu	37	4	166913969	166913969	+	Silent	SNP	C	C	T	rs377042841		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:166913969C>T	ENST00000061240.2	+	3	941	c.294C>T	c.(292-294)gaC>gaT	p.D98D	TLL1_ENST00000513213.1_Silent_p.D98D|TLL1_ENST00000507499.1_Silent_p.D98D	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	98					cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GACTTGGAGACCATGCTATGT	0.363																																					p.D98D		Atlas-SNP	.											.	TLL1	194	.	0			c.C294T						PASS	.						131.0	129.0	130.0					4																	166913969		2203	4299	6502	SO:0001819	synonymous_variant	7092	exon3			TGGAGACCATGCT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.294C>T	4.37:g.166913969C>T		91.0	0.0	0		80.0	4.0	0.05	NM_001204760	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																			.	.	alt		0.363	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
ZBED2	79413	hgsc.bcm.edu	37	3	111312927	111312927	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:111312927G>A	ENST00000317012.4	-	2	1130	c.122C>T	c.(121-123)gCt>gTt	p.A41V	CD96_ENST00000283285.5_Intron|CD96_ENST00000438817.2_Intron|CD96_ENST00000352690.4_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	41							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						AGTGGGCATAGCACTCACAAA	0.532																																					p.A41V		Atlas-SNP	.											.	ZBED2	22	.	0			c.C122T						PASS	.						243.0	203.0	217.0					3																	111312927		2203	4300	6503	SO:0001583	missense	79413	exon2			GGCATAGCACTCA	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"""Zinc fingers, BED-type"""	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.122C>T	3.37:g.111312927G>A	ENSP00000321370:p.Ala41Val	154.0	0.0	0		190.0	76.0	0.4	NM_024508	D3DN62	Missense_Mutation	SNP	ENST00000317012.4	37	CCDS2960.2	.	.	.	.	.	.	.	.	.	.	G	4.764	0.142084	0.09083	.	.	ENSG00000177494	ENST00000317012	.	.	.	3.16	2.27	0.28462	.	.	.	.	.	T	0.25005	0.0607	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19844	-1.0293	8	0.22706	T	0.39	.	6.0802	0.19936	0.1484:0.0:0.8516:0.0	.	41	Q9BTP6	ZBED2_HUMAN	V	41	.	ENSP00000321370:A41V	A	-	2	0	ZBED2	112795617	0.000000	0.05858	0.002000	0.10522	0.053000	0.15095	0.323000	0.19593	0.654000	0.30846	0.563000	0.77884	GCT	.	.	none		0.532	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508	
ETV5	2119	hgsc.bcm.edu	37	3	185797673	185797673	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:185797673G>A	ENST00000306376.5	-	7	829	c.583C>T	c.(583-585)Cga>Tga	p.R195*	ETV5_ENST00000537818.1_Nonsense_Mutation_p.R237*|ETV5-AS1_ENST00000453370.1_RNA|ETV5_ENST00000434744.1_Nonsense_Mutation_p.R195*	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	195					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			TGTGGTGGTCGGGGGACCGCA	0.587			T	"""TMPRSS2, SCL45A3"""	Prostate																																p.R195X		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5	106	.	0			c.C583T						PASS	.						120.0	118.0	119.0					3																	185797673		2203	4300	6503	SO:0001587	stop_gained	2119	exon7			GTGGTCGGGGGAC	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"""ets-related molecule"""	601600	"""ets variant gene 5 (ets-related molecule)"""			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.583C>T	3.37:g.185797673G>A	ENSP00000306894:p.Arg195*	145.0	0.0	0		166.0	74.0	0.445783	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Nonsense_Mutation	SNP	ENST00000306376.5	37	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	G	39	7.294772	0.98192	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	.	.	.	5.34	3.39	0.38822	.	0.818906	0.11352	N	0.572821	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	11.3294	0.49467	0.0:0.0:0.6711:0.3289	.	.	.	.	X	195;195;237	.	ENSP00000306894:R195X	R	-	1	2	ETV5	187280367	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	5.489000	0.66875	1.201000	0.43203	0.563000	0.77884	CGA	.	.	none		0.587	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454	
ESPNL	339768	hgsc.bcm.edu	37	2	239040089	239040089	+	Missense_Mutation	SNP	C	C	T	rs199724430	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:239040089C>T	ENST00000343063.3	+	9	2997	c.2734C>T	c.(2734-2736)Cgc>Tgc	p.R912C	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.R544C|ESPNL_ENST00000409169.1_Missense_Mutation_p.R868C	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	912										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGCCGCCGGCCGCCGGGCCTG	0.692													C|||	11	0.00219649	0.0	0.0	5008	,	,		13571	0.0109		0.0	False		,,,				2504	0.0				p.R912C		Atlas-SNP	.											ESPNL,NS,carcinoma,-1,1	ESPNL	63	1	0			c.C2734T						scavenged	.	C	CYS/ARG	2,4188		0,2,2093	9.0	12.0	11.0		2734	2.9	0.9	2		11	0,8228		0,0,4114	no	missense	ESPNL	NM_194312.2	180	0,2,6207	TT,TC,CC		0.0,0.0477,0.0161	probably-damaging	912/1006	239040089	2,12416	2095	4114	6209	SO:0001583	missense	339768	exon9			GCCGGCCGCCGGG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2734C>T	2.37:g.239040089C>T	ENSP00000339115:p.Arg912Cys	1.0	1.0	1		11.0	6.0	0.545455	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	17.11	3.304542	0.60305	4.77E-4	0.0	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.70749	-0.51;0.58;0.22	4.72	2.87	0.33458	.	0.258957	0.31897	N	0.006898	T	0.72137	0.3423	M	0.68593	2.085	0.46823	D	0.999212	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.959	T	0.73430	-0.3985	10	0.87932	D	0	-35.1335	4.8076	0.13328	0.1532:0.6129:0.1486:0.0853	.	868;912	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	C	912;868;544	ENSP00000339115:R912C;ENSP00000386577:R868C;ENSP00000386579:R544C	ENSP00000339115:R912C	R	+	1	0	ESPNL	238704828	0.042000	0.20092	0.896000	0.35187	0.865000	0.49528	1.688000	0.37690	0.401000	0.25424	0.460000	0.39030	CGC	C|0.998;T|0.002	0.002	strong		0.692	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
SWAP70	23075	hgsc.bcm.edu	37	11	9685820	9685820	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:9685820C>T	ENST00000318950.6	+	1	197	c.94C>T	c.(94-96)Ctc>Ttc	p.L32F	SWAP70_ENST00000447399.2_Missense_Mutation_p.L32F	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	32					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		CAAGTCCCAGCTCAAGGTGGG	0.692																																					p.L32F		Atlas-SNP	.											.	SWAP70	40	.	0			c.C94T						PASS	.						30.0	24.0	26.0					11																	9685820		2179	4272	6451	SO:0001583	missense	23075	exon1			TCCCAGCTCAAGG	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.94C>T	11.37:g.9685820C>T	ENSP00000315630:p.Leu32Phe	121.0	0.0	0		222.0	97.0	0.436937	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750499	0.89753	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	D;T	0.86865	-2.18;2.55	5.5	5.5	0.81552	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93943	0.8061	M	0.81497	2.545	0.80722	D	1	D;P;D	0.76494	0.998;0.891;0.999	D;P;D	0.85130	0.996;0.49;0.997	D	0.94379	0.7603	10	0.87932	D	0	-6.5908	19.0354	0.92974	0.0:1.0:0.0:0.0	.	32;32;32	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	F	32	ENSP00000399056:L32F;ENSP00000315630:L32F	ENSP00000315630:L32F	L	+	1	0	SWAP70	9642396	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.705000	0.54823	2.584000	0.87258	0.563000	0.77884	CTC	.	.	none		0.692	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	
SH3YL1	26751	hgsc.bcm.edu	37	2	218939	218939	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:218939C>T	ENST00000405430.1	-	12	1277	c.901G>A	c.(901-903)Gat>Aat	p.D301N	SH3YL1_ENST00000415006.2_Missense_Mutation_p.D205N|SH3YL1_ENST00000356150.5_Missense_Mutation_p.D301N|SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000403658.1_Missense_Mutation_p.D186N|SH3YL1_ENST00000403657.1_Missense_Mutation_p.D186N|SH3YL1_ENST00000403712.2_Missense_Mutation_p.D282N			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	301	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		AAATTCAAATCCCCAGGCTGC	0.373																																					p.D301N		Atlas-SNP	.											.	SH3YL1	49	.	0			c.G901A						PASS	.						102.0	93.0	96.0					2																	218939		1826	4079	5905	SO:0001583	missense	26751	exon10			TCAAATCCCCAGG		CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"""SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"""			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.901G>A	2.37:g.218939C>T	ENSP00000384269:p.Asp301Asn	111.0	0.0	0		94.0	43.0	0.457447	NM_015677	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Missense_Mutation	SNP	ENST00000405430.1	37		.	.	.	.	.	.	.	.	.	.	C	32	5.170694	0.94807	.	.	ENSG00000035115	ENST00000415006;ENST00000403712;ENST00000403657;ENST00000405430;ENST00000356150;ENST00000403658;ENST00000451005	T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85	6.03	6.03	0.97812	Src homology-3 domain (5);	0.108509	0.64402	D	0.000010	T	0.81969	0.4935	H	0.98487	4.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;1.0;0.997;0.998	D	0.88284	0.2938	10	0.87932	D	0	-11.8105	18.0605	0.89375	0.0:1.0:0.0:0.0	.	186;282;301;205	Q96HL8-4;Q96HL8-2;Q96HL8;Q96HL8-3	.;.;SH3Y1_HUMAN;.	N	205;282;186;301;301;186;214	ENSP00000404143:D205N;ENSP00000384276:D282N;ENSP00000385668:D186N;ENSP00000384269:D301N;ENSP00000348471:D301N;ENSP00000383928:D186N;ENSP00000416312:D214N	ENSP00000348471:D301N	D	-	1	0	SH3YL1	208939	1.000000	0.71417	0.981000	0.43875	0.982000	0.71751	6.441000	0.73439	2.854000	0.98071	0.655000	0.94253	GAT	.	.	none		0.373	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677	
PIANP	196500	hgsc.bcm.edu	37	12	6806573	6806573	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:6806573G>T	ENST00000540656.1	-	3	741	c.403C>A	c.(403-405)Cct>Act	p.P135T	PIANP_ENST00000320591.5_Missense_Mutation_p.P135T|PIANP_ENST00000534837.1_Missense_Mutation_p.P135T	NM_001244015.1	NP_001230944.1	Q8IYJ0	PIANP_HUMAN	PILR alpha associated neural protein	135						integral component of membrane (GO:0016021)											AGCCCATGAGGGGCTGCAAAA	0.602																																					p.P135T		Atlas-SNP	.											.	.	.	.	0			c.C403A						PASS	.						50.0	54.0	53.0					12																	6806573		1940	4123	6063	SO:0001583	missense	196500	exon3			CATGAGGGGCTGC	BC035736	CCDS44818.1, CCDS58205.1	12p13.31	2012-08-17	2012-08-17	2012-08-17	ENSG00000139200	ENSG00000139200			25338	protein-coding gene	gene with protein product	"""PILR-associating neural protein"""		"""chromosome 12 open reading frame 53"""	C12orf53		12975309	Standard	NM_153685		Approved	DKFZp547D2210, PANP	uc001qqf.2	Q8IYJ0	OTTHUMG00000168664	ENST00000540656.1:c.403C>A	12.37:g.6806573G>T	ENSP00000442157:p.Pro135Thr	101.0	0.0	0		109.0	5.0	0.0458716	NM_001244014	A8K0T3|B3KPF7|B3KRI6|Q6UX35	Missense_Mutation	SNP	ENST00000540656.1	37	CCDS44818.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.148879	0.57151	.	.	ENSG00000139200	ENST00000540656;ENST00000320591;ENST00000534837;ENST00000439553;ENST00000545917	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	4.05	4.05	0.47172	.	0.135360	0.50627	D	0.000106	T	0.19846	0.0477	N	0.14661	0.345	0.31623	N	0.650026	P	0.40282	0.711	B	0.27887	0.084	T	0.28650	-1.0037	10	0.72032	D	0.01	-9.1833	8.2372	0.31634	0.1749:0.0:0.8251:0.0	.	135	Q8IYJ0	CL053_HUMAN	T	135;135;135;109;135	ENSP00000442157:P135T;ENSP00000317818:P135T;ENSP00000443919:P135T;ENSP00000444605:P135T	ENSP00000317818:P135T	P	-	1	0	C12orf53	6676834	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.423000	0.59861	1.802000	0.52723	0.305000	0.20034	CCT	.	.	none		0.602	PIANP-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400524.1	NM_153685	
CCAR1	55749	hgsc.bcm.edu	37	10	70549639	70549639	+	Silent	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:70549639G>A	ENST00000265872.6	+	24	3479	c.3360G>A	c.(3358-3360)acG>acA	p.T1120T	CCAR1_ENST00000543719.1_Silent_p.T1105T|CCAR1_ENST00000535016.1_Silent_p.T1105T	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	1120					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						ACTTATCTACGGTAATGGATG	0.284																																					p.T1120T		Atlas-SNP	.											.	CCAR1	118	.	0			c.G3360A						PASS	.						45.0	48.0	47.0					10																	70549639		2201	4293	6494	SO:0001819	synonymous_variant	55749	exon24			ATCTACGGTAATG	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.3360G>A	10.37:g.70549639G>A		158.0	0.0	0		167.0	8.0	0.0479042	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	37	CCDS7282.1																																																																																			.	.	none		0.284	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411694	39411694	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:39411694G>C	ENST00000394008.1	+	1	59	c.57G>C	c.(55-57)tgG>tgC	p.W19C		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	24	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCACCTGCTGGAAGCCCACCA	0.622																																					p.W19C		Atlas-SNP	.											KRTAP9-9,NS,carcinoma,+2,1	KRTAP9-9	24	1	0			c.G57C						scavenged	.																																			SO:0001583	missense	81870	exon1			CTGCTGGAAGCCC	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.57G>C	17.37:g.39411694G>C	ENSP00000377576:p.Trp19Cys	24.0	2.0	0.0833333		15.0	2.0	0.133333	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	0.100	-1.153249	0.01700	.	.	ENSG00000198083	ENST00000394008	T	0.00711	5.8	3.04	-5.55	0.02536	.	.	.	.	.	T	0.00210	0.0006	N	0.00152	-1.975	0.20196	N	0.999925	B	0.02656	0.0	B	0.04013	0.001	T	0.42865	-0.9426	9	0.02654	T	1	.	6.8781	0.24158	0.0:0.2867:0.1571:0.5562	.	24	Q9BYP9	KRA99_HUMAN	C	19	ENSP00000377576:W19C	ENSP00000377576:W19C	W	+	3	0	KRTAP9-9	36665220	0.000000	0.05858	0.005000	0.12908	0.435000	0.31806	-0.843000	0.04350	-1.036000	0.03287	0.456000	0.33151	TGG	.	.	none		0.622	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
FMO5	2330	hgsc.bcm.edu	37	1	146656089	146656089	+	IGR	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:146656089C>T	ENST00000254090.4	-	0	2632				RP11-337C18.8_ENST00000606757.1_RNA|FMO5_ENST00000441068.2_Silent_p.K459K|RP11-337C18.10_ENST00000606856.1_RNA|RP11-337C18.8_ENST00000607149.1_RNA	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	25	all_hematologic(923;0.0487)					ccttaggcccctttattccgg	0.348																																					p.K459K		Atlas-SNP	.											.	FMO5	94	.	0			c.G1377A						PASS	.						98.0	87.0	90.0					1																	146656089		692	1591	2283	SO:0001628	intergenic_variant	2330	exon9			AGGCCCCTTTATT	Z47553	CCDS926.1, CCDS44209.1, CCDS44210.1	1q21.1	2011-08-04			ENSG00000131781	ENSG00000131781			3773	protein-coding gene	gene with protein product		603957				8786146, 9119381	Standard	NM_001461		Approved		uc001epi.2	P49326	OTTHUMG00000014607		1.37:g.146656089C>T		120.0	0.0	0		76.0	4.0	0.0526316	NM_001144829	B2RBG1|C9JJD1|Q8IV22	Silent	SNP	ENST00000254090.4	37	CCDS926.1																																																																																			.	.	none		0.348	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040373.2	NM_001461	
PSG4	5672	hgsc.bcm.edu	37	19	43708388	43708388	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:43708388A>C	ENST00000405312.3	-	2	317	c.80T>G	c.(79-81)tTc>tGc	p.F27C	PSG4_ENST00000244295.9_Missense_Mutation_p.F27C|PSG4_ENST00000433626.2_Missense_Mutation_p.F27C	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	27					female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				CGGATTCCAGAAGTTTAAAAG	0.468																																					p.X27X		Atlas-SNP	.											.	PSG4	129	.	0			c.G80G						PASS	.						107.0	121.0	116.0					19																	43708388		2144	4269	6413	SO:0001583	missense	5672	exon2			TTCCAGAAGTTTA		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.80T>G	19.37:g.43708388A>C	ENSP00000384770:p.Phe27Cys	200.0	0.0	0		190.0	74.0	0.389474	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	N	7.311	0.615088	0.14129	.	.	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626;ENST00000451895	T;T;T;T	0.50813	1.16;0.73;1.87;3.24	1.65	0.446	0.16602	.	.	.	.	.	T	0.34193	0.0889	L	0.33624	1.015	0.09310	N	1	B;B;B	0.28324	0.207;0.154;0.012	B;B;B	0.33254	0.091;0.16;0.033	T	0.36962	-0.9726	9	0.72032	D	0.01	.	3.5161	0.07726	0.6473:0.0:0.0:0.3527	.	27;27;27	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	C	27;27;27;43	ENSP00000244295:F27C;ENSP00000384770:F27C;ENSP00000387864:F27C;ENSP00000388134:F43C	ENSP00000244295:F27C	F	-	2	0	PSG4	48400228	0.058000	0.20735	0.279000	0.24732	0.035000	0.12851	-0.188000	0.09642	0.069000	0.16605	0.145000	0.16022	TTC	.	.	none		0.468	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
ZDBF2	57683	hgsc.bcm.edu	37	2	207174869	207174869	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:207174869A>G	ENST00000374423.3	+	5	6003	c.5617A>G	c.(5617-5619)Aaa>Gaa	p.K1873E		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1873							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TTCGAAGGGGAAAAAAAAGGT	0.413																																					p.K1873E		Atlas-SNP	.											ZDBF2_ENST00000374423,caecum,carcinoma,0,2	ZDBF2	531	2	0			c.A5617G						PASS	.						58.0	57.0	57.0					2																	207174869		1921	4134	6055	SO:0001583	missense	57683	exon5			AAGGGGAAAAAAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5617A>G	2.37:g.207174869A>G	ENSP00000363545:p.Lys1873Glu	95.0	0.0	0		77.0	26.0	0.337662	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	A	4.072	0.011280	0.07912	.	.	ENSG00000204186	ENST00000374423	T	0.38887	1.11	5.48	2.13	0.27403	.	.	.	.	.	T	0.12817	0.0311	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.30268	-0.9984	9	0.12766	T	0.61	.	5.7718	0.18257	0.2703:0.1494:0.5803:0.0	.	1873	Q9HCK1	ZDBF2_HUMAN	E	1873	ENSP00000363545:K1873E	ENSP00000363545:K1873E	K	+	1	0	ZDBF2	206883114	0.934000	0.31675	0.002000	0.10522	0.026000	0.11368	2.260000	0.43267	1.234000	0.43709	0.451000	0.29950	AAA	.	.	none		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
IWS1	55677	hgsc.bcm.edu	37	2	128263223	128263223	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:128263223C>T	ENST00000295321.4	-	3	515	c.256G>A	c.(256-258)Gag>Aag	p.E86K	AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000455721.2_Missense_Mutation_p.E93K|IWS1_ENST00000486662.1_5'UTR	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	86	Glu-rich.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		CTGTGAAGCTCCTCACTTTCA	0.483																																					p.E86K		Atlas-SNP	.											.	IWS1	61	.	0			c.G256A						PASS	.						168.0	169.0	168.0					2																	128263223		2203	4300	6503	SO:0001583	missense	55677	exon3			GAAGCTCCTCACT	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.256G>A	2.37:g.128263223C>T	ENSP00000295321:p.Glu86Lys	129.0	0.0	0		175.0	55.0	0.314286	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901973	0.52227	.	.	ENSG00000163166	ENST00000295321;ENST00000455721;ENST00000409725	T;T	0.33438	1.46;1.41	5.4	5.4	0.78164	.	0.301427	0.32608	N	0.005872	T	0.30916	0.0780	L	0.58101	1.795	0.25294	N	0.98934	B	0.21606	0.058	B	0.12837	0.008	T	0.13282	-1.0515	10	0.19590	T	0.45	-3.4505	16.0792	0.80989	0.0:1.0:0.0:0.0	.	86	Q96ST2	IWS1_HUMAN	K	86;93;91	ENSP00000295321:E86K;ENSP00000399245:E93K	ENSP00000295321:E86K	E	-	1	0	IWS1	127979693	0.993000	0.37304	1.000000	0.80357	0.869000	0.49853	3.916000	0.56416	2.524000	0.85096	0.491000	0.48974	GAG	.	.	none		0.483	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
NMUR1	10316	hgsc.bcm.edu	37	2	232389859	232389859	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:232389859C>T	ENST00000305141.4	-	3	1309	c.1176G>A	c.(1174-1176)atG>atA	p.M392I		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	392					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		TGCCTGTGGTCATCCTGCTGA	0.672																																					p.M392I		Atlas-SNP	.											.	NMUR1	46	.	0			c.G1176A						PASS	.						39.0	40.0	39.0					2																	232389859		2203	4300	6503	SO:0001583	missense	10316	exon3			TGTGGTCATCCTG	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"""GPCR / Class A : Neuromedin U receptors"""	4518	protein-coding gene	gene with protein product		604153	"""G protein-coupled receptor 66"""	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.1176G>A	2.37:g.232389859C>T	ENSP00000305877:p.Met392Ile	125.0	0.0	0		157.0	60.0	0.382166	NM_006056	O43664|Q7LDP6|Q8NE20	Missense_Mutation	SNP	ENST00000305141.4	37	CCDS2486.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.224634	0.39300	.	.	ENSG00000171596	ENST00000305141	T	0.37235	1.21	4.27	3.36	0.38483	.	1.558880	0.04572	N	0.393532	T	0.21103	0.0508	N	0.08118	0	0.20074	N	0.999931	B	0.02656	0.0	B	0.01281	0.0	T	0.16928	-1.0386	10	0.27785	T	0.31	-2.4681	6.9443	0.24510	0.0:0.5308:0.373:0.0962	.	392	Q9HB89	NMUR1_HUMAN	I	392	ENSP00000305877:M392I	ENSP00000305877:M392I	M	-	3	0	NMUR1	232098103	0.995000	0.38212	0.869000	0.34112	0.940000	0.58332	1.786000	0.38694	1.119000	0.41883	0.456000	0.33151	ATG	.	.	none		0.672	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056	
NFKBIA	4792	hgsc.bcm.edu	37	14	35871695	35871695	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:35871695G>A	ENST00000216797.5	-	5	912	c.811C>T	c.(811-813)Cag>Tag	p.Q271*	NFKBIA_ENST00000557100.1_5'UTR|NFKBIA_ENST00000557140.1_Nonsense_Mutation_p.Q228*|NFKBIA_ENST00000557389.1_Nonsense_Mutation_p.Q181*	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	271					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	AGTGTCAGCTGGCCCAGCTGC	0.562																																					p.Q271X		Atlas-SNP	.											.	NFKBIA	28	.	0			c.C811T						PASS	.						88.0	91.0	90.0					14																	35871695		2203	4300	6503	SO:0001587	stop_gained	4792	exon5			TCAGCTGGCCCAG		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"""Ankyrin repeat domain containing"""	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.811C>T	14.37:g.35871695G>A	ENSP00000216797:p.Gln271*	142.0	0.0	0		180.0	46.0	0.255556	NM_020529	B2R8L6	Nonsense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	G	38	7.053020	0.98029	.	.	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-12.2413	15.4515	0.75277	0.0:0.1382:0.8618:0.0	.	.	.	.	X	271;228;181	.	ENSP00000216797:Q271X	Q	-	1	0	NFKBIA	34941446	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.992000	0.40737	2.719000	0.93026	0.655000	0.94253	CAG	.	.	none		0.562	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529	
NAGA	4668	hgsc.bcm.edu	37	22	42463804	42463804	+	Missense_Mutation	SNP	G	G	T	rs140775168	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:42463804G>T	ENST00000396398.3	-	3	821	c.289C>A	c.(289-291)Cgc>Agc	p.R97S	NAGA_ENST00000402937.1_Missense_Mutation_p.R97S|NAGA_ENST00000403363.1_Missense_Mutation_p.R97S	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	97					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						TGAGGGAAGCGCTTGGGATCC	0.607																																					p.R97S		Atlas-SNP	.											.	NAGA	26	.	0			c.C289A						PASS	.						130.0	112.0	118.0					22																	42463804		2203	4300	6503	SO:0001583	missense	4668	exon3			GGAAGCGCTTGGG		CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.289C>A	22.37:g.42463804G>T	ENSP00000379680:p.Arg97Ser	58.0	0.0	0		80.0	32.0	0.4	NM_000262		Missense_Mutation	SNP	ENST00000396398.3	37	CCDS14030.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.210448	0.79240	.	.	ENSG00000198951	ENST00000396398;ENST00000403363;ENST00000402937	D;D;D	0.99820	-6.93;-6.93;-6.93	4.66	3.59	0.41128	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99768	0.9905	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96983	0.9716	10	0.72032	D	0.01	-23.1156	10.2175	0.43177	0.0:0.0:0.5995:0.4005	.	97	P17050	NAGAB_HUMAN	S	97	ENSP00000379680:R97S;ENSP00000385283:R97S;ENSP00000384603:R97S	ENSP00000379680:R97S	R	-	1	0	NAGA	40793750	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.394000	0.34509	2.441000	0.82636	0.561000	0.74099	CGC	G|1.000;C|0.000	.	alt		0.607	NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1		
MGAT5	4249	hgsc.bcm.edu	37	2	135102520	135102520	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:135102520G>A	ENST00000409645.1	+	9	1249	c.997G>A	c.(997-999)Gga>Aga	p.G333R	MGAT5_ENST00000281923.2_Missense_Mutation_p.G333R			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	333					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		GAAGGTTGTAGGAAACCGATC	0.378																																					p.G333R		Atlas-SNP	.											.	MGAT5	84	.	0			c.G997A						PASS	.						125.0	122.0	123.0					2																	135102520		2203	4300	6503	SO:0001583	missense	4249	exon8			GTTGTAGGAAACC	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.997G>A	2.37:g.135102520G>A	ENSP00000386377:p.Gly333Arg	86.0	0.0	0		90.0	32.0	0.355556	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	37	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.578283	0.86645	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.38	5.38	0.77491	.	0.050300	0.85682	D	0.000000	T	0.76666	0.4019	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75428	-0.3321	9	0.46703	T	0.11	-14.1382	19.4972	0.95079	0.0:0.0:1.0:0.0	.	333	Q09328	MGT5A_HUMAN	R	333	.	ENSP00000281923:G333R	G	+	1	0	MGAT5	134818990	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	9.758000	0.98927	2.668000	0.90789	0.563000	0.77884	GGA	.	.	none		0.378	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410	
MTCL1	23255	hgsc.bcm.edu	37	18	8806921	8806921	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr18:8806921T>C	ENST00000306329.11	+	9	3424	c.3424T>C	c.(3424-3426)Ttc>Ctc	p.F1142L	SOGA2_ENST00000359865.3_Missense_Mutation_p.F823L|SOGA2_ENST00000400050.3_Missense_Mutation_p.F782L|SOGA2_ENST00000306285.7_Missense_Mutation_p.F138L|SOGA2_ENST00000518815.1_Missense_Mutation_p.F138L|SOGA2_ENST00000517570.1_Missense_Mutation_p.F782L																							GTTCAGCGCCTTCAAGGCCTT	0.587																																					p.F823L		Atlas-SNP	.											CCDC165,NS,carcinoma,-2,1	.	.	1	0			c.T2467C						scavenged	.						70.0	61.0	64.0					18																	8806921		2203	4300	6503	SO:0001583	missense	23255	exon11			AGCGCCTTCAAGG																												ENST00000306329.11:c.3424T>C	18.37:g.8806921T>C	ENSP00000305027:p.Phe1142Leu	58.0	0.0	0		62.0	3.0	0.0483871	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	T	0.201	-1.045061	0.01997	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.54	4.67	0.58626	.	0.145473	0.32444	N	0.006085	T	0.04543	0.0124	N	0.00621	-1.32	0.23704	N	0.997068	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.39418	-0.9615	10	0.02654	T	1	-19.4729	6.0193	0.19620	0.0:0.6353:0.1402:0.2244	.	1133;823	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	L	844;782;823;782;138	ENSP00000429556:F782L;ENSP00000352927:F823L;ENSP00000382924:F782L;ENSP00000303670:F138L	ENSP00000303670:F138L	F	+	1	0	CCDC165	8796921	0.802000	0.28943	0.123000	0.21794	0.132000	0.20833	1.531000	0.36018	1.461000	0.47929	-0.242000	0.12053	TTC	.	.	none		0.587	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
STAT3	6774	hgsc.bcm.edu	37	17	40474482	40474482	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:40474482T>A	ENST00000264657.5	-	21	2231	c.1919A>T	c.(1918-1920)tAc>tTc	p.Y640F	STAT3_ENST00000404395.3_Missense_Mutation_p.Y640F|STAT3_ENST00000585517.1_Missense_Mutation_p.Y640F|STAT3_ENST00000389272.3_Missense_Mutation_p.Y542F|STAT3_ENST00000588969.1_Missense_Mutation_p.Y640F	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	640	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		CTGCTTTGTGTATGGTTCCAC	0.463									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.Y640F		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,0,46	STAT3	268	46	0			c.A1919T						PASS	.						243.0	213.0	223.0					17																	40474482		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTTGTGTATGGTT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"""SH2 domain containing"""	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1919A>T	17.37:g.40474482T>A	ENSP00000264657:p.Tyr640Phe	228.0	0.0	0		271.0	137.0	0.505535	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813449	0.70912	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89196	-2.48;-2.48;-2.48	4.64	4.64	0.57946	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	N	0.16016	0.355	0.80722	D	1	D;D;D	0.59357	0.982;0.985;0.985	D;D;D	0.78314	0.984;0.991;0.991	T	0.82589	-0.0382	10	0.06891	T	0.86	-37.3581	14.2314	0.65895	0.0:0.0:0.0:1.0	.	640;640;640	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	F	640;542;640	ENSP00000264657:Y640F;ENSP00000373923:Y542F;ENSP00000384943:Y640F	ENSP00000264657:Y640F	Y	-	2	0	STAT3	37728008	1.000000	0.71417	0.964000	0.40570	0.715000	0.41141	7.868000	0.87116	1.953000	0.56701	0.460000	0.39030	TAC	.	.	none		0.463	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
PCLO	27445	hgsc.bcm.edu	37	7	82545106	82545106	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:82545106A>G	ENST00000333891.9	-	7	12533	c.12196T>C	c.(12196-12198)Ttt>Ctt	p.F4066L	PCLO_ENST00000423517.2_Missense_Mutation_p.F4066L|PCLO_ENST00000437081.1_Missense_Mutation_p.F786L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGAAGGCTAAATGCGGTGCTT	0.438																																					p.F4066L		Atlas-SNP	.											.	PCLO	1506	.	0			c.T12196C						PASS	.						94.0	83.0	86.0					7																	82545106		1946	4159	6105	SO:0001583	missense	27445	exon7			GGCTAAATGCGGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.12196T>C	7.37:g.82545106A>G	ENSP00000334319:p.Phe4066Leu	99.0	0.0	0		78.0	31.0	0.397436	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.067747	0.55539	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.16457	2.34;2.34	5.84	5.84	0.93424	.	.	.	.	.	T	0.31040	0.0784	L	0.59436	1.845	0.51482	D	0.999927	P;D;D	0.61697	0.78;0.99;0.99	B;P;P	0.52514	0.192;0.701;0.701	T	0.02378	-1.1168	9	0.87932	D	0	.	16.2109	0.82158	1.0:0.0:0.0:0.0	.	3997;4066;4066	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	L	4066;4066;786	ENSP00000334319:F4066L;ENSP00000388393:F4066L	ENSP00000334319:F4066L	F	-	1	0	PCLO	82383042	1.000000	0.71417	0.984000	0.44739	0.968000	0.65278	9.339000	0.96797	2.230000	0.72887	0.455000	0.32223	TTT	.	.	none		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
DPYD	1806	hgsc.bcm.edu	37	1	97548004	97548004	+	Missense_Mutation	SNP	T	T	C	rs568169006		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:97548004T>C	ENST00000370192.3	-	22	2889	c.2789A>G	c.(2788-2790)cAg>cGg	p.Q930R		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	930					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	TCCAAGGTACTGCAGTGCTTT	0.343																																					p.Q930R		Atlas-SNP	.											.	DPYD	219	.	0			c.A2789G						PASS	.						206.0	194.0	198.0					1																	97548004		2203	4299	6502	SO:0001583	missense	1806	exon22			AGGTACTGCAGTG	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2789A>G	1.37:g.97548004T>C	ENSP00000359211:p.Gln930Arg	116.0	0.0	0		109.0	44.0	0.40367	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	T	6.890	0.533671	0.13188	.	.	ENSG00000188641	ENST00000370192	D	0.89939	-2.59	5.82	3.5	0.40072	.	0.511060	0.21827	N	0.068524	T	0.70789	0.3264	L	0.39245	1.2	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.63651	-0.6589	10	0.31617	T	0.26	-0.5352	6.781	0.23646	0.0:0.1332:0.1289:0.7378	.	930	Q12882	DPYD_HUMAN	R	930	ENSP00000359211:Q930R	ENSP00000359211:Q930R	Q	-	2	0	DPYD	97320592	1.000000	0.71417	0.988000	0.46212	0.110000	0.19582	1.641000	0.37197	0.461000	0.27071	-0.291000	0.09656	CAG	.	.	none		0.343	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067193	46067193	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:46067193G>C	ENST00000334670.8	+	1	863	c.818G>C	c.(817-819)tGc>tCc	p.C273S	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	273						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CCGGCCTCCTGCGTGTCCCTC	0.677																																					p.C273S		Atlas-SNP	.											KRTAP10-11,NS,carcinoma,-1,1	KRTAP10-11	36	1	0			c.G818C						PASS	.						41.0	52.0	48.0					21																	46067193		2200	4292	6492	SO:0001583	missense	386678	exon1			CCTCCTGCGTGTC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.818G>C	21.37:g.46067193G>C	ENSP00000334197:p.Cys273Ser	80.0	0.0	0		134.0	6.0	0.0447761	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	g	10.35	1.326226	0.24080	.	.	ENSG00000243489	ENST00000334670	T	0.00648	5.99	3.93	1.85	0.25348	.	.	.	.	.	T	0.00724	0.0024	L	0.45051	1.395	0.21527	N	0.999652	B	0.21071	0.051	B	0.24541	0.054	T	0.44314	-0.9336	9	0.16896	T	0.51	.	7.0501	0.25069	0.1131:0.3795:0.5075:0.0	.	273	P60412	KR10B_HUMAN	S	273	ENSP00000334197:C273S	ENSP00000334197:C273S	C	+	2	0	KRTAP10-11	44891621	0.000000	0.05858	0.035000	0.18076	0.597000	0.36814	-0.005000	0.12855	0.627000	0.30340	0.462000	0.41574	TGC	.	.	none		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
PIM1	5292	hgsc.bcm.edu	37	6	37138424	37138424	+	Silent	SNP	C	C	T			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:37138424C>T	ENST00000373509.5	+	1	446	c.73C>T	c.(73-75)Ctg>Ttg	p.L25L		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	116					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)	p.L25V(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	CGCCACCAAGCTGGCGCCCGG	0.726			T	BCL6	NHL																																p.L116L		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C346T						scavenged	.						22.0	24.0	24.0					6																	37138424		2196	4289	6485	SO:0001819	synonymous_variant	5292	exon1			ACCAAGCTGGCGC		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.73C>T	6.37:g.37138424C>T		11.0	0.0	0		12.0	3.0	0.25	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
PCDH17	27253	hgsc.bcm.edu	37	13	58207600	58207600	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:58207600G>A	ENST00000377918.3	+	1	946	c.920G>A	c.(919-921)gGc>gAc	p.G307D		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	307	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CGTGTGAAGGGCAATCTGGAC	0.582																																					p.G307D	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											PCDH17,NS,carcinoma,+1,1	PCDH17	304	1	0			c.G920A						PASS	.						64.0	61.0	62.0					13																	58207600		2203	4300	6503	SO:0001583	missense	27253	exon1			TGAAGGGCAATCT	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.920G>A	13.37:g.58207600G>A	ENSP00000367151:p.Gly307Asp	66.0	0.0	0		66.0	15.0	0.227273	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663894	0.67700	.	.	ENSG00000118946	ENST00000377918	T	0.51817	0.69	5.57	4.67	0.58626	Cadherin (4);Cadherin-like (1);	0.044369	0.85682	D	0.000000	T	0.59046	0.2165	L	0.39467	1.215	0.80722	D	1	D;D	0.67145	0.995;0.996	D;D	0.76071	0.978;0.987	T	0.54774	-0.8243	9	.	.	.	.	15.9011	0.79377	0.0:0.1353:0.8647:0.0	.	307;307	O14917-2;O14917	.;PCD17_HUMAN	D	307	ENSP00000367151:G307D	.	G	+	2	0	PCDH17	57105601	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.693000	0.74582	2.640000	0.89533	0.650000	0.86243	GGC	.	.	none		0.582	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
