#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_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
NUP214	8021	hgsc.bcm.edu	37	9	134073007	134073008	+	Frame_Shift_Ins	INS	-	-	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:134073007_134073008insC	ENST00000359428.5	+	29	4270_4271	c.4126_4127insC	c.(4126-4128)gccfs	p.A1376fs	NUP214_ENST00000483497.2_Frame_Shift_Ins_p.A202fs|NUP214_ENST00000411637.2_Frame_Shift_Ins_p.A1366fs|NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000451030.1_Frame_Shift_Ins_p.A1377fs			P35658	NU214_HUMAN	nucleoporin 214kDa	1376	11 X 5 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TAATTTTACTGCCCCCCCGGTG	0.545			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.A1376fs	Pancreas(4;24 48 25510 30394 32571)	Pindel,Atlas-Indel	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.4126_4127insC						PASS	.																																			SO:0001589	frameshift_variant	8021	exon29			.	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4133dupC	9.37:g.134073014_134073014dupC	ENSP00000352400:p.Ala1376fs	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	86	17	0.198	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Frame_Shift_Ins	INS	ENST00000359428.5	37	CCDS6940.1																																																																																			.	.	none		0.545	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
CHD7	55636	hgsc.bcm.edu	37	8	61714117	61714118	+	Frame_Shift_Ins	INS	-	-	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:61714117_61714118insA	ENST00000423902.2	+	6	2886_2887	c.2407_2408insA	c.(2407-2409)gaafs	p.E803fs	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000525508.1_Frame_Shift_Ins_p.E803fs	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	803	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CCCAGTGGTAGAAAAAATTATG	0.391																																					p.E803fs		Pindel,Atlas-Indel	.											.	CHD7	534	.	1	Insertion - In frame(1)	lung(1)	c.2407_2408insA						PASS	.																																			SO:0001589	frameshift_variant	55636	exon6			.	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.2413dupA	8.37:g.61714123_61714123dupA	ENSP00000392028:p.Glu803fs	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	164	28	0.171	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Frame_Shift_Ins	INS	ENST00000423902.2	37	CCDS47865.1																																																																																			.	.	none		0.391	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547094	+	In_Frame_Ins	INS	-	-	CAG	rs10902490|rs113304321|rs528214697	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:132547093_132547094insCAG	ENST00000333577.4	+	48	8398_8399	c.8289_8290insCAG	c.(8290-8292)cag>CAGcag	p.2764_2764Q>QQ	EP400_ENST00000332482.4_In_Frame_Ins_p.2691_2691Q>QQ|EP400_ENST00000389562.2_In_Frame_Ins_p.2727_2727Q>QQ|EP400_ENST00000330386.6_In_Frame_Ins_p.2647_2647Q>QQ|EP400_ENST00000389561.2_In_Frame_Ins_p.2728_2728Q>QQ			Q96L91	EP400_HUMAN	E1A binding protein p400	2764	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2726Q(9)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcaacaacagcagcagca	0.564														1869	0.373203	0.3427	0.513	5008	,	,		15674	0.2391		0.4722	False		,,,				2504	0.3517				p.Q2727delinsQQ		Atlas-Indel	.											EP400,NS,carcinoma,0,15	EP400	370	15	9	Substitution - coding silent(9)	lung(3)|kidney(2)|endometrium(2)|central_nervous_system(2)	c.8181_8182insCAG						PASS	.																																			SO:0001652	inframe_insertion	57634	exon47			.	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8329_8331dupCAG	12.37:g.132547100_132547102dupCAG	ENSP00000333602:p.Gln2784dup	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	In_Frame_Ins	INS	ENST00000333577.4	37																																																																																				.	.	weak		0.564	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
RBM33	155435	hgsc.bcm.edu	37	7	155532534	155532545	+	In_Frame_Del	DEL	CCCACCCCAGCA	CCCACCCCAGCA	-			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	CCCACCCCAGCA	CCCACCCCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:155532534_155532545delCCCACCCCAGCA	ENST00000401878.3	+	12	2061_2072	c.1863_1874delCCCACCCCAGCA	c.(1861-1875)cccccaccccagcac>ccc	p.PPQH630del		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	630	His-rich.|Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		agcaccagcccccaccccagcacccaccacag	0.708																																					p.621_625del		Atlas-Indel	.											.	RBM33	157	.	0			c.1862_1873del						PASS	.			77,2879		15,47,1416						5.1	0.2			6	120,5272		26,68,2602	no	coding	RBM33	NM_053043.2		41,115,4018	A1A1,A1R,RR		2.2255,2.6049,2.3598				197,8151				SO:0001651	inframe_deletion	155435	exon12			.	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1863_1874delCCCACCCCAGCA	7.37:g.155532534_155532545delCCCACCCCAGCA	ENSP00000384160:p.Pro630_His633del	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	In_Frame_Del	DEL	ENST00000401878.3	37	CCDS5941.2																																																																																			.	.	none		0.708	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
FADS6	283985	hgsc.bcm.edu	37	17	72889676	72889677	+	In_Frame_Ins	INS	-	-	GGCTCCGTAGGTTCCATC	rs4319809|rs1625113	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:72889676_72889677insGGCTCCGTAGGTTCCATC	ENST00000310226.6	-	1	31_32	c.17_18insGATGGAACCTACGGAGCC	c.(16-18)ccc>ccGATGGAACCTACGGAGCCc	p.6_6P>PMEPTEP		NM_178128.3	NP_835229.2	Q8N9I5	FADS6_HUMAN	fatty acid desaturase 6	12	3 X 6 AA tandem repeat of M-E-P-T-E-P.				fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|lung(4)	8	all_lung(278;0.172)|Lung NSC(278;0.207)					TAGGTTCCATGGGCTCCGTGGG	0.728																																					p.P6delinsPMEPTEP		Pindel,Atlas-Indel	.											FADS6_ENST00000310226,caecum,carcinoma,0,2	FADS6	55	2	0			c.18_19insGATGGAACCTACGGAGCC						PASS	.																																			SO:0001652	inframe_insertion	283985	exon1			.	AK094411	CCDS54163.1	17q25.1	2014-07-17	2013-01-25			ENSG00000172782		"""Fatty acid desaturases"""	30459	protein-coding gene	gene with protein product			"""fatty acid desaturase domain family, member 6"""				Standard	XM_005257224		Approved		uc002jmd.1	Q8N9I5		ENST00000310226.6:c.17_18insGATGGAACCTACGGAGCC	17.37:g.72889676_72889677insGGCTCCGTAGGTTCCATC	ENSP00000307821:p.MetGluProThrGluPro12dup	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	70	22	0.314	NM_178128	Q17RQ7|Q6XYE1	In_Frame_Ins	INS	ENST00000310226.6	37	CCDS54163.1																																																																																			.	.	none		0.728	FADS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445219.1		
MESP2	145873	hgsc.bcm.edu	37	15	90320121	90320144	+	In_Frame_Del	DEL	AGGGGCAGGGGCAAGGGCAGGGGC	AGGGGCAGGGGCAAGGGCAGGGGC	-	rs56192595|rs200021459|rs199821487	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	AGGGGCAGGGGCAAGGGCAGGGGC	AGGGGCAGGGGCAAGGGCAGGGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr15:90320121_90320144delAGGGGCAGGGGCAAGGGCAGGGGC	ENST00000341735.3	+	1	533_556	c.533_556delAGGGGCAGGGGCAAGGGCAGGGGC	c.(532-558)gaggggcaggggcaagggcaggggcag>gag	p.GQGQGQGQ195del	MESP2_ENST00000558723.1_Intron|MESP2_ENST00000560219.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	195	13 X 2 AA tandem repeats of G-Q.				mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q198_G205delQGQGQGQG(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			ACGCaggcggaggggcaggggcaagggcaggggcaggggcaggg	0.777														3487	0.696286	0.4168	0.7824	5008	,	,		13432	0.8879		0.7654	False		,,,				2504	0.7444				p.178_185del		Atlas-Indel	.											.	MESP2	20	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.532_555del						PASS	.			995,777		385,225,276						0.1	0.0		dbSNP_129	3	3389,1453		1404,581,436	no	coding	MESP2	NM_001039958.1		1789,806,712	A1A1,A1R,RR		30.0083,43.8488,33.7164				4384,2230				SO:0001651	inframe_deletion	145873	exon1			.		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.533_556delAGGGGCAGGGGCAAGGGCAGGGGC	15.37:g.90320121_90320144delAGGGGCAGGGGCAAGGGCAGGGGC	ENSP00000342392:p.Gly195_Gln202del	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	25	0.806452	NM_001039958	Q7RTU2	In_Frame_Del	DEL	ENST00000341735.3	37	CCDS42078.1																																																																																			AGGGGCAGGGGCAAGGGCAGGGGC|0.230;-|0.770	0.770	strong		0.777	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr22:29885567_29885568insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1971_1972	c.1938_1939insAAGTCCCCTGAGAAGGCC	c.(1939-1941)aag>AAGTCCCCTGAGAAGGCCaag	p.647_647K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTGA	0.569																																					p.A646delinsAKSPEKA		Atlas-Indel	.											NEFH,rectum,carcinoma,0,1	NEFH	178	1	0			c.1938_1939insAAGTCCCCTGAGAAGGCC						PASS	.			2816,1448		937,942,253						-5.3	0.0		dbSNP_134	77	5046,3206		1537,1972,617	no	coding	NEFH	NM_021076.3		2474,2914,870	A1A1,A1R,RR		38.8512,33.9587,37.1844				7862,4654				SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	22.37:g.29885567_29885568insAAGTCCCCTGAGAAGGCC	Exception_encountered	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	39	11	0.282051	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	strong		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
NR1H2	7376	hgsc.bcm.edu	37	19	50881822	50881823	+	In_Frame_Ins	INS	-	-	CAG	rs57821899|rs61751954|rs34296657|rs66611742|rs1052533	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:50881822_50881823insCAG	ENST00000253727.5	+	6	751_752	c.516_517insCAG	c.(517-519)cag>CAGcag	p.173_173Q>QQ	NR1H2_ENST00000598168.1_In_Frame_Ins_p.173_173Q>QQ|NR1H2_ENST00000411902.2_In_Frame_Ins_p.76_76Q>QQ|NR1H2_ENST00000593926.1_In_Frame_Ins_p.173_173Q>QQ|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000599105.1_In_Frame_Ins_p.173_173Q>QQ	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	173					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		AGATTCGGAAACAGCAGCAGGA	0.644														1987	0.396765	0.621	0.4294	5008	,	,		16931	0.1677		0.3161	False		,,,				2504	0.3896				p.K172delinsKQ		Pindel	.											.	NR1H2	47	.	0			c.516_517insCAG						PASS	.																																			SO:0001652	inframe_insertion	7376	exon6			.	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.523_525dupCAG	19.37:g.50881829_50881831dupCAG	ENSP00000253727:p.Gln175dup	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	64	12	0.188	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	In_Frame_Ins	INS	ENST00000253727.5	37	CCDS42593.1																																																																																			CAG|1.000	.	weak		0.644	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2		
PALM3	342979	hgsc.bcm.edu	37	19	14167553	14167553	+	Missense_Mutation	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:14167553C>A	ENST00000340790.4	-	3	189	c.190G>T	c.(190-192)Gac>Tac	p.D64Y		NM_001145028.1	NP_001138500.1	A6NDB9	PALM3_HUMAN	paralemmin 3	64					negative regulation of cytokine-mediated signaling pathway (GO:0001960)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)			endometrium(1)|kidney(2)|pancreas(1)|skin(1)	5						GAGGTGGGGTCTTCGGATGGC	0.612																																					p.D64Y		Atlas-SNP	.											.	PALM3	26	.	0			c.G190T						PASS	.						75.0	87.0	83.0					19																	14167553		692	1591	2283	SO:0001583	missense	342979	exon3			TGGGGTCTTCGGA		CCDS46001.1	19p13.12	2010-04-15			ENSG00000187867	ENSG00000187867			33274	protein-coding gene	gene with protein product							Standard	NM_001145028		Approved		uc010xnk.1	A6NDB9		ENST00000340790.4:c.190G>T	19.37:g.14167553C>A	ENSP00000344996:p.Asp64Tyr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	108	39	0.361111	NM_001145028		Missense_Mutation	SNP	ENST00000340790.4	37	CCDS46001.1	.	.	.	.	.	.	.	.	.	.	c	10.84	1.465199	0.26335	.	.	ENSG00000187867	ENST00000340790	T	0.35048	1.33	4.06	2.95	0.34219	.	.	.	.	.	T	0.47358	0.1441	L	0.40543	1.245	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.18618	-1.0331	9	0.87932	D	0	.	9.6574	0.39934	0.0:0.7881:0.2119:0.0	.	64	A6NDB9	PALM3_HUMAN	Y	64	ENSP00000344996:D64Y	ENSP00000344996:D64Y	D	-	1	0	PALM3	14028553	0.776000	0.28616	0.011000	0.14972	0.041000	0.13682	3.756000	0.55205	2.095000	0.63458	0.561000	0.74099	GAC	.	.	none		0.612	PALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458540.1	NM_001145028	
GRIA2	2891	hgsc.bcm.edu	37	4	158142838	158142838	+	Silent	SNP	C	C	T	rs371935251		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:158142838C>T	ENST00000264426.9	+	2	387	c.108C>T	c.(106-108)ggC>ggT	p.G36G	GRIA2_ENST00000504801.1_Intron|GRIA2_ENST00000449365.1_5'UTR|GRIA2_ENST00000393815.2_5'UTR|GRIA2_ENST00000296526.7_Silent_p.G36G|GRIA2_ENST00000507898.1_5'UTR	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	36					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.G36G(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TTCCTAGGGGCGCCGATCAAG	0.537																																					p.G36G		Atlas-SNP	.											GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	2	2	Substitution - coding silent(2)	kidney(2)	c.C108T						PASS	.						95.0	99.0	98.0					4																	158142838		2203	4300	6503	SO:0001819	synonymous_variant	2891	exon2			TAGGGGCGCCGAT		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.108C>T	4.37:g.158142838C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	83	17	0.204819	NM_000826	A8MT92|I6L997|Q96FP6	Silent	SNP	ENST00000264426.9	37	CCDS43274.1																																																																																			.	.	alt		0.537	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
ITGB3	3690	hgsc.bcm.edu	37	17	45369814	45369814	+	Missense_Mutation	SNP	C	C	T	rs145572861	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:45369814C>T	ENST00000559488.1	+	10	1586	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W	ITGB3_ENST00000435993.2_Missense_Mutation_p.R477W|ITGB3_ENST00000560629.1_Missense_Mutation_p.A512V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	524	Cysteine-rich tandem repeats.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CTGCAGCCAGCGGGGCGAGTG	0.617													C|||	2	0.000399361	0.0008	0.0	5008	,	,		18639	0.001		0.0	False		,,,				2504	0.0				p.R524W		Atlas-SNP	.											.	ITGB3	157	.	0			c.C1570T						PASS	.	C	TRP/ARG	5,4401	9.9+/-24.2	0,5,2198	88.0	81.0	84.0		1570	4.4	1.0	17	dbSNP_134	84	0,8600		0,0,4300	yes	missense	ITGB3	NM_000212.2	101	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	524/789	45369814	5,13001	2203	4300	6503	SO:0001583	missense	3690	exon10			AGCCAGCGGGGCG		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1570C>T	17.37:g.45369814C>T	ENSP00000452786:p.Arg524Trp	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	19.68	3.872407	0.72180	0.001135	0.0	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.99329	-5.75	5.38	4.39	0.52855	EGF, extracellular (1);	0.055231	0.64402	D	0.000002	D	0.99450	0.9805	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98771	1.0728	10	0.87932	D	0	.	11.7475	0.51828	0.4384:0.5616:0.0:0.0	.	524	P05106	ITB3_HUMAN	W	524;477	ENSP00000407801:R477W	ENSP00000262017:R524W	R	+	1	2	C17orf57	42724813	0.931000	0.31567	1.000000	0.80357	0.940000	0.58332	0.075000	0.14686	1.240000	0.43803	0.462000	0.41574	CGG	C|1.000;T|0.000	0.000	strong		0.617	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
ETAA1	54465	hgsc.bcm.edu	37	2	67631813	67631813	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:67631813G>A	ENST00000272342.5	+	5	2129	c.1999G>A	c.(1999-2001)Gag>Aag	p.E667K	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	667						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						AAGTATATGTGAGATCAATAA	0.343																																					p.E667K		Atlas-SNP	.											.	ETAA1	88	.	0			c.G1999A						PASS	.						83.0	88.0	86.0					2																	67631813		2202	4295	6497	SO:0001583	missense	54465	exon5			ATATGTGAGATCA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1999G>A	2.37:g.67631813G>A	ENSP00000272342:p.Glu667Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	-	11.45	1.642910	0.29246	.	.	ENSG00000143971	ENST00000272342	T	0.18960	2.18	4.65	-1.19	0.09585	.	1.031440	0.07617	N	0.926447	T	0.12603	0.0306	L	0.41236	1.265	0.09310	N	1	B	0.13145	0.007	B	0.14578	0.011	T	0.38090	-0.9677	10	0.02654	T	1	-1.0365	5.2166	0.15346	0.4149:0.148:0.4372:0.0	.	667	Q9NY74	ETAA1_HUMAN	K	667	ENSP00000272342:E667K	ENSP00000272342:E667K	E	+	1	0	ETAA1	67485317	0.362000	0.24980	0.000000	0.03702	0.424000	0.31475	0.779000	0.26746	-0.078000	0.12730	0.467000	0.42956	GAG	.	.	none		0.343	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
TP53	7157	hgsc.bcm.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs397516437|rs121912651		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R248W	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,adenocarcinoma,+1,1635	TP53	33396	1635	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	c.C742T	GRCh37	CM010465|CM900211	TP53	M	rs121912651	PASS	.						151.0	112.0	125.0					17																	7577539		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCCTCCGGTTCAT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	44	30	0.681818	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG	.	.	weak		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr22:25016911C>T	ENST00000400382.1	+	9	1362	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	GGT1_ENST00000400380.1_Missense_Mutation_p.R203W|GGT1_ENST00000400383.1_Missense_Mutation_p.R203W|GGT1_ENST00000248923.4_Missense_Mutation_p.R203W|GGT1_ENST00000406383.2_Missense_Mutation_p.R203W|GGT1_ENST00000466310.1_Intron			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	203					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.R203W(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	AAAGGTGCTTCGGGAGGGGGA	0.652																																					p.R203W		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	breast(1)	c.C607T						scavenged	.						20.0	22.0	21.0					22																	25016911		1981	4142	6123	SO:0001583	missense	2678	exon9			GTGCTTCGGGAGG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.607C>T	22.37:g.25016911C>T	ENSP00000383232:p.Arg203Trp	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	192	5	0.0260417	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	16.88	3.244872	0.59103	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12	3.94	1.51	0.23008	.	0.465560	0.21948	U	0.066770	T	0.18841	0.0452	M	0.62016	1.91	0.29917	N	0.823045	D	0.76494	0.999	P	0.58970	0.849	T	0.03121	-1.1070	10	0.87932	D	0	-23.2527	10.8877	0.46976	0.3395:0.6605:0.0:0.0	.	203	P19440	GGT1_HUMAN	W	203	ENSP00000248923:R203W;ENSP00000393537:R203W;ENSP00000383232:R203W;ENSP00000383233:R203W;ENSP00000383231:R203W;ENSP00000385975:R203W	ENSP00000248923:R203W	R	+	1	2	GGT1	23346911	0.047000	0.20315	0.042000	0.18584	0.549000	0.35272	1.263000	0.33004	0.735000	0.32537	0.555000	0.69702	CGG	C|0.996;T|0.004	0.004	strong		0.652	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
NPEPL1	79716	hgsc.bcm.edu	37	20	57269610	57269610	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:57269610G>A	ENST00000356091.6	+	3	757	c.469G>A	c.(469-471)Gga>Aga	p.G157R	NPEPL1_ENST00000525967.1_Missense_Mutation_p.G129R|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Missense_Mutation_p.G109R	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	157						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TTTCCTGGTGGGACAAGACAA	0.667																																					p.G157R		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G469A						PASS	.						30.0	32.0	31.0					20																	57269610		1953	4145	6098	SO:0001583	missense	79716	exon3			CTGGTGGGACAAG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.469G>A	20.37:g.57269610G>A	ENSP00000348395:p.Gly157Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.742333	0.49151	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.32023	1.47;1.49;1.48	4.62	3.66	0.41972	.	0.052273	0.85682	D	0.000000	T	0.46639	0.1403	M	0.76328	2.33	0.51233	D	0.999914	P;P;P;D	0.54207	0.823;0.839;0.848;0.965	B;P;B;P	0.57283	0.374;0.583;0.374;0.817	T	0.41858	-0.9485	10	0.18710	T	0.47	-9.0519	13.1398	0.59428	0.0:0.0:0.8389:0.1611	.	157;109;129;157	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	R	129;109;157	ENSP00000434810:G129R;ENSP00000437112:G109R;ENSP00000348395:G157R	ENSP00000348395:G157R	G	+	1	0	NPEPL1	56703017	1.000000	0.71417	0.995000	0.50966	0.107000	0.19398	9.409000	0.97331	0.931000	0.37242	-0.320000	0.08662	GGA	.	.	none		0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145248876	145248876	+	Missense_Mutation	SNP	A	A	G	rs200866084		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:145248876A>G	ENST00000369340.3	+	3	464	c.20A>G	c.(19-21)aAt>aGt	p.N7S	RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.N7S|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.N7S|NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.N7S			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	7	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.N7S(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						ACCTACCACAATGGCACAGGA	0.348																																					p.N7S		Atlas-SNP	.											NOTCH2NL_ENST00000362074,colon,carcinoma,0,2	NOTCH2NL	100	2	2	Substitution - Missense(2)	large_intestine(2)	c.A20G						scavenged	.						11.0	10.0	10.0					1																	145248876		2011	4104	6115	SO:0001583	missense	388677	exon2			ACCACAATGGCAC		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.20A>G	1.37:g.145248876A>G	ENSP00000358346:p.Asn7Ser	Somatic	2693	459	0.170442		WXS	Illumina HiSeq	Phase_I	2613	440	0.168389	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.596096	0.46318	.	.	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	T;T;T	0.63255	-0.03;-0.03;-0.03	3.15	3.15	0.36227	Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.47432	0.1445	L	0.35793	1.09	0.22552	N	0.998997	D;D	0.63880	0.993;0.988	P;P	0.55391	0.775;0.6	T	0.26087	-1.0113	9	0.49607	T	0.09	.	7.9433	0.29971	1.0:0.0:0.0:0.0	.	7;7	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	S	7	ENSP00000354929:N7S;ENSP00000344557:N7S;ENSP00000358346:N7S	ENSP00000344557:N7S	N	+	2	0	NOTCH2NL	143960233	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.487000	0.60293	1.439000	0.47511	0.329000	0.21502	AAT	.	.	weak		0.348	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
DTX1	1840	hgsc.bcm.edu	37	12	113496201	113496201	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:113496201G>A	ENST00000257600.3	+	1	707	c.204G>A	c.(202-204)caG>caA	p.Q68Q		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	68	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TGGACGCCCAGCTTGTGCCCT	0.662																																					p.Q68Q		Atlas-SNP	.											DTX1,NS,lymphoid_neoplasm,+1,1	DTX1	83	1	0			c.G204A						PASS	.						124.0	114.0	117.0					12																	113496201		2203	4300	6503	SO:0001819	synonymous_variant	1840	exon1			CGCCCAGCTTGTG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.204G>A	12.37:g.113496201G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	11	0.34375	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.662	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	rs537300122	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr22:38119902A>G	ENST00000406386.3	+	7	1594	c.1339A>G	c.(1339-1341)Aca>Gca	p.T447A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	447					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T447A(3)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGTAGAGCTACACGAGACAA	0.587													A|||	50	0.00998403	0.0	0.0029	5008	,	,		19561	0.0337		0.0119	False		,,,				2504	0.002				p.T447A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	3	Substitution - Missense(3)	prostate(2)|skin(1)	c.A1339G						scavenged	.						60.0	64.0	63.0					22																	38119902		1870	4095	5965	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1339A>G	22.37:g.38119902A>G	ENSP00000384312:p.Thr447Ala	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	64	5	0.078125	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	5.040	0.193024	0.09599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19806	2.12	2.54	2.54	0.30619	.	.	.	.	.	T	0.23727	0.0574	L	0.36672	1.1	0.19945	N	0.999945	P	0.52463	0.953	P	0.53988	0.739	T	0.07558	-1.0766	9	0.30854	T	0.27	.	6.7436	0.23449	1.0:0.0:0.0:0.0	.	447	Q9H2D6	TARA_HUMAN	A	447	ENSP00000384312:T447A	ENSP00000384312:T447A	T	+	1	0	TRIOBP	36449848	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.062000	0.11674	1.059000	0.40554	0.113000	0.15668	ACA	.	.	none		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
STAT4	6775	hgsc.bcm.edu	37	2	191905872	191905872	+	Silent	SNP	G	G	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:191905872G>T	ENST00000392320.2	-	15	1568	c.1254C>A	c.(1252-1254)ggC>ggA	p.G418G	STAT4_ENST00000358470.4_Silent_p.G418G|STAT4_ENST00000470708.1_5'UTR	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	418					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.G418G(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			CCATGTGACAGCCCTAAGGAA	0.333																																					p.G418G		Atlas-SNP	.											STAT4,rectum,carcinoma,0,1	STAT4	85	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1254A						PASS	.						103.0	97.0	99.0					2																	191905872		2203	4300	6503	SO:0001819	synonymous_variant	6775	exon15			GTGACAGCCCTAA		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"""SH2 domain containing"""	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.1254C>A	2.37:g.191905872G>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	32	0.202532	NM_001243835	Q96NZ6	Silent	SNP	ENST00000392320.2	37	CCDS2310.1																																																																																			.	.	none		0.333	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151	
HRNR	388697	hgsc.bcm.edu	37	1	152186614	152186614	+	Silent	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:152186614C>G	ENST00000368801.2	-	3	7566	c.7491G>C	c.(7489-7491)tcG>tcC	p.S2497S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2497					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCACAGCTCGATGACTGTC	0.557																																					p.S2497S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.G7491C						scavenged	.						1.0	1.0	1.0					1																	152186614		84	271	355	SO:0001819	synonymous_variant	388697	exon3			ACAGCTCGATGAC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7491G>C	1.37:g.152186614C>G		Somatic	616	35	0.0568182		WXS	Illumina HiSeq	Phase_I	546	44	0.0805861	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			.	.	none		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
POM121	9883	hgsc.bcm.edu	37	7	72412427	72412427	+	Missense_Mutation	SNP	G	G	A	rs201876140		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:72412427G>A	ENST00000434423.2	+	11	1895	c.1895G>A	c.(1894-1896)aGc>aAc	p.S632N	POM121_ENST00000257622.4_Missense_Mutation_p.S367N|POM121_ENST00000395270.1_Missense_Mutation_p.S367N|POM121_ENST00000358357.3_Missense_Mutation_p.S367N|POM121_ENST00000446813.1_Missense_Mutation_p.S367N			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	632	Pore side. {ECO:0000255}.				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)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.S367N(2)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				AAGACACCCAGCCTCCTACCC	0.547																																					p.S367N		Atlas-SNP	.											POM121,NS,malignant_melanoma,0,2	POM121	131	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G1100A						scavenged	.						3.0	3.0	3.0					7																	72412427		1270	2943	4213	SO:0001583	missense	9883	exon11			CACCCAGCCTCCT	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.1895G>A	7.37:g.72412427G>A	ENSP00000405562:p.Ser632Asn	Somatic	309	27	0.0873786		WXS	Illumina HiSeq	Phase_I	224	21	0.09375	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	G	7.496	0.651738	0.14516	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.08102	3.13;3.17;3.13;3.17;3.39	2.7	2.7	0.31948	.	0.155531	0.31257	N	0.007975	T	0.09862	0.0242	L	0.58969	1.84	0.43263	D	0.995207	P;P	0.36535	0.557;0.554	B;B	0.35971	0.215;0.157	T	0.12066	-1.0562	10	0.49607	T	0.09	.	10.9555	0.47356	0.0:0.0:1.0:0.0	.	367;632	A8MXF9;Q96HA1	.;P121A_HUMAN	N	367;367;367;367;632	ENSP00000393020:S367N;ENSP00000257622:S367N;ENSP00000378687:S367N;ENSP00000351124:S367N;ENSP00000405562:S632N	ENSP00000257622:S367N	S	+	2	0	POM121	72050363	0.502000	0.26107	0.893000	0.35052	0.018000	0.09664	1.430000	0.34914	1.503000	0.48686	0.173000	0.16961	AGC	.	.	weak		0.547	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
ZNF552	79818	hgsc.bcm.edu	37	19	58320162	58320162	+	Missense_Mutation	SNP	G	G	A	rs576029108	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:58320162G>A	ENST00000391701.1	-	3	639	c.470C>T	c.(469-471)gCg>gTg	p.A157V	ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000599802.1_Intron	NM_024762.3	NP_079038.2	Q9H707	ZN552_HUMAN	zinc finger protein 552	157					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(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		ACACCTCTTCGCAAACAACGC	0.478													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21428	0.0		0.0	False		,,,				2504	0.0				p.A157V		Atlas-SNP	.											ZNF552,NS,carcinoma,+1,1	ZNF552	32	1	0			c.C470T						PASS	.						162.0	155.0	157.0					19																	58320162		2203	4300	6503	SO:0001583	missense	79818	exon3			CTCTTCGCAAACA	AK097041	CCDS12963.1	19q13.43	2013-09-20			ENSG00000178935	ENSG00000178935		"""Zinc fingers, C2H2-type"", ""-"""	26135	protein-coding gene	gene with protein product							Standard	XM_005259267		Approved	FLJ21603	uc002qqg.3	Q9H707	OTTHUMG00000183478	ENST00000391701.1:c.470C>T	19.37:g.58320162G>A	ENSP00000375582:p.Ala157Val	Somatic	462	1	0.0021645		WXS	Illumina HiSeq	Phase_I	302	81	0.268212	NM_024762	B3KUE9|Q6P5A6	Missense_Mutation	SNP	ENST00000391701.1	37	CCDS12963.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.870767	0.00542	.	.	ENSG00000178935	ENST00000391701	T	0.04083	3.71	1.96	-0.803	0.10886	.	.	.	.	.	T	0.01592	0.0051	N	0.04043	-0.29	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46665	-0.9175	9	0.02654	T	1	.	2.7839	0.05368	0.6156:0.0:0.163:0.2214	.	153;157	B7Z1H1;Q9H707	.;ZN552_HUMAN	V	157	ENSP00000375582:A157V	ENSP00000375582:A157V	A	-	2	0	ZNF552	63011974	0.000000	0.05858	0.002000	0.10522	0.029000	0.11900	-0.431000	0.06965	0.022000	0.15160	-1.451000	0.01035	GCG	.	.	none		0.478	ZNF552-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466829.1	NM_024762	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18680514	18680514	+	Splice_Site	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:18680514G>A	ENST00000380548.4	+	11	1680	c.1341G>A	c.(1339-1341)ccG>ccA	p.P447P	ADAMTSL1_ENST00000276935.6_Splice_Site_p.P447P|ADAMTSL1_ENST00000327883.7_Splice_Site_p.P447P|ADAMTSL1_ENST00000380566.4_Silent_p.P430P	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	447	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		AGTGGTCTCCGGTAACTGTGC	0.527																																					p.P447P		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G1341A						PASS	.						116.0	112.0	114.0					9																	18680514		2203	4300	6503	SO:0001630	splice_region_variant	92949	exon11			GTCTCCGGTAACT	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.1341+1G>A	9.37:g.18680514G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	16	0.355556	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			.	.	none		0.527	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		Silent
CBWD3	445571	hgsc.bcm.edu	37	9	70871836	70871836	+	Splice_Site	SNP	C	C	G	rs376362566		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:70871836C>G	ENST00000360171.6	+	5	981		c.e5-1		CBWD3_ENST00000377342.5_Intron	NM_201453.2	NP_958861.2	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3								ATP binding (GO:0005524)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TATATTTTCACGTGCAGTGGC	0.289																																					.		Atlas-SNP	.											CBWD3,rectum,carcinoma,-1,1	CBWD3	10	1	0			c.431-1C>G						scavenged	.						25.0	31.0	29.0					9																	70871836		2190	4250	6440	SO:0001630	splice_region_variant	445571	exon5			TTTTCACGTGCAG	BC069006	CCDS35038.1, CCDS35038.2	9q13	2014-05-06			ENSG00000196873	ENSG00000196873			18519	protein-coding gene	gene with protein product		611080				15233989, 12421752	Standard	XM_005277637		Approved	bA561O23.1	uc004aga.4	Q5JTY5	OTTHUMG00000184383	ENST00000360171.6:c.431-1C>G	9.37:g.70871836C>G		Somatic	1307	15	0.0114767		WXS	Illumina HiSeq	Phase_I	1156	18	0.0155709	NM_201453	B4DNG9|Q6VB91	Splice_Site	SNP	ENST00000360171.6	37	CCDS35038.1	.	.	.	.	.	.	.	.	.	.	c	14.78	2.637800	0.47049	.	.	ENSG00000196873	ENST00000360171;ENST00000447896;ENST00000455061;ENST00000455820;ENST00000377344	.	.	.	3.38	3.38	0.38709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.714	0.51641	0.0:0.1812:0.8188:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBWD3	70061656	1.000000	0.71417	0.991000	0.47740	0.802000	0.45316	7.061000	0.76699	0.543000	0.28864	-0.676000	0.03789	.	C|0.500;G|0.500	0.500	weak		0.289	CBWD3-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052526.1	NM_201453	Intron
REPS1	85021	hgsc.bcm.edu	37	6	139262508	139262508	+	Silent	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:139262508A>G	ENST00000450536.2	-	8	1673	c.1099T>C	c.(1099-1101)Tta>Cta	p.L367L	REPS1_ENST00000409812.2_Silent_p.L367L|REPS1_ENST00000367663.4_Silent_p.L367L|REPS1_ENST00000415951.2_Silent_p.L367L|REPS1_ENST00000258062.5_Silent_p.L367L			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	367	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		TTGGGCATTAAGCTTTCAGGA	0.398																																					p.L367L		Atlas-SNP	.											.	REPS1	58	.	0			c.T1099C						PASS	.						177.0	180.0	179.0					6																	139262508		2203	4300	6503	SO:0001819	synonymous_variant	85021	exon8			GCATTAAGCTTTC		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1099T>C	6.37:g.139262508A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	69	51	0.73913	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Silent	SNP	ENST00000450536.2	37																																																																																				.	.	none		0.398	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3		
OR8K5	219453	hgsc.bcm.edu	37	11	55927085	55927085	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:55927085C>G	ENST00000313447.1	-	1	708	c.709G>C	c.(709-711)Gct>Cct	p.A237P		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A237T(1)		large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				GTGGAGAAAGCCTTTTTCCTG	0.408																																					p.A237P		Atlas-SNP	.											OR8K5,NS,carcinoma,0,2	OR8K5	82	2	1	Substitution - Missense(1)	lung(1)	c.G709C						PASS	.						85.0	80.0	82.0					11																	55927085		2201	4296	6497	SO:0001583	missense	219453	exon1			AGAAAGCCTTTTT	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.709G>C	11.37:g.55927085C>G	ENSP00000323853:p.Ala237Pro	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	143	16	0.111888	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	c	14.32	2.500187	0.44455	.	.	ENSG00000181752	ENST00000313447	T	0.00363	7.83	3.98	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.351885	0.24431	N	0.038600	T	0.01592	0.0051	H	0.99454	4.575	0.32250	N	0.571499	D	0.69078	0.997	D	0.67231	0.95	T	0.02766	-1.1113	10	0.87932	D	0	.	11.6173	0.51096	0.1805:0.8195:0.0:0.0	.	237	Q8NH50	OR8K5_HUMAN	P	237	ENSP00000323853:A237P	ENSP00000323853:A237P	A	-	1	0	OR8K5	55683661	0.994000	0.37717	0.954000	0.39281	0.155000	0.21991	3.064000	0.49986	1.019000	0.39547	-0.377000	0.06932	GCT	.	.	none		0.408	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
PER1	5187	hgsc.bcm.edu	37	17	8053822	8053822	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:8053822C>T	ENST00000317276.4	-	2	440	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	PER1_ENST00000354903.5_Missense_Mutation_p.R52Q|PER1_ENST00000581082.1_Missense_Mutation_p.R68Q	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	68	Interaction with BTRC. {ECO:0000269|PubMed:15917222}.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GTGTGAGCTCCGCTGAGATGC	0.582			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes																													p.R68Q		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.G203A						PASS	.						114.0	103.0	106.0					17																	8053822		2203	4300	6503	SO:0001583	missense	5187	exon2			GAGCTCCGCTGAG	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.203G>A	17.37:g.8053822C>T	ENSP00000314420:p.Arg68Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013101	0.54468	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.36699	2.65;1.24	5.16	3.97	0.46021	.	0.063176	0.64402	D	0.000013	T	0.14013	0.0339	N	0.11064	0.09	0.38309	D	0.943193	B;P;B	0.48640	0.028;0.913;0.44	B;B;B	0.36378	0.006;0.223;0.022	T	0.06789	-1.0807	10	0.13470	T	0.59	-18.8514	7.9228	0.29857	0.0:0.8031:0.0:0.1969	.	68;52;68	Q6IN51;B4DI49;O15534	.;.;PER1_HUMAN	Q	68;52	ENSP00000314420:R68Q;ENSP00000346979:R52Q	ENSP00000314420:R68Q	R	-	2	0	PER1	7994547	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	1.762000	0.38451	2.405000	0.81733	0.563000	0.77884	CGG	.	.	none		0.582	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
BNC2	54796	hgsc.bcm.edu	37	9	16727796	16727796	+	Splice_Site	SNP	T	T	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:16727796T>A	ENST00000380672.4	-	3	386	c.329A>T	c.(328-330)cAg>cTg	p.Q110L	BNC2_ENST00000380666.2_Splice_Site_p.Q110L|BNC2_ENST00000545497.1_Intron|BNC2_ENST00000380667.2_Intron|RP11-62F24.2_ENST00000450445.1_RNA	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GTAACTTACCTGTTGGGACAT	0.373																																					p.Q110L		Atlas-SNP	.											.	BNC2	166	.	0			c.A329T						PASS	.						176.0	168.0	171.0					9																	16727796		2203	4300	6503	SO:0001630	splice_region_variant	54796	exon3			CTTACCTGTTGGG	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.330+1A>T	9.37:g.16727796T>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089390	0.76756	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000456672;ENST00000436939;ENST00000380666;ENST00000540340	T;T;T	0.04015	3.73;3.73;3.73	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.17066	0.0410	L	0.47716	1.5	0.80722	D	1	D;D;D;D	0.63046	0.992;0.981;0.967;0.967	D;D;P;D	0.72982	0.979;0.969;0.901;0.932	T	0.00071	-1.2131	10	0.72032	D	0.01	-18.987	16.8222	0.85835	0.0:0.0:0.0:1.0	.	110;110;68;110	Q06HC4;Q6ZN30-2;Q5H9S4;Q6ZN30	.;.;.;BNC2_HUMAN	L	110;67;110;110;110;110	ENSP00000370047:Q110L;ENSP00000408370:Q67L;ENSP00000370041:Q110L	ENSP00000370041:Q110L	Q	-	2	0	BNC2	16717796	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.470000	0.80973	2.371000	0.80710	0.533000	0.62120	CAG	.	.	none		0.373	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	Missense_Mutation
C1S	716	hgsc.bcm.edu	37	12	7172542	7172542	+	Missense_Mutation	SNP	G	G	A	rs147341600		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:7172542G>A	ENST00000406697.1	+	9	1284	c.656G>A	c.(655-657)cGg>cAg	p.R219Q	C1S_ENST00000402681.3_Missense_Mutation_p.R52Q|C1S_ENST00000360817.5_Missense_Mutation_p.R219Q|C1S_ENST00000328916.3_Missense_Mutation_p.R219Q			P09871	C1S_HUMAN	complement component 1, s subcomponent	219	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GTGACCTTGCGGAGAGAAGAT	0.468																																					p.R219Q	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G656A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	135.0	138.0	137.0		656,656	-2.4	0.1	12	dbSNP_134	137	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	C1S	NM_001734.3,NM_201442.2	43,43	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign,benign	219/689,219/689	7172542	3,13003	2203	4300	6503	SO:0001583	missense	716	exon6			CCTTGCGGAGAGA		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.656G>A	12.37:g.7172542G>A	ENSP00000385035:p.Arg219Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	129	20	0.155039	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	0.179	-1.063860	0.01934	0.0	3.49E-4	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000402681;ENST00000542978	T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29	6.17	-2.39	0.06602	CUB (5);	0.630882	0.13151	N	0.409855	T	0.07279	0.0184	N	0.12611	0.24	0.09310	N	1	B	0.18013	0.025	B	0.14023	0.01	T	0.40194	-0.9576	10	0.02654	T	1	.	12.9992	0.58666	0.6693:0.0:0.3307:0.0	.	219	P09871	C1S_HUMAN	Q	219;219;219;52;52	ENSP00000385035:R219Q;ENSP00000328173:R219Q;ENSP00000354057:R219Q;ENSP00000384171:R52Q;ENSP00000442298:R52Q	ENSP00000328173:R219Q	R	+	2	0	C1S	7042803	0.001000	0.12720	0.060000	0.19600	0.161000	0.22273	-0.248000	0.08854	-0.286000	0.09076	-0.345000	0.07892	CGG	G|1.000;A|0.000	0.000	weak		0.468	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
RGPD4	285190	hgsc.bcm.edu	37	2	108443536	108443536	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:108443536C>G	ENST00000408999.3	+	1	144	c.67C>G	c.(67-69)Cga>Gga	p.R23G	AC096655.2_ENST00000457647.2_lincRNA|RGPD4_ENST00000354986.4_Missense_Mutation_p.R23G	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	23					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						CCCGTCGCCTCGAAAGGTGAG	0.701																																					p.R23G		Atlas-SNP	.											RGPD4,caecum,carcinoma,-1,1	RGPD4	112	1	0			c.C67G						scavenged	.						44.0	61.0	56.0					2																	108443536		692	1591	2283	SO:0001583	missense	285190	exon1			TCGCCTCGAAAGG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.67C>G	2.37:g.108443536C>G	ENSP00000386810:p.Arg23Gly	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	138	2	0.0144928	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	0.319	-0.963323	0.02249	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.41065	1.01;1.01	2.33	1.42	0.22433	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.22666	0.0547	L	0.33485	1.01	0.09310	N	1	D	0.52996	0.957	B	0.30251	0.113	T	0.10109	-1.0644	9	0.51188	T	0.08	-2.4203	7.0687	0.25167	0.4799:0.5201:0.0:0.0	.	23	Q7Z3J3	RGPD4_HUMAN	G	23	ENSP00000347081:R23G;ENSP00000386810:R23G	ENSP00000347081:R23G	R	+	1	2	RGPD4	107809968	0.670000	0.27512	0.021000	0.16686	0.002000	0.02628	0.784000	0.26816	0.094000	0.17404	-1.276000	0.01395	CGA	.	.	none		0.701	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
TAPT1	202018	hgsc.bcm.edu	37	4	16165144	16165144	+	Silent	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:16165144T>C	ENST00000405303.2	-	14	1574	c.1491A>G	c.(1489-1491)gaA>gaG	p.E497E	TAPT1_ENST00000304584.8_3'UTR|TAPT1_ENST00000399920.3_Silent_p.E386E	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	497					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)			NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						CAGACAGGTTTTCTTCTGTGG	0.348																																					p.E497E		Atlas-SNP	.											.	TAPT1	31	.	0			c.A1491G						PASS	.						63.0	59.0	60.0					4																	16165144		1856	4112	5968	SO:0001819	synonymous_variant	202018	exon14			CAGGTTTTCTTCT	AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.1491A>G	4.37:g.16165144T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	177	43	0.242938	NM_153365	Q8N2S3|Q9NZK9	Silent	SNP	ENST00000405303.2	37	CCDS47030.1																																																																																			.	.	none		0.348	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365	
GPATCH4	54865	hgsc.bcm.edu	37	1	156565049	156565049	+	Missense_Mutation	SNP	A	A	C	rs77528517|rs72559129	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:156565049A>C	ENST00000438976.2	-	8	1114	c.1084T>G	c.(1084-1086)Ttt>Gtt	p.F362V	GPATCH4_ENST00000368232.4_Missense_Mutation_p.F357V|GPATCH4_ENST00000497287.1_5'Flank			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	357							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CACCACCTAAAAGTTTCCTCA	0.507																																					p.F362V		Atlas-SNP	.											.	GPATCH4	34	.	0			c.T1084G						PASS	.						192.0	192.0	192.0					1																	156565049		2203	4300	6503	SO:0001583	missense	54865	exon8			ACCTAAAAGTTTC	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"""G patch domain containing"""	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.1084T>G	1.37:g.156565049A>C	ENSP00000396441:p.Phe362Val	Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	280	14	0.05	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	37	CCDS44245.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.368|0.368	-0.935701|-0.935701	0.02340|0.02340	.|.	.|.	ENSG00000160818|ENSG00000160818	ENST00000368229|ENST00000368232;ENST00000438976	.|.	.|.	.|.	3.86|3.86	-2.77|-2.77	0.05877|0.05877	.|.	.|.	.|.	.|.	.|.	.|T	.|0.03220	.|0.0094	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.13594	.|0.008	.|B	.|0.14023	.|0.01	.|T	.|0.41980	.|-0.9478	.|7	.|0.02654	.|T	.|1	.|.	6.2915|6.2915	0.21063|0.21063	0.4516:0.0:0.4207:0.1278|0.4516:0.0:0.4207:0.1278	.|.	.|362	.|E9PAV9	.|.	.|V	-1|357;362	.|.	.|ENSP00000357215:F357V	.|F	-|-	.|1	.|0	GPATCH4|GPATCH4	154831673|154831673	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.008000|0.008000	0.06430|0.06430	0.130000|0.130000	0.15850|0.15850	-0.571000|-0.571000	0.06014|0.06014	-0.379000|-0.379000	0.06801|0.06801	.|TTT	A|0.333;C|0.333;G|0.333	0.333	strong		0.507	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725	
FAM181B	220382	hgsc.bcm.edu	37	11	82444591	82444591	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:82444591C>T	ENST00000329203.3	-	1	315	c.181G>A	c.(181-183)Gag>Aag	p.E61K		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	61										large_intestine(1)|lung(2)|prostate(1)	4						CGGGTGGCCTCGCGCACGTCC	0.662																																					p.E61K		Atlas-SNP	.											.	FAM181B	14	.	0			c.G181A						PASS	.						25.0	22.0	23.0					11																	82444591		2202	4300	6502	SO:0001583	missense	220382	exon1			TGGCCTCGCGCAC	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.181G>A	11.37:g.82444591C>T	ENSP00000365295:p.Glu61Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	42	0.65625	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253538	0.59212	.	.	ENSG00000182103	ENST00000329203	T	0.34275	1.37	3.79	2.88	0.33553	.	0.080008	0.48767	N	0.000165	T	0.31263	0.0791	L	0.50333	1.59	0.50632	D	0.999889	P	0.45902	0.868	B	0.40677	0.337	T	0.05468	-1.0883	9	.	.	.	.	11.2366	0.48944	0.0:0.9085:0.0:0.0915	.	61	A6NEQ2	F181B_HUMAN	K	61	ENSP00000365295:E61K	.	E	-	1	0	FAM181B	82122239	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	6.310000	0.72830	0.794000	0.33899	-0.391000	0.06502	GAG	.	.	none		0.662	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
SRPR	6734	hgsc.bcm.edu	37	11	126134971	126134971	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:126134971G>A	ENST00000332118.6	-	11	1562	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	SRPR_ENST00000530680.1_5'Flank|SRPR_ENST00000532259.1_Missense_Mutation_p.R442W	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	470					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		CTCAAACGCCGGGTGTGTGTA	0.542																																					p.R470W		Atlas-SNP	.											.	SRPR	60	.	0			c.C1408T						PASS	.						67.0	61.0	63.0					11																	126134971		2201	4299	6500	SO:0001583	missense	6734	exon11			AACGCCGGGTGTG	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1408C>T	11.37:g.126134971G>A	ENSP00000328023:p.Arg470Trp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	17	0.25	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	37	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	G	34	5.364665	0.95877	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	5.26	5.26	0.73747	ATPase, AAA+ type, core (1);Signal recognition particle, SRP54 subunit, GTPase (2);	0.112768	0.64402	D	0.000006	D	0.85596	0.5733	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.88160	0.2857	9	0.87932	D	0	-12.8572	19.0619	0.93096	0.0:0.0:1.0:0.0	.	442;470	E9PJS4;P08240	.;SRPR_HUMAN	W	470;442	.	ENSP00000328023:R470W	R	-	1	2	SRPR	125640181	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.411000	0.97342	2.744000	0.94065	0.650000	0.86243	CGG	.	.	none		0.542	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
LMNB1	4001	hgsc.bcm.edu	37	5	126113530	126113530	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:126113530C>T	ENST00000261366.5	+	1	691	c.330C>T	c.(328-330)tgC>tgT	p.C110C	LMNB1_ENST00000395354.1_Silent_p.C110C|RP11-434D11.4_ENST00000509185.2_lincRNA|LMNB1_ENST00000460265.1_3'UTR	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	110	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	lamin filament (GO:0005638)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		TGGGCAAGTGCAAGGCGGAAC	0.711																																					p.C110C		Atlas-SNP	.											.	LMNB1	49	.	0			c.C330T						PASS	.						4.0	4.0	4.0					5																	126113530		1956	3851	5807	SO:0001819	synonymous_variant	4001	exon1			CAAGTGCAAGGCG	L37737	CCDS4140.1	5q23.2	2013-01-16			ENSG00000113368	ENSG00000113368		"""Intermediate filaments type V, lamins"""	6637	protein-coding gene	gene with protein product		150340				7557986, 8838815	Standard	NM_005573		Approved		uc003kud.2	P20700	OTTHUMG00000128969	ENST00000261366.5:c.330C>T	5.37:g.126113530C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_005573	B2R6J6|Q3SYN7|Q96EI6	Silent	SNP	ENST00000261366.5	37	CCDS4140.1																																																																																			.	.	none		0.711	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573	
SEC24B	10427	hgsc.bcm.edu	37	4	110384430	110384430	+	Silent	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:110384430T>C	ENST00000265175.5	+	2	562	c.507T>C	c.(505-507)tcT>tcC	p.S169S	SEC24B_ENST00000504968.2_Silent_p.S200S|SEC24B_ENST00000399100.2_Silent_p.S169S	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	169					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CTGCCAGCTCTTCTGTTGCGT	0.478																																					p.S169S		Atlas-SNP	.											.	SEC24B	186	.	0			c.T507C						PASS	.						328.0	314.0	318.0					4																	110384430		2031	4188	6219	SO:0001819	synonymous_variant	10427	exon2			CAGCTCTTCTGTT	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.507T>C	4.37:g.110384430T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	187	38	0.203209	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	37	CCDS47124.1																																																																																			.	.	none		0.478	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
PYDC1	260434	hgsc.bcm.edu	37	16	31230671	31230671	+	5'Flank	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:31230671T>C	ENST00000302964.3	-	0	0				TRIM72_ENST00000322122.3_Missense_Mutation_p.L183P|PYDC1_ENST00000568383.1_5'Flank	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1						innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CGGGTGTTCCTGGCTGCACTG	0.652																																					p.L183P		Atlas-SNP	.											.	TRIM72	32	.	0			c.T548C						PASS	.						51.0	54.0	53.0					16																	31230671		2197	4299	6496	SO:0001631	upstream_gene_variant	493829	exon4			TGTTCCTGGCTGC		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"""pyrin domain containing 1"""			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407		16.37:g.31230671T>C	Exception_encountered	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	62	11	0.177419	NM_001008274	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	37	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.242510	0.79912	.	.	ENSG00000177238	ENST00000322122	T	0.72725	-0.68	5.37	5.37	0.77165	.	0.117745	0.36893	N	0.002344	T	0.80470	0.4629	M	0.61703	1.905	0.80722	D	1	D	0.71674	0.998	P	0.62649	0.905	T	0.82806	-0.0275	10	0.87932	D	0	.	14.3504	0.66697	0.0:0.0:0.0:1.0	.	183	Q6ZMU5	TRI72_HUMAN	P	183	ENSP00000312675:L183P	ENSP00000312675:L183P	L	+	2	0	TRIM72	31138172	1.000000	0.71417	0.996000	0.52242	0.745000	0.42441	4.888000	0.63164	2.024000	0.59613	0.533000	0.62120	CTG	.	.	none		0.652	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901	
UAP1	6675	hgsc.bcm.edu	37	1	162560143	162560143	+	Missense_Mutation	SNP	A	A	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:162560143A>T	ENST00000367925.1	+	7	1232	c.1200A>T	c.(1198-1200)gaA>gaT	p.E400D	UAP1_ENST00000367924.1_Missense_Mutation_p.E400D|UAP1_ENST00000271469.3_Missense_Mutation_p.E400D|RP11-359K18.4_ENST00000609669.1_RNA|UAP1_ENST00000367926.4_Missense_Mutation_p.E400D			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	400					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|UDP-N-acetylglucosamine diphosphorylase activity (GO:0003977)			breast(2)|cervix(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)|skin(2)|stomach(1)	22	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TATTGCGAGAAGATGAGTTTT	0.408																																					p.E400D		Atlas-SNP	.											UAP1,NS,carcinoma,0,1	UAP1	47	1	0			c.A1200T						scavenged	.						186.0	180.0	182.0					1																	162560143		2203	4300	6503	SO:0001583	missense	6675	exon8			GCGAGAAGATGAG	AB011004	CCDS1240.1	1q23.2	2014-07-31	2014-07-31		ENSG00000117143	ENSG00000117143	2.7.7.23		12457	protein-coding gene	gene with protein product		602862		SPAG2		9603950, 8025165	Standard	NM_003115		Approved	AGX1, AgX	uc001gce.4	Q16222	OTTHUMG00000034419	ENST00000367925.1:c.1200A>T	1.37:g.162560143A>T	ENSP00000356902:p.Glu400Asp	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	172	4	0.0232558	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Missense_Mutation	SNP	ENST00000367925.1	37		.	.	.	.	.	.	.	.	.	.	A	17.86	3.491783	0.64074	.	.	ENSG00000117143	ENST00000367926;ENST00000271469;ENST00000367925;ENST00000367924	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	4.93	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.08492	0.0211	L	0.60067	1.865	0.48975	D	0.999737	B	0.29136	0.234	B	0.37989	0.262	T	0.14392	-1.0474	9	0.33940	T	0.23	-30.3462	5.911	0.19029	0.7288:0.0:0.2712:0.0	.	400	Q16222-2	.	D	400	ENSP00000356903:E400D;ENSP00000271469:E400D;ENSP00000356902:E400D;ENSP00000356901:E400D	ENSP00000271469:E400D	E	+	3	2	UAP1	160826767	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.324000	0.43831	0.921000	0.36994	0.533000	0.62120	GAA	.	.	none		0.408	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115	
BTG2	7832	hgsc.bcm.edu	37	1	203274827	203274827	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:203274827C>G	ENST00000290551.4	+	1	164	c.93C>G	c.(91-93)agC>agG	p.S31R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	31					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)			GCTGCGTGAGCGAGCAGAGGC	0.711																																					p.S31R		Atlas-SNP	.											.	BTG2	16	.	0			c.C93G						PASS	.						16.0	16.0	16.0					1																	203274827		2157	4235	6392	SO:0001583	missense	7832	exon1			CGTGAGCGAGCAG		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.93C>G	1.37:g.203274827C>G	ENSP00000290551:p.Ser31Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	13	0.19697	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.683961	0.47991	.	.	ENSG00000159388	ENST00000290551	T	0.23754	1.89	4.66	3.75	0.43078	Anti-proliferative protein (3);	0.175253	0.47455	D	0.000221	T	0.26304	0.0642	L	0.59436	1.845	0.37789	D	0.92728	B	0.16802	0.019	B	0.28916	0.096	T	0.14980	-1.0453	10	0.54805	T	0.06	-0.1987	7.4459	0.27211	0.0:0.7394:0.1689:0.0917	.	31	P78543	BTG2_HUMAN	R	31	ENSP00000290551:S31R	ENSP00000290551:S31R	S	+	3	2	BTG2	201541450	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	0.692000	0.25482	1.191000	0.43056	0.478000	0.44815	AGC	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
LAMB1	3912	hgsc.bcm.edu	37	7	107603364	107603364	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:107603364G>A	ENST00000222399.6	-	15	2073	c.1843C>T	c.(1843-1845)Cgc>Tgc	p.R615C	LAMB1_ENST00000393561.1_Missense_Mutation_p.R639C|LAMB1_ENST00000393560.1_Missense_Mutation_p.R615C	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	615	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)	p.R615C(1)		NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GGCTCGTAGCGAATTAGGATG	0.453																																					p.R615C		Atlas-SNP	.											LAMB1,NS,carcinoma,0,1	LAMB1	185	1	1	Substitution - Missense(1)	lung(1)	c.C1843T						scavenged	.						83.0	83.0	83.0					7																	107603364		2203	4300	6503	SO:0001583	missense	3912	exon15			CGTAGCGAATTAG	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1843C>T	7.37:g.107603364G>A	ENSP00000222399:p.Arg615Cys	Somatic	216	2	0.00925926		WXS	Illumina HiSeq	Phase_I	203	51	0.251232	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688937	0.68271	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.52295	0.82;0.83;0.67	4.72	4.72	0.59763	Laminin IV (1);	.	.	.	.	T	0.68485	0.3006	M	0.77103	2.36	0.80722	D	1	D;P;B	0.89917	1.0;0.682;0.296	D;B;B	0.63488	0.915;0.107;0.055	T	0.74714	-0.3572	9	0.87932	D	0	.	17.7011	0.88295	0.0:0.0:1.0:0.0	.	615;615;639	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	C	639;615;615	ENSP00000377191:R639C;ENSP00000222399:R615C;ENSP00000377190:R615C	ENSP00000222399:R615C	R	-	1	0	LAMB1	107390600	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.480000	0.81109	2.181000	0.69327	0.563000	0.77884	CGC	.	.	none		0.453	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
PCDHB5	26167	hgsc.bcm.edu	37	5	140517068	140517068	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:140517068G>A	ENST00000231134.5	+	1	2269	c.2052G>A	c.(2050-2052)tcG>tcA	p.S684S		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	684					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCCGACTCGCTCACTGTCT	0.697																																					p.S684S		Atlas-SNP	.											PCDHB5,NS,carcinoma,+1,1	PCDHB5	184	1	0			c.G2052A						PASS	.						68.0	72.0	70.0					5																	140517068		2199	4295	6494	SO:0001819	synonymous_variant	26167	exon1			CGACTCGCTCACT	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2052G>A	5.37:g.140517068G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	37	CCDS4247.1																																																																																			.	.	none		0.697	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455866	5455866	+	Missense_Mutation	SNP	G	G	A	rs375118147		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:5455866G>A	ENST00000222033.4	+	1	441	c.364G>A	c.(364-366)Gtc>Atc	p.V122I		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	122						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		GCTGTTCGGCGTCCCCCTGGC	0.682																																					p.V122I		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G364A						PASS	.	G	ILE/VAL	0,4210		0,0,2105	47.0	55.0	53.0		364	-0.8	0.0	19		53	1,8419		0,1,4209	no	missense	ZNRF4	NM_181710.3	29	0,1,6314	AA,AG,GG		0.0119,0.0,0.0079	benign	122/430	5455866	1,12629	2105	4210	6315	SO:0001583	missense	148066	exon1			TTCGGCGTCCCCC	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.364G>A	19.37:g.5455866G>A	ENSP00000222033:p.Val122Ile	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	26	7	0.269231	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	.	.	.	.	.	.	.	.	.	.	G	2.855	-0.237362	0.05944	0.0	1.19E-4	ENSG00000105428	ENST00000222033	T	0.04862	3.54	4.55	-0.827	0.10802	.	0.557882	0.16640	U	0.205677	T	0.04048	0.0113	L	0.40543	1.245	0.09310	N	1	B	0.30211	0.273	B	0.17722	0.019	T	0.35943	-0.9768	10	0.37606	T	0.19	.	3.753	0.08573	0.0962:0.4131:0.3402:0.1505	.	122	Q8WWF5	ZNRF4_HUMAN	I	122	ENSP00000222033:V122I	ENSP00000222033:V122I	V	+	1	0	ZNRF4	5406866	0.073000	0.21202	0.001000	0.08648	0.045000	0.14185	0.594000	0.24014	0.004000	0.14682	-0.424000	0.05967	GTC	.	.	weak		0.682	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
MAP1B	4131	hgsc.bcm.edu	37	5	71492363	71492363	+	Missense_Mutation	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:71492363C>A	ENST00000296755.7	+	5	3479	c.3181C>A	c.(3181-3183)Cag>Aag	p.Q1061K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1061					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGCCGAGGAGCAGTATGGATT	0.527																																					p.Q1061K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C3181A						PASS	.						102.0	106.0	104.0					5																	71492363		2203	4300	6503	SO:0001583	missense	4131	exon5			GAGGAGCAGTATG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3181C>A	5.37:g.71492363C>A	ENSP00000296755:p.Gln1061Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	0.783	-0.761567	0.02996	.	.	ENSG00000131711	ENST00000296755	T	0.03386	3.95	5.86	4.91	0.64330	.	0.186043	0.38164	N	0.001796	T	0.01730	0.0055	N	0.01874	-0.695	0.33778	D	0.623966	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44651	-0.9314	10	0.12430	T	0.62	-19.5589	13.6838	0.62504	0.2629:0.7371:0.0:0.0	.	935;1061	A2BDK6;P46821	.;MAP1B_HUMAN	K	1061	ENSP00000296755:Q1061K	ENSP00000296755:Q1061K	Q	+	1	0	MAP1B	71528119	0.918000	0.31147	0.998000	0.56505	0.626000	0.37791	1.922000	0.40045	2.784000	0.95788	0.655000	0.94253	CAG	.	.	none		0.527	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
CTSC	1075	hgsc.bcm.edu	37	11	88070757	88070757	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:88070757G>A	ENST00000227266.5	-	1	198	c.84C>T	c.(82-84)gcC>gcT	p.A28A	CTSC_ENST00000393301.4_5'UTR|CTSC_ENST00000524463.1_Silent_p.A28A|CTSC_ENST00000529974.1_Silent_p.A28A	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	28					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGGTGCAGTTGGCAGGTGTGT	0.667																																					p.A28A		Atlas-SNP	.											.	CTSC	46	.	0			c.C84T						PASS	.						19.0	19.0	19.0					11																	88070757		2196	4287	6483	SO:0001819	synonymous_variant	1075	exon1			GCAGTTGGCAGGT	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.84C>T	11.37:g.88070757G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	194	23	0.118557	NM_148170	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Silent	SNP	ENST00000227266.5	37	CCDS8282.1																																																																																			.	.	none		0.667	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
ABCG4	64137	hgsc.bcm.edu	37	11	119031694	119031694	+	Nonsense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:119031694C>T	ENST00000449422.2	+	15	2007	c.1819C>T	c.(1819-1821)Cga>Tga	p.R607*	ABCG4_ENST00000531739.1_Nonsense_Mutation_p.R607*|ABCG4_ENST00000307417.3_Nonsense_Mutation_p.R607*	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	607	ABC transmembrane type-2.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		GAGCATCCTCCGAGCGCTGGA	0.577																																					p.R607X		Atlas-SNP	.											.	ABCG4	77	.	0			c.C1819T						PASS	.						109.0	95.0	99.0					11																	119031694		2200	4295	6495	SO:0001587	stop_gained	64137	exon15			ATCCTCCGAGCGC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1819C>T	11.37:g.119031694C>T	ENSP00000406874:p.Arg607*	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	164	41	0.25	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Nonsense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	C	40	8.193064	0.98699	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	.	.	.	5.42	5.42	0.78866	.	0.245301	0.41605	D	0.000850	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-1.6587	14.8887	0.70590	0.144:0.856:0.0:0.0	.	.	.	.	X	607	.	ENSP00000304111:R607X	R	+	1	2	ABCG4	118536904	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	3.098000	0.50259	2.552000	0.86080	0.561000	0.74099	CGA	.	.	none		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
GUF1	60558	hgsc.bcm.edu	37	4	44680787	44680787	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:44680787A>G	ENST00000281543.5	+	1	342	c.148A>G	c.(148-150)Agc>Ggc	p.S50G	GUF1_ENST00000506793.1_Intron	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						CAGGCTCTACAGCTCCGCAGA	0.622																																					p.S50G		Atlas-SNP	.											.	GUF1	72	.	0			c.A148G						PASS	.						13.0	15.0	15.0					4																	44680787		2199	4292	6491	SO:0001583	missense	60558	exon1			CTCTACAGCTCCG		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.148A>G	4.37:g.44680787A>G	ENSP00000281543:p.Ser50Gly	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	242	37	0.152893	NM_021927		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607169	0.28623	.	.	ENSG00000151806	ENST00000281543	T	0.70164	-0.46	4.01	-5.1	0.02911	.	1.118960	0.06514	N	0.738611	T	0.36026	0.0952	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.09207	-1.0685	10	0.32370	T	0.25	0.5496	0.4147	0.00447	0.2657:0.1519:0.2865:0.296	.	50	Q8N442	GUF1_HUMAN	G	50	ENSP00000281543:S50G	ENSP00000281543:S50G	S	+	1	0	GUF1	44375544	0.004000	0.15560	0.002000	0.10522	0.081000	0.17604	-0.295000	0.08298	-0.969000	0.03573	0.533000	0.62120	AGC	.	.	none		0.622	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33041313	33041313	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:33041313G>C	ENST00000419277.1	-	2	164	c.35C>G	c.(34-36)gCt>gGt	p.A12G	HLA-DPB1_ENST00000418931.2_5'Flank|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.A12G|HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPB1_ENST00000535465.1_5'Flank	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	12					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CAAGATCACAGCTCTGATATG	0.557																																					p.A12G		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C35G						PASS	.						191.0	175.0	181.0					6																	33041313		1511	2709	4220	SO:0001583	missense	3113	exon1			ATCACAGCTCTGA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.35C>G	6.37:g.33041313G>C	ENSP00000393566:p.Ala12Gly	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582133	0.28180	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337;ENST00000417724	T;T;T	0.02656	4.56;4.56;4.21	4.1	1.19	0.21007	.	0.640274	0.14756	U	0.300279	T	0.00875	0.0029	L	0.41710	1.295	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.47235	-0.9133	10	0.87932	D	0	.	3.6194	0.08090	0.2214:0.0:0.5695:0.2091	.	12	P20036	DPA1_HUMAN	G	12	ENSP00000393566:A12G;ENSP00000402872:A12G;ENSP00000390929:A12G	ENSP00000398134:A12G	A	-	2	0	HLA-DPA1	33149291	0.000000	0.05858	0.000000	0.03702	0.126000	0.20510	-0.331000	0.07914	-0.010000	0.14271	-0.148000	0.13756	GCT	.	.	none		0.557	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85459141	85459141	+	Silent	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:85459141T>G	ENST00000393217.2	+	9	2554	c.2493T>G	c.(2491-2493)acT>acG	p.T831T		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	831										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GTGGATTAACTTCTTTGCACA	0.363																																					p.T831T		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.T2493G						PASS	.						126.0	121.0	123.0					12																	85459141		2203	4300	6503	SO:0001819	synonymous_variant	84125	exon9			ATTAACTTCTTTG	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.2493T>G	12.37:g.85459141T>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	96	28	0.291667	NM_001079910	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	37	CCDS41816.1																																																																																			.	.	none		0.363	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
TPTE2	93492	hgsc.bcm.edu	37	13	20056679	20056679	+	Missense_Mutation	SNP	T	T	G	rs200244531		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr13:20056679T>G	ENST00000400230.2	-	4	172	c.128A>C	c.(127-129)gAa>gCa	p.E43A	TPTE2_ENST00000382977.4_Missense_Mutation_p.E43A|TPTE2_ENST00000382975.4_Missense_Mutation_p.E43A|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000382978.1_Missense_Mutation_p.E43A|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000457266.2_Missense_Mutation_p.E43A|TPTE2_ENST00000400103.2_Missense_Mutation_p.E43A			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	43					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.E43A(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GGAAAGTCGTTCTAACATACT	0.313																																					p.E43A		Atlas-SNP	.											TPTE2_ENST00000400230,NS,carcinoma,0,1	TPTE2	225	1	1	Substitution - Missense(1)	kidney(1)	c.A128C						scavenged	.						52.0	51.0	51.0					13																	20056679		2201	4299	6500	SO:0001583	missense	93492	exon5			AGTCGTTCTAACA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.128A>C	13.37:g.20056679T>G	ENSP00000383089:p.Glu43Ala	Somatic	346	3	0.00867052		WXS	Illumina HiSeq	Phase_I	234	6	0.025641	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	T	2.387	-0.340821	0.05243	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548	D;D;D;D;D;D	0.94931	-3.56;-3.53;-3.47;-3.47;-3.56;-3.53	2.06	0.858	0.19030	.	0.878504	0.09602	U	0.780065	D	0.86159	0.5866	N	0.21448	0.665	0.09310	N	1	B;B	0.28850	0.225;0.0	B;B	0.19946	0.027;0.0	T	0.74598	-0.3612	9	.	.	.	-0.5937	3.8365	0.08896	0.0:0.192:0.0:0.808	.	43;43	A8MX64;Q6XPS3	.;TPTE2_HUMAN	A	43	ENSP00000372438:E43A;ENSP00000382974:E43A;ENSP00000383089:E43A;ENSP00000372437:E43A;ENSP00000372435:E43A;ENSP00000442218:E43A	.	E	-	2	0	TPTE2	18954679	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.422000	0.21296	0.241000	0.21283	0.383000	0.25322	GAA	.	.	weak		0.313	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
FOXO3	2309	hgsc.bcm.edu	37	6	108985092	108985092	+	Silent	SNP	C	C	G	rs200866771		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:108985092C>G	ENST00000343882.6	+	3	1360	c.1056C>G	c.(1054-1056)gcC>gcG	p.A352A	FOXO3_ENST00000540898.1_Silent_p.A132A|FOXO3_ENST00000406360.1_Silent_p.A352A	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	352				PMLYSSSASLSPSVSKP -> AHALQHVSQPVTFSKQA (in Ref. 6; CAA04860). {ECO:0000305}.	antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A352A(2)		central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		GCAGCTCAGCCAGCCTGTCAC	0.572																																					p.A352A		Atlas-SNP	.											FOXO3,NS,carcinoma,0,3	FOXO3	67	3	2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|prostate(1)	c.C1056G						scavenged	.						63.0	54.0	57.0					6																	108985092		2203	4300	6503	SO:0001819	synonymous_variant	2309	exon2			CTCAGCCAGCCTG	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"""Forkhead boxes"""	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.1056C>G	6.37:g.108985092C>G		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	47	9	0.191489	NM_001455	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Silent	SNP	ENST00000343882.6	37	CCDS5068.1																																																																																			C|0.999;G|0.001	0.001	weak		0.572	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2		
DTX1	1840	hgsc.bcm.edu	37	12	113496024	113496024	+	Silent	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:113496024G>C	ENST00000257600.3	+	1	530	c.27G>C	c.(25-27)ctG>ctC	p.L9L		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	9					cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						ACGGTGGGCTGATGCCTGTGA	0.697																																					p.L9L		Atlas-SNP	.											.	DTX1	83	.	0			c.G27C						PASS	.						48.0	39.0	42.0					12																	113496024		2200	4298	6498	SO:0001819	synonymous_variant	1840	exon1			TGGGCTGATGCCT	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.27G>C	12.37:g.113496024G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.697	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
GBX2	2637	hgsc.bcm.edu	37	2	237076128	237076128	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:237076128C>T	ENST00000306318.4	-	1	884	c.487G>A	c.(487-489)Gcc>Acc	p.A163T	GBX2_ENST00000551105.1_Missense_Mutation_p.A163T|GBX2_ENST00000465889.1_5'Flank|AC079135.1_ENST00000415226.1_RNA|AC079135.1_ENST00000483218.1_RNA	NM_001485.2	NP_001476.2	P52951	GBX2_HUMAN	gastrulation brain homeobox 2	163				LPPAHPHHQIPSLPTGFCSSLAQGMALTSTLMATLPGGFSA SPQHQEAAAARKFAPQPLPGGGNFDKAEALQADAEDGKGFL AKEGSLLAFSAAETVQASLVGAVRGQGKDESKVEDDPKG -> CRPHTLTTRSPACPQASAPAWRRAWRSPLRSWPRSPAA SPRRPSTRRRQRPASSRRSRCPAAVTSTRRRRCRLTRRTAK ASWPKRARCSPSPRPRRCRLRSSGLSEGKGKTSQRWKTTRS (in Ref. 1; AAC03241). {ECO:0000305}.	autonomic nervous system development (GO:0048483)|axon guidance (GO:0007411)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellum development (GO:0021549)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|patterning of blood vessels (GO:0001569)|rhombomere 2 development (GO:0021568)|thalamus development (GO:0021794)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Breast(86;0.00235)|Renal(207;0.00339)|all_hematologic(139;0.00357)|all_lung(227;0.0616)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|Lung NSC(271;0.179)		Epithelial(121;4.5e-25)|OV - Ovarian serous cystadenocarcinoma(60;5.16e-11)|BRCA - Breast invasive adenocarcinoma(100;3.4e-05)|Lung(119;0.00195)|LUSC - Lung squamous cell carcinoma(224;0.00471)		GCGGAGAAGGCGAGCAGCGAG	0.756																																					p.A163T		Atlas-SNP	.											.	GBX2	20	.	0			c.G487A						PASS	.						13.0	13.0	13.0					2																	237076128		2138	4210	6348	SO:0001583	missense	2637	exon1			AGAAGGCGAGCAG	AF118452	CCDS2515.1	2q37.2	2012-03-09	2005-12-22		ENSG00000168505	ENSG00000168505		"""Homeoboxes / ANTP class : HOXL subclass"""	4186	protein-coding gene	gene with protein product		601135	"""gastrulation brain homeo box 2"""			9346236, 8838315	Standard	XM_005246071		Approved		uc002vvw.1	P52951	OTTHUMG00000133294	ENST00000306318.4:c.487G>A	2.37:g.237076128C>T	ENSP00000302251:p.Ala163Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001485	B2RPH7|O43833|Q53RX5|Q9Y5Y1	Missense_Mutation	SNP	ENST00000306318.4	37	CCDS2515.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940228	0.52972	.	.	ENSG00000168505	ENST00000306318;ENST00000551105	D	0.91894	-2.93	4.6	2.48	0.30137	.	0.334685	0.28360	N	0.015636	T	0.79112	0.4391	N	0.08118	0	0.32887	D	0.511398	B;B	0.30824	0.296;0.146	B;B	0.22601	0.04;0.011	T	0.77955	-0.2393	10	0.33141	T	0.24	-9.731	8.0352	0.30488	0.384:0.4985:0.1175:0.0	.	163;163	F8VY47;P52951	.;GBX2_HUMAN	T	163	ENSP00000302251:A163T	ENSP00000302251:A163T	A	-	1	0	GBX2	236740867	0.032000	0.19561	1.000000	0.80357	0.974000	0.67602	0.010000	0.13242	0.890000	0.36211	0.462000	0.41574	GCC	.	.	none		0.756	GBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257078.3	NM_001485	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056330	26056330	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26056330C>G	ENST00000343677.2	-	1	369	c.327G>C	c.(325-327)aaG>aaC	p.K109N		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	109	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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)	p.K109N(1)		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						AGGCTGCCTTCTTGTTGAGTT	0.557																																					p.K109N		Atlas-SNP	.											HIST1H1C,colon,carcinoma,0,2	HIST1H1C	80	2	1	Substitution - Missense(1)	ovary(1)	c.G327C						PASS	.						80.0	87.0	85.0					6																	26056330		2203	4300	6503	SO:0001583	missense	3006	exon1			TGCCTTCTTGTTG	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.327G>C	6.37:g.26056330C>G	ENSP00000339566:p.Lys109Asn	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	180	38	0.211111	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746067	0.89663	.	.	ENSG00000187837	ENST00000343677	T	0.11821	2.74	5.54	5.54	0.83059	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.107876	0.64402	D	0.000008	T	0.49029	0.1533	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66524	-0.5902	10	0.87932	D	0	-3.6427	18.8173	0.92081	0.0:1.0:0.0:0.0	.	109	P16403	H12_HUMAN	N	109	ENSP00000339566:K109N	ENSP00000339566:K109N	K	-	3	2	HIST1H1C	26164309	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	3.924000	0.56476	2.763000	0.94921	0.655000	0.94253	AAG	.	.	none		0.557	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
TUBB8	347688	hgsc.bcm.edu	37	10	93876	93876	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr10:93876G>A	ENST00000309812.4	-	4	518	c.456C>T	c.(454-456)ctC>ctT	p.L152L	TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.L80L	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	152					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.L152L(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GGATCTTACTGAGCAGAAGGG	0.592																																					p.L152L	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,NS,carcinoma,0,1	TUBB8	62	1	1	Substitution - coding silent(1)	cervix(1)	c.C456T						scavenged	.						106.0	94.0	98.0					10																	93876		2203	4300	6503	SO:0001819	synonymous_variant	347688	exon4			CTTACTGAGCAGA	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.456C>T	10.37:g.93876G>A		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	67	7	0.104478	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			A|1.000;|0.000	1.000	weak		0.592	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609323	84609323	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:84609323C>T	ENST00000344803.2	+	4	3985	c.3938C>T	c.(3937-3939)aCa>aTa	p.T1313I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1313					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGGCTGGGGACATCCCAACGC	0.527																																					p.T1313I		Atlas-SNP	.											.	.	.	.	0			c.C3938T						PASS	.						30.0	30.0	30.0					9																	84609323		1936	4134	6070	SO:0001583	missense	389763	exon4			TGGGGACATCCCA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3938C>T	9.37:g.84609323C>T	ENSP00000341988:p.Thr1313Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396019	0.25205	.	.	ENSG00000214929	ENST00000344803	T	0.18016	2.24	3.02	-0.0902	0.13666	.	0.543984	0.13848	U	0.358549	T	0.08133	0.0203	N	0.24115	0.695	0.09310	N	1	P	0.37101	0.582	B	0.33339	0.162	T	0.23762	-1.0179	10	0.35671	T	0.21	-4.7927	3.1663	0.06536	0.0:0.4943:0.229:0.2767	.	1313	Q6ZQQ2	F75D1_HUMAN	I	1313	ENSP00000341988:T1313I	ENSP00000341988:T1313I	T	+	2	0	FAM75D1	83799143	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.381000	0.07417	-0.010000	0.14271	0.655000	0.94253	ACA	.	.	none		0.527	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
OR51I2	390064	hgsc.bcm.edu	37	11	5475352	5475352	+	Missense_Mutation	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:5475352T>C	ENST00000341449.2	+	1	715	c.634T>C	c.(634-636)Ttt>Ctt	p.F212L	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	212					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGGACCTGTTTTTTATCTT	0.478																																					p.F212L		Atlas-SNP	.											.	OR51I2	76	.	0			c.T634C						PASS	.						382.0	325.0	345.0					11																	5475352		2201	4297	6498	SO:0001583	missense	390064	exon1			GACCTGTTTTTTA	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.634T>C	11.37:g.5475352T>C	ENSP00000341987:p.Phe212Leu	Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	338	51	0.150888	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.840977	0.00573	.	.	ENSG00000187918	ENST00000341449	T	0.32515	1.45	5.58	-10.1	0.00402	GPCR, rhodopsin-like superfamily (1);	1.199250	0.06023	N	0.651698	T	0.04363	0.0120	N	0.00358	-1.6	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17289	-1.0374	10	0.02654	T	1	.	3.6162	0.08078	0.2624:0.4828:0.0785:0.1763	.	212	Q9H344	O51I2_HUMAN	L	212	ENSP00000341987:F212L	ENSP00000341987:F212L	F	+	1	0	OR51I2	5431928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.134000	0.00148	-1.504000	0.01810	-0.256000	0.11100	TTT	.	.	none		0.478	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
STAT3	6774	hgsc.bcm.edu	37	17	40475063	40475063	+	Missense_Mutation	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:40475063T>C	ENST00000264657.5	-	20	2159	c.1847A>G	c.(1846-1848)gAa>gGa	p.E616G	STAT3_ENST00000404395.3_Missense_Mutation_p.E616G|STAT3_ENST00000389272.3_Missense_Mutation_p.E518G|STAT3_ENST00000588969.1_Missense_Mutation_p.E616G|STAT3_ENST00000585517.1_Missense_Mutation_p.E616G	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)	616	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)		GACGCCTCCTTCTTTGCTGCT	0.562									Hyperimmunoglobulin E Recurrent Infection Syndrome		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E616G		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,-1,1	STAT3	268	1	0			c.A1847G						PASS	.						129.0	120.0	123.0					17																	40475063		2203	4300	6503	SO:0001583	missense	6774	exon20	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	CCTCCTTCTTTGC	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.1847A>G	17.37:g.40475063T>C	ENSP00000264657:p.Glu616Gly	Somatic	87	0	0	893	WXS	Illumina HiSeq	Phase_I	76	25	0.328947	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175244	0.78564	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89343	-2.5;-2.5;-2.5	5.29	5.29	0.74685	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.86016	0.5832	L	0.49126	1.545	0.80722	D	1	P;P;P	0.44344	0.8;0.833;0.833	B;B;B	0.39258	0.195;0.295;0.295	D	0.87270	0.2285	10	0.52906	T	0.07	-26.4272	15.3873	0.74711	0.0:0.0:0.0:1.0	.	616;616;616	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	G	616;518;616	ENSP00000264657:E616G;ENSP00000373923:E518G;ENSP00000384943:E616G	ENSP00000264657:E616G	E	-	2	0	STAT3	37728589	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.846000	0.86887	2.221000	0.72209	0.533000	0.62120	GAA	.	.	none		0.562	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
GCNT1	2650	hgsc.bcm.edu	37	9	79118237	79118237	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:79118237G>A	ENST00000376730.4	+	4	1423	c.940G>A	c.(940-942)Gac>Aac	p.D314N	GCNT1_ENST00000536223.1_Missense_Mutation_p.D314N|GCNT1_ENST00000444201.2_Missense_Mutation_p.D314N|GCNT1_ENST00000442371.1_Missense_Mutation_p.D314N	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	314	Catalytic. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						GTGGGCACAAGACACATACAG	0.488																																					p.D314N		Atlas-SNP	.											.	GCNT1	52	.	0			c.G940A						PASS	.						74.0	74.0	74.0					9																	79118237		2203	4300	6503	SO:0001583	missense	2650	exon4			GCACAAGACACAT	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.940G>A	9.37:g.79118237G>A	ENSP00000365920:p.Asp314Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	g	33	5.233247	0.95207	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.21621	-1.0240	9	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	314	Q02742	GCNT1_HUMAN	N	314	ENSP00000440883:D314N;ENSP00000415454:D314N;ENSP00000390703:D314N;ENSP00000365920:D314N	.	D	+	1	0	GCNT1	78308057	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GAC	.	.	none		0.488	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
BCL11A	53335	hgsc.bcm.edu	37	2	60688036	60688036	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:60688036C>T	ENST00000335712.6	-	4	2238	c.2011G>A	c.(2011-2013)Gat>Aat	p.D671N	BCL11A_ENST00000538214.1_Missense_Mutation_p.D637N|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.D637N|BCL11A_ENST00000537768.1_Missense_Mutation_p.D340N|BCL11A_ENST00000356842.4_Missense_Mutation_p.D671N|BCL11A_ENST00000477659.1_5'UTR	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	671					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGGAAGGGATCTTTGAGCTGC	0.637			T	IGH@	B-CLL																																p.D671N		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.G2011A						PASS	.						39.0	48.0	45.0					2																	60688036		2202	4295	6497	SO:0001583	missense	53335	exon4			AGGGATCTTTGAG	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.2011G>A	2.37:g.60688036C>T	ENSP00000338774:p.Asp671Asn	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	7	0.102941	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768661	0.49680	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.13307	2.6;3.28;2.72;3.32;3.23	5.93	5.93	0.95920	.	0.125598	0.51477	D	0.000100	T	0.30070	0.0753	L	0.50333	1.59	0.58432	D	0.999998	D;P;P;P;D	0.61697	0.99;0.805;0.61;0.947;0.969	P;B;B;P;P	0.61940	0.794;0.26;0.328;0.798;0.896	T	0.00677	-1.1614	10	0.16896	T	0.51	-2.2696	20.3465	0.98790	0.0:1.0:0.0:0.0	.	637;340;637;671;671	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	N	671;696;637;340;671;637	ENSP00000349300:D671N;ENSP00000438303:D637N;ENSP00000443712:D340N;ENSP00000338774:D671N;ENSP00000351307:D637N	ENSP00000338774:D671N	D	-	1	0	BCL11A	60541540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.798000	0.96311	0.655000	0.94253	GAT	.	.	none		0.637	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
BTG1	694	hgsc.bcm.edu	37	12	92539203	92539203	+	Silent	SNP	G	G	A	rs369374957		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:92539203G>A	ENST00000256015.3	-	1	470	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	37					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)	p.L37L(1)		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)				AAGGTCTGCAGCTGTCGCTCG	0.677			T	MYC	BCLL																																p.L37L		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C109T						PASS	.						38.0	41.0	40.0					12																	92539203		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			TCTGCAGCTGTCG		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.109C>T	12.37:g.92539203G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	alt		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
ENPP2	5168	hgsc.bcm.edu	37	8	120631489	120631489	+	Silent	SNP	A	A	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:120631489A>T	ENST00000075322.6	-	5	532	c.474T>A	c.(472-474)ccT>ccA	p.P158P	ENPP2_ENST00000522826.1_Silent_p.P158P|ENPP2_ENST00000427067.2_Silent_p.P154P|ENPP2_ENST00000259486.6_Silent_p.P158P	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	158					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CTTACCCTGCAGGGCATTCTG	0.348																																					p.P158P	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.T474A						PASS	.						98.0	92.0	94.0					8																	120631489		2203	4300	6503	SO:0001819	synonymous_variant	5168	exon5			CCCTGCAGGGCAT	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.474T>A	8.37:g.120631489A>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_001130863	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			.	.	none		0.348	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
MCOLN1	57192	hgsc.bcm.edu	37	19	7593558	7593558	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:7593558G>A	ENST00000264079.6	+	8	1078	c.953G>A	c.(952-954)cGc>cAc	p.R318H		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	318					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTCTGCGCCCGCTCACTCCTT	0.637																																					p.R318H		Atlas-SNP	.											MCOLN1,colon,carcinoma,+1,1	MCOLN1	54	1	0			c.G953A						PASS	.						151.0	94.0	113.0					19																	7593558		2203	4300	6503	SO:0001583	missense	57192	exon8			GCGCCCGCTCACT	AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.953G>A	19.37:g.7593558G>A	ENSP00000264079:p.Arg318His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_020533	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	ENST00000264079.6	37	CCDS12180.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170229	0.78452	.	.	ENSG00000090674	ENST00000264079;ENST00000394321	D	0.83992	-1.79	5.32	5.32	0.75619	.	0.050554	0.85682	D	0.000000	D	0.91436	0.7297	M	0.87682	2.9	0.80722	D	1	D;D	0.63880	0.993;0.976	D;P	0.63381	0.914;0.717	D	0.92856	0.6301	10	0.87932	D	0	.	16.4854	0.84183	0.0:0.0:1.0:0.0	.	283;318	Q9GZU1-2;Q9GZU1	.;MCLN1_HUMAN	H	318;283	ENSP00000264079:R318H	ENSP00000264079:R318H	R	+	2	0	MCOLN1	7499558	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	7.602000	0.82796	2.492000	0.84095	0.563000	0.77884	CGC	.	.	none		0.637	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651412	1651412	+	Silent	SNP	G	G	C	rs569811286		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:1651412G>C	ENST00000399676.2	+	1	380	c.342G>C	c.(340-342)ggG>ggC	p.G114G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	114	8 X 4 AA repeats of C-C-X-P.			Missing (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.G114G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCTGTGGGGGGTCCAAGGGGG	0.706													N|||	1	0.000199681	0.0	0.0	5008	,	,		3556	0.001		0.0	False		,,,				2504	0.0				p.G114G		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,+1,2	KRTAP5-5	86	2	1	Substitution - coding silent(1)	prostate(1)	c.G342C						scavenged	.						20.0	31.0	27.0					11																	1651412		2083	4147	6230	SO:0001819	synonymous_variant	439915	exon1			TGGGGGGTCCAAG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.342G>C	11.37:g.1651412G>C		Somatic	61	2	0.0327869		WXS	Illumina HiSeq	Phase_I	60	3	0.05	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			.	.	none		0.706	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
MAP1S	55201	hgsc.bcm.edu	37	19	17838807	17838807	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:17838807C>T	ENST00000324096.4	+	5	2765	c.2614C>T	c.(2614-2616)Cgc>Tgc	p.R872C	MAP1S_ENST00000544059.2_Missense_Mutation_p.R846C|CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_3'UTR	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	872	Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCCCAACTCACGCGCTGCCGC	0.682																																					p.R872C		Atlas-SNP	.											.	MAP1S	74	.	0			c.C2614T						PASS	.						8.0	10.0	10.0					19																	17838807		2151	4207	6358	SO:0001583	missense	55201	exon5			AACTCACGCGCTG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2614C>T	19.37:g.17838807C>T	ENSP00000325313:p.Arg872Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	68	20	0.294118	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467034	0.43839	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.19105	2.17;2.17	4.99	-3.27	0.05048	.	2.214490	0.01791	N	0.032329	T	0.12220	0.0297	N	0.14661	0.345	0.09310	N	1	P;P	0.52692	0.955;0.955	B;B	0.41723	0.365;0.365	T	0.20874	-1.0262	10	0.56958	D	0.05	-1.5835	4.9983	0.14251	0.3404:0.2807:0.3789:0.0	.	846;872	B4DH53;Q66K74	.;MAP1S_HUMAN	C	872;846	ENSP00000325313:R872C;ENSP00000439243:R846C	ENSP00000325313:R872C	R	+	1	0	MAP1S	17699807	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.283000	0.18846	-0.338000	0.08413	-1.053000	0.02334	CGC	.	.	none		0.682	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
CILP2	148113	hgsc.bcm.edu	37	19	19651184	19651184	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:19651184G>A	ENST00000291495.5	+	3	420	c.335G>A	c.(334-336)cGc>cAc	p.R112H	CILP2_ENST00000586018.1_Missense_Mutation_p.R118H	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	112						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						GTCGGCGAGCGCGTGCACTTG	0.721																																					p.R112H		Atlas-SNP	.											.	CILP2	84	.	0			c.G335A						PASS	.						5.0	6.0	6.0					19																	19651184		2017	4033	6050	SO:0001583	missense	148113	exon3			GCGAGCGCGTGCA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.335G>A	19.37:g.19651184G>A	ENSP00000291495:p.Arg112His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615674	0.87359	.	.	ENSG00000160161	ENST00000291495	T	0.17370	2.28	4.27	4.27	0.50696	.	0.142510	0.44097	D	0.000481	T	0.28632	0.0709	L	0.42245	1.32	0.35344	D	0.786743	D;D	0.71674	0.994;0.998	P;D	0.66716	0.866;0.946	T	0.25984	-1.0116	10	0.42905	T	0.14	-2.4888	9.6583	0.39939	0.0:0.0:0.7916:0.2083	.	112;112	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	H	112	ENSP00000291495:R112H	ENSP00000291495:R112H	R	+	2	0	CILP2	19512184	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	3.229000	0.51278	1.937000	0.56155	0.306000	0.20318	CGC	.	.	none		0.721	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
NPEPL1	79716	hgsc.bcm.edu	37	20	57269609	57269609	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:57269609G>A	ENST00000356091.6	+	3	756	c.468G>A	c.(466-468)gtG>gtA	p.V156V	NPEPL1_ENST00000525967.1_Silent_p.V128V|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Silent_p.V108V	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	156						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TTTTCCTGGTGGGACAAGACA	0.667																																					p.V156V		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G468A						PASS	.						30.0	32.0	32.0					20																	57269609		1950	4143	6093	SO:0001819	synonymous_variant	79716	exon3			CCTGGTGGGACAA	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.468G>A	20.37:g.57269609G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			.	.	none		0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
SHANK2	22941	hgsc.bcm.edu	37	11	70505972	70505972	+	Silent	SNP	C	C	T	rs141960453		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:70505972C>T	ENST00000423696.2	-	7	921	c.885G>A	c.(883-885)gcG>gcA	p.A295A	SHANK2_ENST00000449833.2_Silent_p.A86A|SHANK2_ENST00000409530.1_Silent_p.A85A|SHANK2_ENST00000357171.3_Silent_p.A86A|SHANK2_ENST00000449116.2_Silent_p.A86A|SHANK2_ENST00000409161.1_Silent_p.A85A|SHANK2_ENST00000338508.4_Silent_p.A675A			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	295	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CGGCTTGCCACGCCACCCCAC	0.577																																					p.A86A		Atlas-SNP	.											.	SHANK2	340	.	0			c.G258A						PASS	.	T	,	4,4396	8.1+/-20.4	0,4,2196	129.0	105.0	113.0		1876,258	-10.0	0.2	11	dbSNP_134	113	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	SHANK2	NM_012309.3,NM_133266.3	,	0,4,6490	TT,TC,CC		0.0,0.0909,0.0308	,	674/1850,86/1262	70505972	4,12984	2200	4294	6494	SO:0001819	synonymous_variant	22941	exon2			TTGCCACGCCACC	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.885G>A	11.37:g.70505972C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	139	83	0.597122	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Silent	SNP	ENST00000423696.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	9.731|9.731	1.162196|1.162196	0.21538|0.21538	9.09E-4|9.09E-4	0.0|0.0	ENSG00000162105|ENSG00000162105	ENST00000426687|ENST00000412252	.|.	.|.	.|.	5.0|5.0	-9.99|-9.99	0.00435|0.00435	.|.	.|.	.|.	.|.	.|.	T|T	0.35595|0.35595	0.0937|0.0937	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45920|0.45920	-0.9228|-0.9228	4|4	.|.	.|.	.|.	.|.	3.5758|3.5758	0.07934|0.07934	0.1331:0.0985:0.2003:0.5681|0.1331:0.0985:0.2003:0.5681	.|.	.|.	.|.	.|.	H|M	84|85	.|.	.|.	R|V	-|-	2|1	0|0	SHANK2|SHANK2	70183620|70183620	0.000000|0.000000	0.05858|0.05858	0.244000|0.244000	0.24202|0.24202	0.980000|0.980000	0.70556|0.70556	-1.990000|-1.990000	0.01479|0.01479	-3.107000|-3.107000	0.00243|0.00243	-0.733000|-0.733000	0.03571|0.03571	CGT|GTG	C|1.000;T|0.000	0.000	weak		0.577	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
NOTCH2	4853	hgsc.bcm.edu	37	1	120611964	120611964	+	Missense_Mutation	SNP	G	G	C	rs11810554	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:120611964G>C	ENST00000256646.2	-	1	276	c.57C>G	c.(55-57)tgC>tgG	p.C19W		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	19					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.C19W(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGGGGGCCGCGCAGCACAGCC	0.766			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.C19W		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	NOTCH2,brain,glioma,0,1	NOTCH2	348	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C57G						scavenged	.						6.0	8.0	8.0					1																	120611964		1705	3721	5426	SO:0001583	missense	4853	exon1	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGCCGCGCAGCAC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.57C>G	1.37:g.120611964G>C	ENSP00000256646:p.Cys19Trp	Somatic	5	1	0.2		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	697|697	0.3191391941391941|0.3191391941391941	81|81	0.16463414634146342|0.16463414634146342	112|112	0.30939226519337015|0.30939226519337015	224|224	0.3916083916083916|0.3916083916083916	280|280	0.36939313984168864|0.36939313984168864	G|G	6.292|6.292	0.421956|0.421956	0.11928|0.11928	.|.	.|.	ENSG00000134250|ENSG00000134250	ENST00000538680|ENST00000256646	.|T	.|0.57436	.|0.4	3.09|3.09	2.04|2.04	0.26737|0.26737	.|.	.|.	.|.	.|.	.|.	T|T	0.14917|0.14917	0.0360|0.0360	N|N	0.14661|0.14661	0.345|0.345	0.26751|0.26751	N|N	0.970205|0.970205	.|B;B	.|0.09022	.|0.001;0.002	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.14337|0.14337	-1.0476|-1.0476	6|9	0.87932|0.37606	D|T	0|0.19	.|.	6.7594|6.7594	0.23532|0.23532	0.0:0.0:0.7206:0.2794|0.0:0.0:0.7206:0.2794	rs11810554|rs11810554	.|19;19	.|Q6IQ50;Q04721	.|.;NOTC2_HUMAN	G|W	36|19	.|ENSP00000256646:C19W	ENSP00000439516:A36G|ENSP00000256646:C19W	A|C	-|-	2|3	0|2	NOTCH2|NOTCH2	120413487|120413487	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.313000|0.313000	0.28021|0.28021	0.766000|0.766000	0.26560|0.26560	1.760000|1.760000	0.52011|0.52011	0.184000|0.184000	0.17185|0.17185	GCG|TGC	G|0.681;C|0.319	0.319	strong		0.766	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
CD79B	974	hgsc.bcm.edu	37	17	62006798	62006798	+	Missense_Mutation	SNP	T	T	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:62006798T>A	ENST00000006750.3	-	5	679	c.587A>T	c.(586-588)tAc>tTc	p.Y196F	CD79B_ENST00000392795.3_Missense_Mutation_p.Y197F|CD79B_ENST00000349817.2_Missense_Mutation_p.Y92F	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	196	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.Y196C(1)|p.Y196F(1)|p.Y196S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CCTTACCTCGTAGGTGTGATC	0.632			"""Mis, O"""		DLBCL																																p.Y197F		Atlas-SNP	.		Dom	yes		17	17q23	974	"""CD79b molecule, immunoglobulin-associated beta"""		L	CD79B,NS,lymphoid_neoplasm,-1,13	CD79B	38	13	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.A590T						scavenged	.						93.0	74.0	81.0					17																	62006798		2203	4300	6503	SO:0001583	missense	974	exon5			ACCTCGTAGGTGT	L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1699	protein-coding gene	gene with protein product		147245	"""CD79B antigen (immunoglobulin-associated beta)"""	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.587A>T	17.37:g.62006798T>A	ENSP00000006750:p.Tyr196Phe	Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	51	40	0.784314	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930227	0.52866	.	.	ENSG00000007312	ENST00000349817;ENST00000392795;ENST00000006750	D;D;D	0.96587	-4.06;-4.06;-4.06	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.95601	0.8570	N	0.24115	0.695	0.43426	D	0.995588	D;D	0.76494	0.996;0.999	D;D	0.85130	0.986;0.997	D	0.95387	0.8478	10	0.87932	D	0	-12.4743	9.5968	0.39578	0.0:0.0:0.0:1.0	.	92;196	P40259-2;P40259	.;CD79B_HUMAN	F	92;197;196	ENSP00000245862:Y92F;ENSP00000376544:Y197F;ENSP00000006750:Y196F	ENSP00000006750:Y196F	Y	-	2	0	CD79B	59360530	0.997000	0.39634	0.977000	0.42913	0.245000	0.25701	3.902000	0.56310	1.782000	0.52362	0.358000	0.22013	TAC	.	.	none		0.632	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1		
KCND2	3751	hgsc.bcm.edu	37	7	119915438	119915438	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:119915438C>T	ENST00000331113.4	+	1	1717	c.752C>T	c.(751-753)gCg>gTg	p.A251V		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	251					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CTGGCTGCAGCGCCTAGTCGT	0.532																																					p.A251V		Atlas-SNP	.											.	KCND2	194	.	0			c.C752T						PASS	.						183.0	151.0	162.0					7																	119915438		2203	4300	6503	SO:0001583	missense	3751	exon1			CTGCAGCGCCTAG	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.752C>T	7.37:g.119915438C>T	ENSP00000333496:p.Ala251Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	183	27	0.147541	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143439	0.77888	.	.	ENSG00000184408	ENST00000331113	D	0.97831	-4.56	5.57	5.57	0.84162	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98463	0.9488	M	0.67625	2.065	0.54753	D	0.999986	D	0.89917	1.0	D	0.78314	0.991	D	0.98623	1.0668	9	.	.	.	.	19.5635	0.95382	0.0:1.0:0.0:0.0	.	251	Q9NZV8	KCND2_HUMAN	V	251	ENSP00000333496:A251V	.	A	+	2	0	KCND2	119702674	1.000000	0.71417	0.195000	0.23364	0.955000	0.61496	5.999000	0.70665	2.636000	0.89361	0.557000	0.71058	GCG	.	.	none		0.532	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281	
PIM1	5292	hgsc.bcm.edu	37	6	37139203	37139203	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37139203G>C	ENST00000373509.5	+	4	916	c.543G>C	c.(541-543)gaG>gaC	p.E181D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.E181D(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)	ATCGCGGCGAGCTCAAGCTCA	0.637			T	BCL6	NHL																																p.E272D		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.G816C						PASS	.						32.0	33.0	32.0					6																	37139203		2203	4300	6503	SO:0001583	missense	5292	exon4			CGGCGAGCTCAAG		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.543G>C	6.37:g.37139203G>C	ENSP00000362608:p.Glu181Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	10	0.15625	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354972	0.24512	.	.	ENSG00000137193	ENST00000373509	T	0.66099	-0.19	4.36	3.47	0.39725	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.207237	0.40554	N	0.001073	T	0.26412	0.0645	L	0.45698	1.435	0.33559	D	0.597158	B	0.13594	0.008	B	0.19946	0.027	T	0.07558	-1.0766	10	0.08837	T	0.75	.	5.5129	0.16890	0.3296:0.0:0.6704:0.0	.	272	P11309	PIM1_HUMAN	D	181	ENSP00000362608:E181D	ENSP00000362608:E181D	E	+	3	2	PIM1	37247181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.006000	0.40874	1.020000	0.39573	0.448000	0.29417	GAG	.	.	none		0.637	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1253976	1253976	+	Missense_Mutation	SNP	A	A	G	rs76956995		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:1253976A>G	ENST00000529681.1	+	17	2099	c.2041A>G	c.(2041-2043)Agc>Ggc	p.S681G	MUC5B_ENST00000447027.1_Missense_Mutation_p.S684G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	681					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGTACAGCTCAGCGACTGGAG	0.687																																					p.S681G		Atlas-SNP	.											MUC5B,colon,carcinoma,0,4	MUC5B	473	4	0			c.A2041G						scavenged	.						22.0	25.0	24.0					11																	1253976		2121	4235	6356	SO:0001583	missense	727897	exon17			CAGCTCAGCGACT	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2041A>G	11.37:g.1253976A>G	ENSP00000436812:p.Ser681Gly	Somatic	70	3	0.0428571		WXS	Illumina HiSeq	Phase_I	79	14	0.177215	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	A	5.230	0.228008	0.09916	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76578	-1.03;-1.03	4.6	-7.0	0.01599	Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.70605	0.3243	N	0.25144	0.715	0.09310	N	1	B;D;D	0.59357	0.425;0.985;0.985	B;P;P	0.54499	0.131;0.675;0.754	T	0.69614	-0.5098	9	0.87932	D	0	.	10.9271	0.47197	0.2958:0.5687:0.1355:0.0	.	681;1340;684	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	681;684;682;717	ENSP00000436812:S681G;ENSP00000415793:S684G	ENSP00000343037:S682G	S	+	1	0	MUC5B	1210552	0.000000	0.05858	0.011000	0.14972	0.067000	0.16453	-4.642000	0.00204	-1.098000	0.03038	0.260000	0.18958	AGC	.	.	weak		0.687	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SDK2	54549	hgsc.bcm.edu	37	17	71434182	71434182	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:71434182G>A	ENST00000392650.3	-	7	837	c.837C>T	c.(835-837)gcC>gcT	p.A279A	SDK2_ENST00000388726.3_Silent_p.A279A	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	279	Ig-like C2-type 3.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CGTAGTAGCCGGCGTCACTGC	0.632																																					p.A279A		Atlas-SNP	.											.	SDK2	219	.	0			c.C837T						PASS	.						28.0	38.0	35.0					17																	71434182		692	1591	2283	SO:0001819	synonymous_variant	54549	exon7			GTAGCCGGCGTCA	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.837C>T	17.37:g.71434182G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	2.222	-0.378123	0.05000	.	.	ENSG00000069188	ENST00000416616	.	.	.	5.05	-0.688	0.11317	.	.	.	.	.	T	0.53802	0.1819	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44421	-0.9329	4	.	.	.	.	7.8147	0.29252	0.3879:0.104:0.5081:0.0	.	.	.	.	W	184	.	.	R	-	1	2	SDK2	68945777	0.123000	0.22298	0.968000	0.41197	0.041000	0.13682	-0.401000	0.07232	-0.292000	0.08999	-2.620000	0.00156	CGG	.	.	none		0.632	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
IZUMO3	100129669	hgsc.bcm.edu	37	9	24545061	24545061	+	Splice_Site	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:24545061T>G	ENST00000543880.2	-	3	533		c.e3-2		IZUMO3_ENST00000604921.1_Splice_Site|RP11-20A20.2_ENST00000602851.1_lincRNA			Q5VZ72	IZUM3_HUMAN	IZUMO family member 3							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)										TAAAGACACCTAAGAGGGAGT	0.373																																					.		Atlas-SNP	.											.	.	.	.	0			c.302-2A>C						PASS	.																																			SO:0001630	splice_region_variant	100129669	exon4			GACACCTAAGAGG		CCDS65020.1	9p21.3	2014-02-17	2010-07-29	2010-07-29	ENSG00000205442	ENSG00000205442		"""-"""	31421	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 134"""	C9orf134		19658160, 22957301	Standard	NM_001271706		Approved	bA20A20.1	uc031tdg.1	Q5VZ72	OTTHUMG00000019704	ENST00000543880.2:c.302-2A>C	9.37:g.24545061T>G		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_001271706		Splice_Site	SNP	ENST00000543880.2	37		.	.	.	.	.	.	.	.	.	.	T	9.766	1.171331	0.21621	.	.	ENSG00000205442	ENST00000412335;ENST00000543880;ENST00000418122	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9251	0.52814	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	IZUMO3	24535061	0.997000	0.39634	0.942000	0.38095	0.158000	0.22134	3.370000	0.52372	2.308000	0.77769	0.533000	0.62120	.	.	.	none		0.373	IZUMO3-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000467652.1	NM_001271706	Intron
CGN	57530	hgsc.bcm.edu	37	1	151508789	151508789	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:151508789G>A	ENST00000271636.7	+	19	3407	c.3274G>A	c.(3274-3276)Gag>Aag	p.E1092K		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	1086					transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GATTGAAGACGAGCGGCAGCA	0.473																																					p.E1092K		Atlas-SNP	.											.	CGN	106	.	0			c.G3274A						PASS	.						64.0	65.0	64.0					1																	151508789		2203	4300	6503	SO:0001583	missense	57530	exon19			GAAGACGAGCGGC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.3274G>A	1.37:g.151508789G>A	ENSP00000271636:p.Glu1092Lys	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	179	37	0.206704	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793437	0.90453	.	.	ENSG00000143375	ENST00000271636	T	0.80738	-1.41	5.65	5.65	0.86999	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.89955	0.6865	M	0.85197	2.74	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	D	0.90900	0.4768	10	0.87932	D	0	-26.5062	18.2859	0.90114	0.0:0.0:1.0:0.0	.	1086	Q9P2M7	CING_HUMAN	K	1092	ENSP00000271636:E1092K	ENSP00000271636:E1092K	E	+	1	0	CGN	149775413	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.054000	0.93866	2.679000	0.91253	0.655000	0.94253	GAG	.	.	none		0.473	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
MYD88	4615	hgsc.bcm.edu	37	3	38182641	38182641	+	Nonstop_Mutation	SNP	T	T	C	rs387907272		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:38182641T>C	ENST00000495303.1	+	3	483	c.478T>C	c.(478-480)Tga>Cga	p.*160R	MYD88_ENST00000424893.1_Missense_Mutation_p.L220P|MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000443433.2_Nonstop_Mutation_p.*205R|MYD88_ENST00000396334.3_Missense_Mutation_p.L265P|MYD88_ENST00000417037.2_Missense_Mutation_p.L273P	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.L265P(188)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAAGCGACTGATCCCCATC	0.552			Mis		ABC-DLBCL								T|||	1	0.000199681	0.0	0.0	5008	,	,		22034	0.0		0.001	False		,,,				2504	0.0				p.X205R		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	188	Substitution - Missense(188)	haematopoietic_and_lymphoid_tissue(188)	c.T613C						PASS	.						148.0	119.0	129.0					3																	38182641		2203	4300	6503	SO:0001578	stop_lost	4615	exon4			AGCGACTGATCCC	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"""myeloid differentiation primary response gene (88)"""			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.478T>C	3.37:g.38182641T>C	ENSP00000417848:p.*160Argext*8	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	92	76	0.826087	NM_001172569	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.85|18.85	3.710754|3.710754	0.68730|0.68730	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000495303;ENST00000443433	T;T;T;T|.	0.15487|.	2.42;2.42;2.42;2.42|.	5.74|5.74	5.74|5.74	0.90152|0.90152	Toll/interleukin-1 receptor homology (TIR) domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71676|.	0.3368|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.998;0.999;0.999|.	T|.	0.70626|.	-0.4820|.	9|.	0.87932|.	D|.	0|.	-17.9268|-17.9268	15.535|15.535	0.75996|0.75996	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	207;252;241|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	P|R	273;265;220;272;241|160;205	ENSP00000401399:L273P;ENSP00000379625:L265P;ENSP00000389979:L220P;ENSP00000391753:L272P|.	ENSP00000379625:L265P|.	L|X	+|+	2|1	0|0	MYD88|MYD88	38157645|38157645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.639000|7.639000	0.83342|0.83342	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468	
RFX5	5993	hgsc.bcm.edu	37	1	151318690	151318690	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:151318690C>T	ENST00000290524.4	-	3	285	c.107G>A	c.(106-108)gGt>gAt	p.G36D	RFX5_ENST00000368870.2_Missense_Mutation_p.G36D|RFX5_ENST00000452513.2_Missense_Mutation_p.G36D|RP11-126K1.6_ENST00000455503.1_RNA|RFX5_ENST00000478564.1_5'UTR|RFX5_ENST00000452671.2_Missense_Mutation_p.G36D	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	36	N-terminal domain.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CGAAATGGTACCTCGGAGCCT	0.547																																					p.G36D		Atlas-SNP	.											.	RFX5	69	.	0			c.G107A						PASS	.						119.0	120.0	120.0					1																	151318690		2203	4300	6503	SO:0001583	missense	5993	exon3			ATGGTACCTCGGA		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.107G>A	1.37:g.151318690C>T	ENSP00000290524:p.Gly36Asp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	16	0.179775	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	37	CCDS994.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383663	0.82792	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513;ENST00000392746;ENST00000422595;ENST00000450506;ENST00000458484;ENST00000430227;ENST00000412774;ENST00000437327;ENST00000436271	T;T;T;T;T;T;D;D	0.82167	0.31;0.31;0.31;0.28;0.32;-0.58;-1.58;-1.58	4.98	4.98	0.66077	.	0.118290	0.56097	D	0.000027	D	0.85561	0.5725	L	0.51422	1.61	0.47547	D	0.999453	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.96	D	0.85596	0.1249	10	0.49607	T	0.09	-8.8161	13.6052	0.62044	0.0:1.0:0.0:0.0	.	36;36	B7Z848;P48382	.;RFX5_HUMAN	D	36	ENSP00000290524:G36D;ENSP00000357864:G36D;ENSP00000389130:G36D;ENSP00000398388:G36D;ENSP00000376502:G36D;ENSP00000399095:G36D;ENSP00000398666:G36D;ENSP00000409187:G36D	ENSP00000290524:G36D	G	-	2	0	RFX5	149585314	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.461000	0.66699	2.591000	0.87537	0.491000	0.48974	GGT	.	.	none		0.547	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449	
FRG1	2483	hgsc.bcm.edu	37	4	190878569	190878569	+	Missense_Mutation	SNP	T	T	C	rs575384276		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:190878569T>C	ENST00000226798.4	+	6	671	c.449T>C	c.(448-450)tTg>tCg	p.L150S	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	150					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L150S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ATGGCTTTGTTGGCCTCAAAT	0.358																																					p.L150S		Atlas-SNP	.											FRG1,NS,carcinoma,0,2	FRG1	76	2	1	Substitution - Missense(1)	prostate(1)	c.T449C						scavenged	.						13.0	18.0	16.0					4																	190878569		2139	4261	6400	SO:0001583	missense	2483	exon6			CTTTGTTGGCCTC	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.449T>C	4.37:g.190878569T>C	ENSP00000226798:p.Leu150Ser	Somatic	239	4	0.0167364		WXS	Illumina HiSeq	Phase_I	212	9	0.0424528	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	15.24	2.773472	0.49786	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.50813	1.86;0.73	4.19	4.19	0.49359	Actin cross-linking (1);	0.139630	0.48286	D	0.000199	T	0.55417	0.1919	M	0.78456	2.415	0.80722	D	1	B	0.31680	0.335	B	0.41299	0.353	T	0.60393	-0.7272	10	0.54805	T	0.06	-2.69	11.5749	0.50856	0.0:0.0:0.0:1.0	.	150	Q14331	FRG1_HUMAN	S	150;22;87	ENSP00000226798:L150S;ENSP00000435943:L87S	ENSP00000226798:L150S	L	+	2	0	FRG1	191115563	1.000000	0.71417	0.991000	0.47740	0.482000	0.33219	7.788000	0.85771	1.677000	0.50941	0.373000	0.22412	TTG	.	.	none		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
VPS13C	54832	hgsc.bcm.edu	37	15	62256044	62256044	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr15:62256044G>C	ENST00000261517.5	-	32	3394	c.3321C>G	c.(3319-3321)atC>atG	p.I1107M	VPS13C_ENST00000395896.4_Missense_Mutation_p.I1107M|VPS13C_ENST00000395898.3_Missense_Mutation_p.I1064M|VPS13C_ENST00000249837.3_Missense_Mutation_p.I1064M	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CTTGAATCTTGATTTCGGCGA	0.343																																					p.I1107M		Atlas-SNP	.											.	VPS13C	506	.	0			c.C3321G						PASS	.						117.0	107.0	110.0					15																	62256044		2202	4300	6502	SO:0001583	missense	54832	exon32			AATCTTGATTTCG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3321C>G	15.37:g.62256044G>C	ENSP00000261517:p.Ile1107Met	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	149	127	0.852349	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.941870	0.53079	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46819	0.86;0.86;0.86	5.66	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.67979	0.2951	M	0.70595	2.14	0.51012	D	0.999901	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.976;0.986;0.99;0.997	T	0.68704	-0.5338	10	0.48119	T	0.1	.	17.3263	0.87248	0.0:0.0:0.8664:0.1336	.	1064;1107;1064;1107	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	M	1064;1107;1107;1107	ENSP00000249837:I1064M;ENSP00000261517:I1107M;ENSP00000379233:I1107M	ENSP00000249837:I1064M	I	-	3	3	VPS13C	60043336	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	2.484000	0.45242	2.656000	0.90262	0.655000	0.94253	ATC	.	.	none		0.343	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ITPKB	3707	hgsc.bcm.edu	37	1	226925103	226925103	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:226925103C>T	ENST00000272117.3	-	1	56	c.57G>A	c.(55-57)gaG>gaA	p.E19E	ITPKB_ENST00000429204.1_Silent_p.E19E|ITPKB_ENST00000366784.1_Silent_p.E19E			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	19					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CGCTCTTCATCTCGTTGGCGC	0.697																																					p.E19E	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,scalp,carcinoma,-2,1	ITPKB	158	1	0			c.G57A						PASS	.						15.0	18.0	17.0					1																	226925103		2084	4139	6223	SO:0001819	synonymous_variant	3707	exon2			CTTCATCTCGTTG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.57G>A	1.37:g.226925103C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			.	.	none		0.697	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
MGAM	8972	hgsc.bcm.edu	37	7	141759688	141759688	+	Silent	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:141759688T>C	ENST00000549489.2	+	33	4076	c.3981T>C	c.(3979-3981)ccT>ccC	p.P1327P	MGAM_ENST00000475668.2_Silent_p.P1327P	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1327	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.P1327P(2)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGACACAGCCTTATCCTGCCT	0.463																																					p.P1327P		Atlas-SNP	.											MGAM_ENST00000549489,NS,carcinoma,0,5	MGAM	767	5	2	Substitution - coding silent(2)	prostate(2)	c.T3981C						scavenged	.						50.0	43.0	45.0					7																	141759688		1935	4135	6070	SO:0001819	synonymous_variant	8972	exon33			ACAGCCTTATCCT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3981T>C	7.37:g.141759688T>C		Somatic	218	3	0.0137615		WXS	Illumina HiSeq	Phase_I	118	6	0.0508475	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	none		0.463	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
FAM189B	10712	hgsc.bcm.edu	37	1	155220451	155220451	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:155220451G>A	ENST00000361361.2	-	9	1635	c.1126C>T	c.(1126-1128)Ctc>Ttc	p.L376F	FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000368368.3_Missense_Mutation_p.L358F|FAM189B_ENST00000350210.2_Missense_Mutation_p.L280F	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	376						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						TCCAGGCTGAGGCAGTAGCCG	0.701																																					p.L376F		Atlas-SNP	.											.	FAM189B	51	.	0			c.C1126T						PASS	.						14.0	17.0	16.0					1																	155220451		2171	4254	6425	SO:0001583	missense	10712	exon9			GGCTGAGGCAGTA	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 2"""	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.1126C>T	1.37:g.155220451G>A	ENSP00000354958:p.Leu376Phe	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.397776	0.83120	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361;ENST00000323361	T;T;T	0.19669	2.13;2.41;2.41	4.21	4.21	0.49690	.	0.237014	0.27319	N	0.019901	T	0.16811	0.0404	N	0.08118	0	0.35127	D	0.767568	D;D;D;D	0.89917	1.0;0.995;0.997;0.995	D;D;D;D	0.85130	0.997;0.979;0.986;0.969	T	0.21552	-1.0242	10	0.59425	D	0.04	.	14.442	0.67323	0.0:0.0:1.0:0.0	.	141;358;280;376	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	F	280;358;376;86	ENSP00000307128:L280F;ENSP00000357352:L358F;ENSP00000354958:L376F	ENSP00000323164:L86F	L	-	1	0	FAM189B	153487075	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.426000	0.66476	2.351000	0.79841	0.563000	0.77884	CTC	.	.	none		0.701	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589	
PIM1	5292	hgsc.bcm.edu	37	6	37139086	37139086	+	Missense_Mutation	SNP	G	G	C	rs33989191	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37139086G>C	ENST00000373509.5	+	4	799	c.426G>C	c.(424-426)gaG>gaC	p.E142D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			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)	TGCAAGAGGAGCTGGCCCGCA	0.617			T	BCL6	NHL								G|||	11	0.00219649	0.0083	0.0	5008	,	,		16103	0.0		0.0	False		,,,				2504	0.0				p.E233D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G699C						PASS	.	G	ASP/GLU	38,4368	40.8+/-73.8	0,38,2165	59.0	70.0	66.0		426	3.3	1.0	6	dbSNP_126	66	0,8600		0,0,4300	yes	missense	PIM1	NM_002648.3	45	0,38,6465	CC,CG,GG		0.0,0.8625,0.2922	benign	142/314	37139086	38,12968	2203	4300	6503	SO:0001583	missense	5292	exon4			AGAGGAGCTGGCC		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.426G>C	6.37:g.37139086G>C	ENSP00000362608:p.Glu142Asp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	80	14	0.175	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	2.740	-0.262501	0.05791	0.008625	0.0	ENSG00000137193	ENST00000373509	T	0.65916	-0.18	4.19	3.31	0.37934	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.376195	0.26224	N	0.025611	T	0.17959	0.0431	N	0.04373	-0.215	0.38312	D	0.943293	B	0.02656	0.0	B	0.04013	0.001	T	0.07986	-1.0744	10	0.10902	T	0.67	.	13.2969	0.60303	0.0:0.4445:0.5555:0.0	rs33989191	233	P11309	PIM1_HUMAN	D	142	ENSP00000362608:E142D	ENSP00000362608:E142D	E	+	3	2	PIM1	37247064	1.000000	0.71417	1.000000	0.80357	0.416000	0.31233	2.500000	0.45381	0.949000	0.37715	0.448000	0.29417	GAG	G|0.998;C|0.002	0.002	strong		0.617	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
C2orf71	388939	hgsc.bcm.edu	37	2	29296353	29296353	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:29296353C>T	ENST00000331664.5	-	1	774	c.775G>A	c.(775-777)Gag>Aag	p.E259K		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	259					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TCCTGGGGCTCTCTTTTCTTC	0.562																																					p.E259K		Atlas-SNP	.											.	C2orf71	146	.	0			c.G775A						PASS	.						64.0	66.0	65.0					2																	29296353		1984	4173	6157	SO:0001583	missense	388939	exon1			GGGGCTCTCTTTT		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.775G>A	2.37:g.29296353C>T	ENSP00000332809:p.Glu259Lys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	53	8	0.150943	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581641	0.28180	.	.	ENSG00000179270	ENST00000331664	T	0.21932	1.98	5.62	5.62	0.85841	.	0.385689	0.28560	N	0.014902	T	0.22627	0.0546	L	0.45581	1.43	0.09310	N	1	P	0.39022	0.655	B	0.34452	0.183	T	0.13202	-1.0518	10	0.51188	T	0.08	-17.6579	19.6596	0.95859	0.0:1.0:0.0:0.0	.	259	A6NGG8	CB071_HUMAN	K	259	ENSP00000332809:E259K	ENSP00000332809:E259K	E	-	1	0	C2orf71	29149857	0.502000	0.26107	0.409000	0.26459	0.181000	0.23173	1.766000	0.38491	2.648000	0.89879	0.561000	0.74099	GAG	.	.	none		0.562	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
PUS1	80324	hgsc.bcm.edu	37	12	132426407	132426407	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:132426407A>G	ENST00000376649.3	+	5	1615	c.1115A>G	c.(1114-1116)cAc>cGc	p.H372R	PUS1_ENST00000542167.2_Missense_Mutation_p.H319R|PUS1_ENST00000443358.2_Missense_Mutation_p.H344R|PUS1_ENST00000440818.2_Missense_Mutation_p.H344R|PUS1_ENST00000535067.1_Intron	NM_025215.5	NP_079491.2	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1	372					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|tRNA pseudouridine synthesis (GO:0031119)	mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|pseudouridylate synthase activity (GO:0004730)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	11	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)		AAGGAGGAGCACATCTACCCC	0.612																																					p.H372R	Esophageal Squamous(102;671 2009 17384 45666)	Atlas-SNP	.											.	PUS1	47	.	0			c.A1115G						PASS	.						93.0	66.0	75.0					12																	132426407		2203	4300	6503	SO:0001583	missense	80324	exon5			AGGAGCACATCTA	AF116238	CCDS9275.2, CCDS31928.1	12q24	2004-05-17			ENSG00000177192	ENSG00000177192			15508	protein-coding gene	gene with protein product		608109				10094309	Standard	NM_001002019		Approved		uc001ujf.3	Q9Y606	OTTHUMG00000128507	ENST00000376649.3:c.1115A>G	12.37:g.132426407A>G	ENSP00000365837:p.His372Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_025215	A8K877|B3KQC1|Q8WYT2|Q9BU44	Missense_Mutation	SNP	ENST00000376649.3	37	CCDS9275.2	.	.	.	.	.	.	.	.	.	.	A	12.24	1.877457	0.33162	.	.	ENSG00000177192	ENST00000443358;ENST00000376649;ENST00000322060;ENST00000440818;ENST00000542167	T;T;T;T;T	0.54675	0.57;0.56;0.57;0.57;0.56	5.17	5.17	0.71159	.	0.357746	0.33075	N	0.005309	T	0.49321	0.1550	L	0.51914	1.62	0.37582	D	0.919854	B;B	0.19073	0.016;0.033	B;B	0.19946	0.026;0.027	T	0.53005	-0.8499	10	0.48119	T	0.1	-8.4957	14.9932	0.71406	1.0:0.0:0.0:0.0	.	319;372	F5H1S9;Q9Y606	.;TRUA_HUMAN	R	344;372;344;344;319	ENSP00000392451:H344R;ENSP00000365837:H372R;ENSP00000324726:H344R;ENSP00000400032:H344R;ENSP00000438948:H319R	ENSP00000324726:H344R	H	+	2	0	PUS1	130992360	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	7.383000	0.79741	1.947000	0.56498	0.402000	0.26972	CAC	.	.	none		0.612	PUS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250313.2	NM_025215	
AKAP4	8852	hgsc.bcm.edu	37	X	49957130	49957130	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chrX:49957130C>G	ENST00000376056.2	-	5	2357	c.2207G>C	c.(2206-2208)gGt>gCt	p.G736A	AKAP4_ENST00000376058.2_Missense_Mutation_p.G362A|AKAP4_ENST00000358526.2_Missense_Mutation_p.G745A|AKAP4_ENST00000376064.3_Missense_Mutation_p.G736A|AKAP4_ENST00000481402.1_5'UTR					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					TGGCATTGCACCACTGTGAAT	0.483																																					p.G745A		Atlas-SNP	.											.	AKAP4	131	.	0			c.G2234C						PASS	.						103.0	68.0	80.0					X																	49957130		2203	4300	6503	SO:0001583	missense	8852	exon5			ATTGCACCACTGT	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"""A-kinase anchor proteins"""	374	protein-coding gene	gene with protein product	"""A-kinase anchor protein 82 kDa"", ""testis-specific gene HI"", ""protein kinase A anchoring protein 4"", ""cancer/testis antigen 99"""	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.2207G>C	X.37:g.49957130C>G	ENSP00000365224:p.Gly736Ala	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	133	97	0.729323	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	37	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	C	5.691	0.311971	0.10789	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064	T;T;T;T	0.04551	3.6;3.6;3.6;3.6	4.3	-5.82	0.02333	A-kinase anchor 110kDa, C-terminal (1);	1.644940	0.03577	N	0.229552	T	0.01800	0.0057	N	0.01874	-0.695	0.09310	N	1	B;B	0.30326	0.001;0.276	B;B	0.32393	0.001;0.145	T	0.41142	-0.9525	9	.	.	.	1.0666	5.0654	0.14580	0.1045:0.144:0.5559:0.1956	.	745;362	Q5JQC9;A6ND82	AKAP4_HUMAN;.	A	736;362;745;736	ENSP00000365224:G736A;ENSP00000365226:G362A;ENSP00000351327:G745A;ENSP00000365232:G736A	.	G	-	2	0	AKAP4	49843870	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.084000	0.01363	-1.165000	0.02786	-0.295000	0.09555	GGT	.	.	none		0.483	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886	
HMCN1	83872	hgsc.bcm.edu	37	1	186007087	186007087	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:186007087C>G	ENST00000271588.4	+	37	6000	c.5771C>G	c.(5770-5772)gCt>gGt	p.A1924G	HMCN1_ENST00000367492.2_Missense_Mutation_p.A1924G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1924	Ig-like C2-type 17.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGGAAGATGCTGGAAAAATG	0.383																																					p.A1924G		Atlas-SNP	.											.	HMCN1	797	.	0			c.C5771G						PASS	.						135.0	127.0	130.0					1																	186007087		2203	4300	6503	SO:0001583	missense	83872	exon37			AAGATGCTGGAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5771C>G	1.37:g.186007087C>G	ENSP00000271588:p.Ala1924Gly	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	88	16	0.181818	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	2.881	-0.231818	0.05983	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66099	-0.18;-0.19	5.52	4.6	0.57074	Immunoglobulin-like (1);	0.233532	0.43747	N	0.000525	T	0.35913	0.0948	N	0.01705	-0.755	0.37687	D	0.923692	B	0.09022	0.002	B	0.09377	0.004	T	0.22871	-1.0204	10	0.18710	T	0.47	.	16.2196	0.82251	0.0:0.867:0.133:0.0	.	1924	Q96RW7	HMCN1_HUMAN	G	1924	ENSP00000271588:A1924G;ENSP00000356462:A1924G	ENSP00000271588:A1924G	A	+	2	0	HMCN1	184273710	0.820000	0.29190	0.096000	0.21009	0.007000	0.05969	3.307000	0.51888	1.306000	0.44926	0.555000	0.69702	GCT	.	.	none		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
LRRC4C	57689	hgsc.bcm.edu	37	11	40137801	40137801	+	Missense_Mutation	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:40137801T>C	ENST00000278198.2	-	2	2005	c.42A>G	c.(40-42)atA>atG	p.I14M	LRRC4C_ENST00000530763.1_Missense_Mutation_p.I14M|LRRC4C_ENST00000528697.1_Missense_Mutation_p.I14M|LRRC4C_ENST00000527150.1_Missense_Mutation_p.I14M			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	14					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ACCTAGGACCTATCATTATCT	0.473																																					p.I14M		Atlas-SNP	.											LRRC4C,NS,carcinoma,-1,1	LRRC4C	190	1	0			c.A42G						scavenged	.						103.0	104.0	103.0					11																	40137801		2203	4300	6503	SO:0001583	missense	57689	exon7			AGGACCTATCATT	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.42A>G	11.37:g.40137801T>C	ENSP00000278198:p.Ile14Met	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	206	3	0.0145631	NM_001258419	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.157634	0.57368	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763;ENST00000533474	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.76	5.76	0.90799	.	0.051765	0.64402	D	0.000001	T	0.35278	0.0926	N	0.14661	0.345	0.44539	D	0.997491	P	0.36616	0.561	B	0.32289	0.143	T	0.24870	-1.0148	10	0.35671	T	0.21	.	15.2431	0.73485	0.0:0.0:0.0:1.0	.	14	Q9HCJ2	LRC4C_HUMAN	M	14	ENSP00000278198:I14M;ENSP00000436976:I14M;ENSP00000437132:I14M;ENSP00000434761:I14M	ENSP00000278198:I14M	I	-	3	3	LRRC4C	40094377	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.194000	0.70268	0.528000	0.53228	ATA	.	.	none		0.473	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
SOX7	83595	hgsc.bcm.edu	37	8	10587841	10587841	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:10587841G>A	ENST00000304501.1	-	1	181	c.103C>T	c.(103-105)Ccc>Tcc	p.P35S	CTD-2135J3.3_ENST00000519568.1_RNA|SOX7_ENST00000554914.1_Intron|SOX7_ENST00000553390.1_Intron|CTD-2135J3.3_ENST00000506149.2_RNA	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	35					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		Tcccccgggggccgggggacg	0.701																																					p.P35S		Atlas-SNP	.											.	SOX7	50	.	0			c.C103T						PASS	.						10.0	14.0	13.0					8																	10587841		2170	4260	6430	SO:0001583	missense	83595	exon1			CCGGGGGCCGGGG	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.103C>T	8.37:g.10587841G>A	ENSP00000301921:p.Pro35Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	84	31	0.369048	NM_031439	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	.	.	.	.	.	.	.	.	.	.	g	3.164	-0.171510	0.06421	.	.	ENSG00000171056	ENST00000304501	D	0.98531	-4.98	3.47	1.26	0.21427	High mobility group, superfamily (1);	0.278361	0.35407	U	0.003229	D	0.91294	0.7255	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	D	0.83684	0.0173	10	0.08837	T	0.75	.	6.9316	0.24444	0.0:0.1745:0.6208:0.2047	.	35	Q9BT81	SOX7_HUMAN	S	35	ENSP00000301921:P35S	ENSP00000301921:P35S	P	-	1	0	SOX7	10625251	0.001000	0.12720	0.029000	0.17559	0.300000	0.27592	0.569000	0.23638	0.616000	0.30141	0.450000	0.29827	CCC	.	.	none		0.701	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
PCDHGA7	56108	hgsc.bcm.edu	37	5	140764507	140764507	+	Missense_Mutation	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:140764507T>C	ENST00000518325.1	+	1	2041	c.2041T>C	c.(2041-2043)Tcc>Ccc	p.S681P	PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_5'Flank|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	681	Cadherin 6. {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)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTTGAGCCCTCCGACGGTCC	0.627																																					p.S681P		Atlas-SNP	.											PCDHGA7,NS,carcinoma,-2,1	PCDHGA7	130	1	0			c.T2041C						scavenged	.						56.0	63.0	61.0					5																	140764507		2201	4299	6500	SO:0001583	missense	56108	exon1			GAGCCCTCCGACG	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.2041T>C	5.37:g.140764507T>C	ENSP00000430024:p.Ser681Pro	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	53	2	0.0377358	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	3.083	-0.188590	0.06299	.	.	ENSG00000253537	ENST00000518325	T	0.52754	0.65	5.12	-8.1	0.01086	Cadherin (1);	.	.	.	.	T	0.19604	0.0471	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.34675	-0.9819	9	0.02654	T	1	.	7.8448	0.29419	0.1708:0.3145:0.0:0.5147	.	681;681	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	P	681	ENSP00000430024:S681P	ENSP00000430024:S681P	S	+	1	0	PCDHGA7	140744691	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.178000	0.03093	-1.919000	0.01071	-0.256000	0.11100	TCC	.	.	none		0.627	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
NBPF10	100132406	hgsc.bcm.edu	37	1	145296403	145296403	+	Silent	SNP	C	C	T	rs4996269	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:145296403C>T	ENST00000342960.5	+	3	360	c.325C>T	c.(325-327)Cta>Tta	p.L109L	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	109						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCTGACCCAGCTAAGGGAGAA	0.517																																					p.L109L		Atlas-SNP	.											NBPF10,NS,carcinoma,0,1	NBPF10	221	1	0			c.C325T						scavenged	.																																			SO:0001819	synonymous_variant	100132406	exon3			ACCCAGCTAAGGG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.325C>T	1.37:g.145296403C>T		Somatic	117	2	0.017094		WXS	Illumina HiSeq	Phase_I	140	11	0.0785714	NM_001039703	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	CCDS53355.1																																																																																			T|0.001;G|0.956	0.001	strong		0.517	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
MUC5B	727897	hgsc.bcm.edu	37	11	1253980	1253980	+	Missense_Mutation	SNP	A	A	G	rs202127660		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:1253980A>G	ENST00000529681.1	+	17	2103	c.2045A>G	c.(2044-2046)gAc>gGc	p.D682G	MUC5B_ENST00000447027.1_Missense_Mutation_p.D685G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	682					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGCTCAGCGACTGGAGGGAC	0.682																																					p.D682G		Atlas-SNP	.											MUC5B,caecum,carcinoma,0,2	MUC5B	473	2	0			c.A2045G						scavenged	.						21.0	24.0	23.0					11																	1253980		2116	4228	6344	SO:0001583	missense	727897	exon17			TCAGCGACTGGAG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2045A>G	11.37:g.1253980A>G	ENSP00000436812:p.Asp682Gly	Somatic	66	2	0.030303		WXS	Illumina HiSeq	Phase_I	74	10	0.135135	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	A	7.541	0.660740	0.14645	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76060	-0.99;-0.99	4.6	2.72	0.32119	Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.50103	0.1596	N	0.02960	-0.455	0.24874	N	0.992269	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45920	-0.9228	9	0.87932	D	0	.	8.6635	0.34108	0.2416:0.0:0.7584:0.0	.	682;1341;685	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	682;685;683;718	ENSP00000436812:D682G;ENSP00000415793:D685G	ENSP00000343037:D683G	D	+	2	0	MUC5B	1210556	0.999000	0.42202	0.632000	0.29296	0.070000	0.16714	2.607000	0.46300	0.373000	0.24621	-1.983000	0.00453	GAC	.	.	weak		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NAV3	89795	hgsc.bcm.edu	37	12	78400358	78400358	+	Missense_Mutation	SNP	T	T	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:78400358T>A	ENST00000397909.2	+	8	1213	c.1040T>A	c.(1039-1041)aTg>aAg	p.M347K	NAV3_ENST00000536525.2_Missense_Mutation_p.M347K|NAV3_ENST00000266692.7_Missense_Mutation_p.M347K|NAV3_ENST00000228327.6_Missense_Mutation_p.M347K			Q8IVL0	NAV3_HUMAN	neuron navigator 3	347						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ACCTCCACCATGTTGACTGTA	0.562										HNSCC(70;0.22)																											p.M347K		Atlas-SNP	.											.	NAV3	506	.	0			c.T1040A						PASS	.						61.0	63.0	62.0					12																	78400358		2101	4221	6322	SO:0001583	missense	89795	exon8			CCACCATGTTGAC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1040T>A	12.37:g.78400358T>A	ENSP00000381007:p.Met347Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	89	16	0.179775	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.57|17.57	3.423239|3.423239	0.62733|0.62733	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000550503|ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	.|T;T;T;T;T	.|0.39592	.|1.07;1.07;1.07;1.07;1.07	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	.|0.000000	.|0.48767	.|U	.|0.000174	T|T	0.57621|0.57621	0.2066|0.2066	L|L	0.52011|0.52011	1.625|1.625	0.80722|0.80722	D|D	1|1	.|D;D	.|0.62365	.|0.973;0.991	.|D;P	.|0.64042	.|0.921;0.73	T|T	0.60255|0.60255	-0.7299|-0.7299	5|10	.|0.72032	.|D	.|0.01	-19.3128|-19.3128	15.804|15.804	0.78477|0.78477	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|347;347	.|Q8IVL0;Q8IVL0-2	.|NAV3_HUMAN;.	Q|K	170|347	.|ENSP00000446628:M347K;ENSP00000446132:M347K;ENSP00000381007:M347K;ENSP00000228327:M347K;ENSP00000266692:M347K	.|ENSP00000228327:M347K	H|M	+|+	3|2	2|0	NAV3|NAV3	76924489|76924489	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.632000|0.632000	0.37999|0.37999	5.998000|5.998000	0.70653|0.70653	2.138000|2.138000	0.66242|0.66242	0.459000|0.459000	0.35465|0.35465	CAT|ATG	.	.	none		0.562	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
SON	6651	hgsc.bcm.edu	37	21	34922547	34922547	+	Missense_Mutation	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr21:34922547T>C	ENST00000356577.4	+	3	1485	c.1010T>C	c.(1009-1011)cTa>cCa	p.L337P	SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Missense_Mutation_p.L337P|SON_ENST00000381679.4_Missense_Mutation_p.L337P|SON_ENST00000290239.6_Missense_Mutation_p.L337P	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	337					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						ATTGAAGCGCTAAGATTGCCA	0.502											OREG0003564	type=REGULATORY REGION|Gene=AK074269|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.L337P		Atlas-SNP	.											.	SON	343	.	0			c.T1010C						PASS	.						105.0	110.0	108.0					21																	34922547		2203	4300	6503	SO:0001583	missense	6651	exon3			AAGCGCTAAGATT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.1010T>C	21.37:g.34922547T>C	ENSP00000348984:p.Leu337Pro	Somatic	70	0	0	851	WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672860	0.29693	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.16597	2.52;2.5;2.49;2.33	5.54	0.00568	0.14064	.	0.517188	0.16322	N	0.219526	T	0.21062	0.0507	L	0.29908	0.895	0.30562	N	0.764394	D;D;B	0.89917	0.999;1.0;0.126	D;D;B	0.69824	0.925;0.966;0.069	T	0.13872	-1.0493	10	0.36615	T	0.2	.	4.9548	0.14033	0.463:0.0843:0.0:0.4526	.	337;337;337	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	P	337	ENSP00000348984:L337P;ENSP00000290239:L337P;ENSP00000300278:L337P;ENSP00000371095:L337P	ENSP00000290239:L337P	L	+	2	0	SON	33844417	0.001000	0.12720	0.908000	0.35775	0.992000	0.81027	-0.017000	0.12590	0.059000	0.16252	-0.527000	0.04329	CTA	.	.	none		0.502	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
PIM1	5292	hgsc.bcm.edu	37	6	37138402	37138402	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138402C>T	ENST00000373509.5	+	1	424	c.51C>T	c.(49-51)tgC>tgT	p.C17C		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	108					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)			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)	CCGCGCCCTGCAACGACCTGC	0.721			T	BCL6	NHL																																p.C108C		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C324T						PASS	.						27.0	28.0	28.0					6																	37138402		2201	4296	6497	SO:0001819	synonymous_variant	5292	exon1			GCCCTGCAACGAC		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.51C>T	6.37:g.37138402C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	60	16	0.266667	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
PIM1	5292	hgsc.bcm.edu	37	6	37138563	37138563	+	Missense_Mutation	SNP	C	C	A	rs34095970		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138563C>A	ENST00000373509.5	+	2	470	c.97C>A	c.(97-99)Ccc>Acc	p.P33T		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	124					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)			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)	GGAGAAGGAGCCCCTGGAGTC	0.701			T	BCL6	NHL																																p.P124T		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C370A						PASS	.						21.0	31.0	28.0					6																	37138563		2155	4262	6417	SO:0001583	missense	5292	exon2			AAGGAGCCCCTGG		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.97C>A	6.37:g.37138563C>A	ENSP00000362608:p.Pro33Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.517268	0.44763	.	.	ENSG00000137193	ENST00000373509	T	0.69040	-0.37	4.64	3.75	0.43078	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	T	0.27419	0.0673	N	0.08118	0	0.48571	D	0.999676	B	0.09022	0.002	B	0.06405	0.002	T	0.11060	-1.0603	10	0.23302	T	0.38	.	12.1438	0.54012	0.0:0.9152:0.0:0.0848	.	124	P11309	PIM1_HUMAN	T	33	ENSP00000362608:P33T	ENSP00000362608:P33T	P	+	1	0	PIM1	37246541	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.980000	0.40618	2.294000	0.77228	0.549000	0.68633	CCC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
KIRREL3	84623	hgsc.bcm.edu	37	11	126299147	126299147	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:126299147C>T	ENST00000525144.2	-	15	1982	c.1733G>A	c.(1732-1734)cGa>cAa	p.R578Q	KIRREL3_ENST00000529097.2_Missense_Mutation_p.R566Q|KIRREL3_ENST00000416561.2_Missense_Mutation_p.R45Q	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	578					hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AATTTCCACTCGGATATCATT	0.453																																					p.R578Q		Atlas-SNP	.											.	KIRREL3	183	.	0			c.G1733A						PASS	.						97.0	101.0	99.0					11																	126299147		1946	4141	6087	SO:0001583	missense	84623	exon15			TCCACTCGGATAT	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1733G>A	11.37:g.126299147C>T	ENSP00000435466:p.Arg578Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	108	19	0.175926	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	C	36	5.627850	0.96671	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	T;T;T	0.79554	-0.67;-0.42;-1.28	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	D	0.86871	0.6037	L	0.46157	1.445	0.58432	D	0.999999	D;D	0.71674	0.998;0.995	D;P	0.66602	0.945;0.837	D	0.87215	0.2250	10	0.66056	D	0.02	-4.7594	19.7415	0.96232	0.0:1.0:0.0:0.0	.	566;578	E9PRX9;Q8IZU9	.;KIRR3_HUMAN	Q	578;566;45	ENSP00000435466:R578Q;ENSP00000434081:R566Q;ENSP00000408692:R45Q	ENSP00000408692:R45Q	R	-	2	0	KIRREL3	125804357	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.487000	0.81328	2.668000	0.90789	0.561000	0.74099	CGA	.	.	none		0.453	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
LGALS13	29124	hgsc.bcm.edu	37	19	40095831	40095831	+	Missense_Mutation	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:40095831C>A	ENST00000221797.4	+	3	151	c.106C>A	c.(106-108)Ctg>Atg	p.L36M		NM_013268.2	NP_037400.1	Q9UHV8	PP13_HUMAN	lectin, galactoside-binding, soluble, 13	36	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			lung(5)|ovary(1)|urinary_tract(1)	7	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			TGACCCACAGCTGCAGGTGGA	0.517																																					p.L36M		Atlas-SNP	.											.	LGALS13	22	.	0			c.C106A						PASS	.						143.0	112.0	122.0					19																	40095831		2203	4300	6503	SO:0001583	missense	29124	exon3			CCACAGCTGCAGG	AF117383	CCDS33024.1	19q13.2	2014-03-19	2008-07-25		ENSG00000105198	ENSG00000105198		"""Lectins, galactoside-binding"""	15449	protein-coding gene	gene with protein product	"""galectin 13"""	608717				6856484, 10527825	Standard	NM_013268		Approved	PP13, PLAC8	uc002omb.3	Q9UHV8	OTTHUMG00000183073	ENST00000221797.4:c.106C>A	19.37:g.40095831C>A	ENSP00000221797:p.Leu36Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	78	19	0.24359	NM_013268	C5HZ15	Missense_Mutation	SNP	ENST00000221797.4	37	CCDS33024.1	.	.	.	.	.	.	.	.	.	.	.	11.18	1.562868	0.27915	.	.	ENSG00000105198	ENST00000221797	T	0.05996	3.36	0.744	-1.35	0.09114	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.15998	0.0385	M	0.66506	2.035	0.19775	N	0.99996	D	0.60160	0.987	D	0.65874	0.939	T	0.09015	-1.0694	8	0.56958	D	0.05	.	.	.	.	.	36	Q9UHV8	PP13_HUMAN	M	36	ENSP00000221797:L36M	ENSP00000221797:L36M	L	+	1	2	LGALS13	44787671	0.038000	0.19896	0.434000	0.26772	0.452000	0.32318	-1.528000	0.02225	-0.386000	0.07821	0.305000	0.20034	CTG	.	.	none		0.517	LGALS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464968.1	NM_013268	
PRB4	5545	hgsc.bcm.edu	37	12	11461692	11461692	+	Silent	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:11461692T>C	ENST00000535904.1	-	3	258	c.225A>G	c.(223-225)ccA>ccG	p.P75P	PRB4_ENST00000445719.2_Silent_p.P75P|PRB4_ENST00000279575.1_Silent_p.P75P			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	96	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.			Missing (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						CTGGCTTTCCTGGAGGAGGTG	0.612										HNSCC(22;0.051)																											p.P75P		Atlas-SNP	.											PRB4,caecum,carcinoma,-1,2	PRB4	59	2	0			c.A225G						scavenged	.						291.0	319.0	310.0					12																	11461692		2203	4300	6503	SO:0001819	synonymous_variant	5545	exon3			CTTTCCTGGAGGA		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.225A>G	12.37:g.11461692T>C		Somatic	229	3	0.0131004		WXS	Illumina HiSeq	Phase_I	272	15	0.0551471	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Silent	SNP	ENST00000535904.1	37	CCDS8641.1																																																																																			.	.	none		0.612	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723	
PKHD1	5314	hgsc.bcm.edu	37	6	51523890	51523890	+	Silent	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:51523890A>G	ENST00000371117.3	-	61	11309	c.11034T>C	c.(11032-11034)atT>atC	p.I3678I		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3678					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ATAAGGATGAAATCATTCCAG	0.418																																					p.I3678I		Atlas-SNP	.											.	PKHD1	927	.	0			c.T11034C						PASS	.						173.0	161.0	165.0					6																	51523890		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon61			GGATGAAATCATT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11034T>C	6.37:g.51523890A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	15	0.170455	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			.	.	none		0.418	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857872	149857872	+	Missense_Mutation	SNP	G	G	C	rs587684290		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:149857872G>C	ENST00000369155.2	-	1	360	c.319C>G	c.(319-321)Ctg>Gtg	p.L107V	BOLA1_ENST00000369153.2_5'Flank|HIST2H2AC_ENST00000331380.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	107					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)			TGCTTGGCCAGCTCGCCGGGC	0.687																																					p.L107V		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.C319G						PASS	.						23.0	28.0	26.0					1																	149857872		2197	4277	6474	SO:0001583	missense	8349	exon1			TGGCCAGCTCGCC	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.319C>G	1.37:g.149857872G>C	ENSP00000358151:p.Leu107Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	37	CCDS936.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.565889	0.65651	.	.	ENSG00000184678	ENST00000369155	T	0.50813	0.73	5.92	5.02	0.67125	Histone-fold (2);	0.000000	0.64402	D	0.000017	T	0.53674	0.1811	H	0.97940	4.11	0.34129	D	0.665045	B	0.34226	0.443	B	0.33295	0.161	T	0.69548	-0.5116	10	0.66056	D	0.02	.	13.8428	0.63449	0.0738:0.0:0.9262:0.0	.	107	Q16778	H2B2E_HUMAN	V	107	ENSP00000358151:L107V	ENSP00000358151:L107V	L	-	1	2	HIST2H2BE	148124496	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.648000	0.67930	1.519000	0.48950	0.585000	0.79938	CTG	.	.	none		0.687	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528	
TEX13A	56157	hgsc.bcm.edu	37	X	104464743	104464743	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chrX:104464743C>T	ENST00000413579.1	-	2	450	c.339G>A	c.(337-339)aaG>aaA	p.K113K	IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.K113K|TEX13A_ENST00000372575.1_Silent_p.K113K|IL1RAPL2_ENST00000344799.4_Intron			Q9BXU3	TX13A_HUMAN	testis expressed 13A	113							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GCTCCCTGAGCTTCTTCAGGT	0.607																																					p.K113K		Atlas-SNP	.											.	TEX13A	55	.	0			c.G339A						PASS	.						33.0	34.0	34.0					X																	104464743		2169	4253	6422	SO:0001819	synonymous_variant	56157	exon2			CCTGAGCTTCTTC	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.339G>A	X.37:g.104464743C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	37																																																																																				.	.	none		0.607	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
ZNF285	26974	hgsc.bcm.edu	37	19	44891217	44891217	+	Missense_Mutation	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:44891217T>C	ENST00000330997.4	-	4	1254	c.1190A>G	c.(1189-1191)gAg>gGg	p.E397G	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.E397G|ZNF285_ENST00000591679.1_Missense_Mutation_p.E404G	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	397					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E397G(2)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GTAGGGCTTCTCTCCAGTGTG	0.483																																					p.E397G		Atlas-SNP	.											ZNF285,NS,carcinoma,0,2	ZNF285	86	2	2	Substitution - Missense(2)	prostate(2)	c.A1190G						scavenged	.						57.0	56.0	57.0					19																	44891217		2203	4300	6503	SO:0001583	missense	26974	exon4			GGCTTCTCTCCAG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1190A>G	19.37:g.44891217T>C	ENSP00000333595:p.Glu397Gly	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	3	0.0441176	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812415	0.70912	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.27557	1.66	3.36	3.36	0.38483	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.53012	0.1770	M	0.75150	2.29	0.34602	D	0.716652	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.933	T	0.67393	-0.5682	9	0.87932	D	0	.	11.1099	0.48226	0.0:0.0:0.0:1.0	.	421;397	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	G	420;397	ENSP00000333595:E397G	ENSP00000333595:E397G	E	-	2	0	ZNF285	49583057	1.000000	0.71417	0.745000	0.31077	0.941000	0.58515	7.429000	0.80309	1.308000	0.44962	0.248000	0.18094	GAG	.	.	none		0.483	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
PABPC1	26986	hgsc.bcm.edu	37	8	101730000	101730000	+	Splice_Site	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:101730000C>A	ENST00000318607.5	-	3	1632		c.e3+1		PABPC1_ENST00000519596.1_5'Flank|PABPC1_ENST00000519004.1_Splice_Site|PABPC1_ENST00000522387.1_Splice_Site	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TTATAACTTACACTTTGCGAT	0.323																																					.		Atlas-SNP	.											.	PABPC1	76	.	0			c.503+1G>T						PASS	.						47.0	45.0	46.0					8																	101730000		2203	4299	6502	SO:0001630	splice_region_variant	26986	exon4			AACTTACACTTTG	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.503+1G>T	8.37:g.101730000C>A		Somatic	385	1	0.0025974		WXS	Illumina HiSeq	Phase_I	334	117	0.350299	NM_002568	Q15097|Q93004	Splice_Site	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499709	0.64298	.	.	ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000519100;ENST00000523555	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5422	0.91033	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PABPC1	101799176	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.756000	0.85195	2.456000	0.83038	0.563000	0.77884	.	.	.	none		0.323	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	Intron
ADAMTS18	170692	hgsc.bcm.edu	37	16	77401400	77401400	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:77401400C>T	ENST00000282849.5	-	4	1134	c.716G>A	c.(715-717)cGa>cAa	p.R239Q	ADAMTS18_ENST00000567121.1_5'UTR	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	239					eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						CTCTGTCTCTCGACTCTGAGA	0.478																																					p.R239Q		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G716A						PASS	.						87.0	81.0	83.0					16																	77401400		2198	4300	6498	SO:0001583	missense	170692	exon4			GTCTCTCGACTCT	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.716G>A	16.37:g.77401400C>T	ENSP00000282849:p.Arg239Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	0.260	-1.000444	0.02128	.	.	ENSG00000140873	ENST00000282849;ENST00000449265	T;T	0.60171	0.21;2.84	4.72	-5.52	0.02560	.	0.875294	0.10159	N	0.708571	T	0.16514	0.0397	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36065	-0.9763	10	0.05436	T	0.98	.	4.9243	0.13885	0.0857:0.2003:0.4601:0.2538	.	239	Q8TE60	ATS18_HUMAN	Q	239	ENSP00000282849:R239Q;ENSP00000392540:R239Q	ENSP00000282849:R239Q	R	-	2	0	ADAMTS18	75958901	0.001000	0.12720	0.013000	0.15412	0.205000	0.24178	-0.509000	0.06336	-0.592000	0.05851	-3.097000	0.00064	CGA	.	.	none		0.478	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
MCC	4163	hgsc.bcm.edu	37	5	112419851	112419851	+	Missense_Mutation	SNP	C	C	T	rs373730711		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:112419851C>T	ENST00000302475.4	-	8	1575	c.1012G>A	c.(1012-1014)Gaa>Aaa	p.E338K	MCC_ENST00000408903.3_Missense_Mutation_p.E528K|MCC_ENST00000515367.2_Missense_Mutation_p.E275K|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	338					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		GATGACGATTCGGACCTTGTC	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		19552	0.0		0.0	False		,,,				2504	0.001				p.E528K		Atlas-SNP	.											.	MCC	234	.	0			c.G1582A						PASS	.	C	LYS/GLU,LYS/GLU	1,4403	2.1+/-5.4	0,1,2201	178.0	162.0	168.0		1582,1012	5.5	0.6	5		168	0,8600		0,0,4300	no	missense,missense	MCC	NM_001085377.1,NM_002387.2	56,56	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	528/1020,338/830	112419851	1,13003	2202	4300	6502	SO:0001583	missense	4163	exon10			ACGATTCGGACCT		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1012G>A	5.37:g.112419851C>T	ENSP00000305617:p.Glu338Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	94	30	0.319149	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836563	0.50951	2.27E-4	0.0	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.33865	2.56;2.57;1.39	5.47	5.47	0.80525	.	0.060761	0.64402	D	0.000007	T	0.29976	0.0750	N	0.14661	0.345	0.58432	D	0.999998	P;P;D;P	0.56521	0.892;0.738;0.976;0.817	B;B;P;B	0.45856	0.099;0.139;0.495;0.099	T	0.05225	-1.0898	10	0.35671	T	0.21	-5.0905	19.3251	0.94258	0.0:1.0:0.0:0.0	.	338;300;528;338	B7Z6G0;B3KTX0;P23508-2;P23508	.;.;.;CRCM_HUMAN	K	338;275;528	ENSP00000305617:E338K;ENSP00000421615:E275K;ENSP00000386227:E528K	ENSP00000305617:E338K	E	-	1	0	MCC	112447750	1.000000	0.71417	0.619000	0.29118	0.283000	0.27025	5.961000	0.70356	2.574000	0.86865	0.563000	0.77884	GAA	.	.	weak		0.448	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr18:14542654C>A	ENST00000358970.5	-	1	491	c.492G>T	c.(490-492)acG>acT	p.T164T	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	164								p.T164T(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGTTCATGTCCGTGTCCCTGA	0.592																																					p.T164T		Atlas-SNP	.											POTEC,NS,carcinoma,-1,5	POTEC	129	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G492T						scavenged	.						260.0	241.0	247.0					18																	14542654		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			CATGTCCGTGTCC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.492G>T	18.37:g.14542654C>A		Somatic	452	5	0.0110619		WXS	Illumina HiSeq	Phase_I	294	6	0.0204082	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	none		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
BTG2	7832	hgsc.bcm.edu	37	1	203274831	203274831	+	Missense_Mutation	SNP	C	C	A	rs530501274		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:203274831C>A	ENST00000290551.4	+	1	168	c.97C>A	c.(97-99)Cag>Aag	p.Q33K	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	33					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)			CGTGAGCGAGCAGAGGCTTAA	0.706																																					p.Q33K		Atlas-SNP	.											.	BTG2	16	.	0			c.C97A						PASS	.						15.0	16.0	16.0					1																	203274831		2150	4221	6371	SO:0001583	missense	7832	exon1			AGCGAGCAGAGGC		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.97C>A	1.37:g.203274831C>A	ENSP00000290551:p.Gln33Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070481	0.55539	.	.	ENSG00000159388	ENST00000290551	T	0.22134	1.97	4.66	3.72	0.42706	Anti-proliferative protein (3);	0.270105	0.31145	N	0.008179	T	0.17959	0.0431	L	0.45581	1.43	0.42010	D	0.99093	B	0.24533	0.105	B	0.26094	0.066	T	0.05099	-1.0906	10	0.28530	T	0.3	-10.9891	8.7243	0.34460	0.1715:0.6626:0.1659:0.0	.	33	P78543	BTG2_HUMAN	K	33	ENSP00000290551:Q33K	ENSP00000290551:Q33K	Q	+	1	0	BTG2	201541454	1.000000	0.71417	0.994000	0.49952	0.847000	0.48162	2.921000	0.48852	1.144000	0.42321	0.478000	0.44815	CAG	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
BMPER	168667	hgsc.bcm.edu	37	7	33945290	33945290	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:33945290C>T	ENST00000297161.2	+	2	439	c.65C>T	c.(64-66)aCg>aTg	p.T22M	BMPER_ENST00000426693.1_Missense_Mutation_p.T22M	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	22					blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CCTGGGATTACGTGCTGCGTC	0.657																																					p.T22M		Atlas-SNP	.											BMPER,NS,carcinoma,-1,1	BMPER	131	1	0			c.C65T						PASS	.						53.0	49.0	50.0					7																	33945290		2203	4300	6503	SO:0001583	missense	168667	exon2			GGATTACGTGCTG		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.65C>T	7.37:g.33945290C>T	ENSP00000297161:p.Thr22Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	15	0.180723	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	37	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.386045	0.61956	.	.	ENSG00000164619	ENST00000297161;ENST00000426693;ENST00000436222	T;T	0.19532	2.14;2.14	3.65	3.65	0.41850	.	0.272984	0.29119	N	0.013098	T	0.21427	0.0516	L	0.39898	1.24	0.29655	N	0.843626	D	0.63046	0.992	P	0.47044	0.535	T	0.06935	-1.0799	10	0.66056	D	0.02	.	10.617	0.45456	0.1929:0.8071:0.0:0.0	.	22	Q8N8U9	BMPER_HUMAN	M	22	ENSP00000297161:T22M;ENSP00000393950:T22M	ENSP00000297161:T22M	T	+	2	0	BMPER	33911815	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.575000	0.53870	2.014000	0.59158	0.557000	0.71058	ACG	.	.	none		0.657	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
DTX1	1840	hgsc.bcm.edu	37	12	113496139	113496139	+	Missense_Mutation	SNP	A	A	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:113496139A>T	ENST00000257600.3	+	1	645	c.142A>T	c.(142-144)Att>Ttt	p.I48F		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	48	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						GTGCCACCACATTGAGAACGT	0.652																																					p.I48F		Atlas-SNP	.											.	DTX1	83	.	0			c.A142T						PASS	.						110.0	96.0	100.0					12																	113496139		2203	4300	6503	SO:0001583	missense	1840	exon1			CACCACATTGAGA	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.142A>T	12.37:g.113496139A>T	ENSP00000257600:p.Ile48Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	19	0.311475	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824981	0.90955	.	.	ENSG00000135144	ENST00000257600	T	0.64438	-0.1	3.9	3.9	0.45041	WWE domain (2);WWE domain, subgroup (1);	0.000000	0.64402	U	0.000001	T	0.79275	0.4418	M	0.84683	2.71	0.53688	D	0.999976	D	0.69078	0.997	D	0.79108	0.992	T	0.82697	-0.0329	10	0.87932	D	0	-2.9711	11.9027	0.52692	1.0:0.0:0.0:0.0	.	48	Q86Y01	DTX1_HUMAN	F	48	ENSP00000257600:I48F	ENSP00000257600:I48F	I	+	1	0	DTX1	111980522	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	8.407000	0.90218	1.644000	0.50603	0.454000	0.30748	ATT	.	.	none		0.652	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
MUC4	4585	hgsc.bcm.edu	37	3	195509611	195509611	+	Missense_Mutation	SNP	A	A	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:195509611A>T	ENST00000463781.3	-	2	9299	c.8840T>A	c.(8839-8841)gTc>gAc	p.V2947D	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V2947D|MUC4_ENST00000349607.4_Intron	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.V2947D(3)		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)		AGTGTCGGTGACAGGAAGAGG	0.592																																					p.V2947D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	skin(2)|endometrium(1)	c.T8840A						scavenged	.						10.0	8.0	9.0					3																	195509611		654	1505	2159	SO:0001583	missense	4585	exon2			TCGGTGACAGGAA	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.8840T>A	3.37:g.195509611A>T	ENSP00000417498:p.Val2947Asp	Somatic	240	3	0.0125		WXS	Illumina HiSeq	Phase_I	140	4	0.0285714	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	.	.	.	.	.	.	.	.	.	.	a	4.900	0.167345	0.09339	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.5;1.49	.	.	.	.	.	.	.	.	T	0.24509	0.0594	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	D	0.68483	0.958	T	0.10154	-1.0642	7	.	.	.	.	1.3928	0.02254	0.3276:0.0:0.3249:0.3475	.	2819	E7ESK3	.	D	2947	ENSP00000417498:V2947D;ENSP00000420243:V2947D	.	V	-	2	0	MUC4	196994390	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.286000	0.08399	-0.000000	0.14550	0.000000	0.15137	GTC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156969	26156969	+	Silent	SNP	G	G	A	rs376044340		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26156969G>A	ENST00000304218.3	+	1	411	c.351G>A	c.(349-351)aaG>aaA	p.K117K	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	117					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GGGAAGCCAAGCCTAAGGCTA	0.642																																					p.K117K		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G351A						PASS	.	G		0,4404		0,0,2202	24.0	31.0	29.0		351	1.7	1.0	6		29	2,8598		0,2,4298	no	coding-synonymous	HIST1H1E	NM_005321.2		0,2,6500	AA,AG,GG		0.0233,0.0,0.0154		117/220	26156969	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	3008	exon1			AGCCAAGCCTAAG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.351G>A	6.37:g.26156969G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	88	23	0.261364	NM_005321	Q4VB25	Silent	SNP	ENST00000304218.3	37	CCDS4586.1																																																																																			.	.	weak		0.642	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
ERBB4	2066	hgsc.bcm.edu	37	2	212587162	212587162	+	Missense_Mutation	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:212587162T>G	ENST00000342788.4	-	7	1149	c.839A>C	c.(838-840)aAt>aCt	p.N280T	ERBB4_ENST00000402597.1_Missense_Mutation_p.N280T|ERBB4_ENST00000484474.1_5'Flank|ERBB4_ENST00000436443.1_Missense_Mutation_p.N280T	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	280	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GTACTTTGCATTGAAATTGTG	0.378										TSP Lung(8;0.080)																											p.N280T		Atlas-SNP	.											.	ERBB4	480	.	0			c.A839C						PASS	.						180.0	164.0	170.0					2																	212587162		2203	4300	6503	SO:0001583	missense	2066	exon7			TTTGCATTGAAAT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.839A>C	2.37:g.212587162T>G	ENSP00000342235:p.Asn280Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	128	21	0.164062	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.24|14.24	2.476435|2.476435	0.44044|0.44044	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	.|T;T;T	.|0.28255	.|1.62;1.62;1.62	5.83|5.83	5.83|5.83	0.93111|0.93111	.|Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.|0.175798	.|0.64402	.|D	.|0.000007	T|T	0.44519|0.44519	0.1297|0.1297	L|L	0.58428|0.58428	1.81|1.81	0.37517|0.37517	D|D	0.917396|0.917396	.|B;B;B;B;B	.|0.26635	.|0.021;0.15;0.155;0.021;0.026	.|B;B;B;B;B	.|0.43386	.|0.03;0.418;0.257;0.03;0.056	T|T	0.47005|0.47005	-0.9150|-0.9150	5|10	.|0.35671	.|T	.|0.21	.|.	16.1946|16.1946	0.82018|0.82018	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|280;280;139;280;280	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	L|T	280|280	.|ENSP00000342235:N280T;ENSP00000403204:N280T;ENSP00000385565:N280T	.|ENSP00000342235:N280T	M|N	-|-	1|2	0|0	ERBB4|ERBB4	212295407|212295407	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	6.018000|6.018000	0.70811|0.70811	2.228000|2.228000	0.72767|0.72767	0.528000|0.528000	0.53228|0.53228	ATG|AAT	.	.	none		0.378	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
UBE2A	7319	hgsc.bcm.edu	37	X	118717088	118717088	+	Splice_Site	SNP	A	A	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chrX:118717088A>C	ENST00000371558.2	+	6	504		c.e6-1		UBE2A_ENST00000371569.5_Splice_Site|UBE2A_ENST00000346330.3_Splice_Site	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						TTGTCTCTTTAGTCTCTGTTG	0.388								Rad6 pathway																													.		Atlas-SNP	.											.	UBE2A	43	.	0			c.241-2A>C						PASS	.						99.0	89.0	93.0					X																	118717088		2203	4300	6503	SO:0001630	splice_region_variant	7319	exon5			CTCTTTAGTCTCT	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"""Ubiquitin-conjugating enzymes E2"""	12472	protein-coding gene	gene with protein product		312180	"""ubiquitin-conjugating enzyme E2A (RAD6 homolog)"""			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.331-1A>C	X.37:g.118717088A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	42	34	0.809524	NM_181762	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Splice_Site	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.362521	0.41902	.	.	ENSG00000077721	ENST00000371558;ENST00000346330;ENST00000371569	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3672	0.66815	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE2A	118601116	1.000000	0.71417	0.966000	0.40874	0.444000	0.32077	9.329000	0.96413	1.992000	0.58205	0.412000	0.27726	.	.	.	none		0.388	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336	Intron
LRP2	4036	hgsc.bcm.edu	37	2	170060578	170060578	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:170060578A>G	ENST00000263816.3	-	42	8204	c.7919T>C	c.(7918-7920)aTc>aCc	p.I2640T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2640					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AACAGTGTTGATTCCCCTGGG	0.463																																					p.I2640T		Atlas-SNP	.											.	LRP2	751	.	0			c.T7919C						PASS	.						186.0	189.0	188.0					2																	170060578		2203	4300	6503	SO:0001583	missense	4036	exon42			GTGTTGATTCCCC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.7919T>C	2.37:g.170060578A>G	ENSP00000263816:p.Ile2640Thr	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	151	84	0.556291	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.906247	0.52333	.	.	ENSG00000081479	ENST00000263816	D	0.91295	-2.82	5.58	5.58	0.84498	Six-bladed beta-propeller, TolB-like (1);	0.163861	0.52532	D	0.000062	D	0.94548	0.8244	H	0.97340	3.985	0.80722	D	1	P	0.47762	0.9	B	0.43225	0.412	D	0.95521	0.8594	10	0.51188	T	0.08	.	15.7383	0.77863	1.0:0.0:0.0:0.0	.	2640	P98164	LRP2_HUMAN	T	2640	ENSP00000263816:I2640T	ENSP00000263816:I2640T	I	-	2	0	LRP2	169768824	1.000000	0.71417	0.006000	0.13384	0.007000	0.05969	9.238000	0.95380	2.116000	0.64780	0.533000	0.62120	ATC	.	.	none		0.463	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156900	26156900	+	Silent	SNP	G	G	A	rs549787183		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26156900G>A	ENST00000304218.3	+	1	342	c.282G>A	c.(280-282)gtG>gtA	p.V94V	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	94	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GCACCCTGGTGCAGACCAAGG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		15327	0.0		0.001	False		,,,				2504	0.0				p.V94V		Atlas-SNP	.											HIST1H1E,NS,carcinoma,+2,1	HIST1H1E	69	1	0			c.G282A						PASS	.						51.0	55.0	53.0					6																	26156900		2203	4300	6503	SO:0001819	synonymous_variant	3008	exon1			CCTGGTGCAGACC	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.282G>A	6.37:g.26156900G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	41	0.394231	NM_005321	Q4VB25	Silent	SNP	ENST00000304218.3	37	CCDS4586.1																																																																																			.	.	none		0.607	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
CHMP2B	25978	hgsc.bcm.edu	37	3	87295015	87295015	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:87295015A>G	ENST00000263780.4	+	3	516	c.278A>G	c.(277-279)aAt>aGt	p.N93S	CHMP2B_ENST00000472024.1_3'UTR|CHMP2B_ENST00000471660.1_Missense_Mutation_p.N52S|CHMP2B_ENST00000494980.1_Intron	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	93					cell death (GO:0008219)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	12	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		AAAGTGATGAATTCCCAAATG	0.323																																					p.N93S		Atlas-SNP	.											.	CHMP2B	28	.	0			c.A278G						PASS	.						81.0	87.0	85.0					3																	87295015		2203	4300	6503	SO:0001583	missense	25978	exon3			TGATGAATTCCCA	BC001553	CCDS2918.1, CCDS58840.1	3p12.1	2011-09-21	2011-09-21		ENSG00000083937	ENSG00000083937		"""Charged multivesicular body proteins"""	24537	protein-coding gene	gene with protein product	"""VPS2 homolog B (S. cerevisiae)"""	609512	"""chromatin modifying protein 2B"""			11559748	Standard	NM_014043		Approved	DKFZP564O123, CHMP2.5, VPS2B	uc003dqp.4	Q9UQN3	OTTHUMG00000158982	ENST00000263780.4:c.278A>G	3.37:g.87295015A>G	ENSP00000263780:p.Asn93Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	159	27	0.169811	NM_014043	B4DJG8|Q53HC7|Q9Y4U6	Missense_Mutation	SNP	ENST00000263780.4	37	CCDS2918.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.983107	0.34942	.	.	ENSG00000083937	ENST00000471660;ENST00000263780	T;T	0.71817	-0.6;-0.6	5.02	5.02	0.67125	.	0.142259	0.64402	D	0.000006	T	0.57755	0.2075	L	0.40543	1.245	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.52411	-0.8579	10	0.18710	T	0.47	-9.1359	9.2981	0.37829	0.9186:0.0:0.0814:0.0	.	52;93	B4DJG8;Q9UQN3	.;CHM2B_HUMAN	S	52;93	ENSP00000419998:N52S;ENSP00000263780:N93S	ENSP00000263780:N93S	N	+	2	0	CHMP2B	87377705	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.039000	0.70972	1.861000	0.53984	0.533000	0.62120	AAT	.	.	none		0.323	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043	
COL6A5	256076	hgsc.bcm.edu	37	3	130116569	130116569	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:130116569G>A	ENST00000432398.2	+	9	4205	c.3711G>A	c.(3709-3711)ggG>ggA	p.G1237G	COL6A5_ENST00000265379.6_Silent_p.G1237G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1237	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TGAGCTGTGGGGCTGGCACAG	0.542																																					p.G1237G		Atlas-SNP	.											.	COL6A5	205	.	0			c.G3711A						PASS	.						103.0	94.0	97.0					3																	130116569		692	1591	2283	SO:0001819	synonymous_variant	256076	exon9			CTGTGGGGCTGGC	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.3711G>A	3.37:g.130116569G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				.	.	none		0.542	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
DPY19L1	23333	hgsc.bcm.edu	37	7	35009120	35009120	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:35009120G>A	ENST00000310974.4	-	9	864	c.720C>T	c.(718-720)agC>agT	p.S240S	DPY19L1_ENST00000462134.2_5'UTR	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	240						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.S240S(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						GTGCAATCAAGCTTCCTCTAT	0.358																																					p.S240S		Atlas-SNP	.											DPY19L1,NS,carcinoma,0,2	DPY19L1	56	2	2	Substitution - coding silent(2)	kidney(2)	c.C720T						scavenged	.						81.0	76.0	77.0					7																	35009120		1833	4097	5930	SO:0001819	synonymous_variant	23333	exon9			AATCAAGCTTCCT	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.720C>T	7.37:g.35009120G>A		Somatic	466	14	0.0300429		WXS	Illumina HiSeq	Phase_I	432	15	0.0347222	NM_015283	O94954|Q4G151	Silent	SNP	ENST00000310974.4	37	CCDS43567.1																																																																																			.	.	none		0.358	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
ATP1A3	478	hgsc.bcm.edu	37	19	42485704	42485704	+	Missense_Mutation	SNP	G	G	A	rs150785666	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:42485704G>A	ENST00000302102.5	-	11	1537	c.1387C>T	c.(1387-1389)Cgc>Tgc	p.R463C	ATP1A3_ENST00000602133.1_Missense_Mutation_p.R433C|ATP1A3_ENST00000545399.1_Missense_Mutation_p.R476C|ATP1A3_ENST00000543770.1_Missense_Mutation_p.R474C	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	463					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						TTCTTGTTGCGTTCACGCATC	0.552																																					p.R476C		Atlas-SNP	.											.	ATP1A3	117	.	0			c.C1426T						PASS	.	G	CYS/ARG	3,4403	6.2+/-15.9	0,3,2200	113.0	96.0	102.0		1387	3.9	1.0	19	dbSNP_134	102	7,8593	5.7+/-21.5	0,7,4293	yes	missense	ATP1A3	NM_152296.3	180	0,10,6493	AA,AG,GG		0.0814,0.0681,0.0769	possibly-damaging	463/1014	42485704	10,12996	2203	4300	6503	SO:0001583	missense	478	exon11			TGTTGCGTTCACG		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"""ATPases / P-type"""	801	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-3"", ""sodium pump subunit alpha-3"", ""sodium-potassium ATPase catalytic subunit alpha-3"""	182350	"""dystonia 12"""	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.1387C>T	19.37:g.42485704G>A	ENSP00000302397:p.Arg463Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	37	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.824059	0.71143	6.81E-4	8.14E-4	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	D;D;D;D	0.96073	-3.9;-3.9;-3.9;-3.9	3.88	3.88	0.44766	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.240845	0.39834	N	0.001256	D	0.94896	0.8350	L	0.37750	1.13	0.54753	D	0.999989	P;P;D;P	0.71674	0.951;0.628;0.998;0.679	P;P;P;P	0.62813	0.762;0.483;0.907;0.617	D	0.94166	0.7419	10	0.87932	D	0	.	9.0984	0.36653	0.0:0.0:0.7817:0.2183	.	476;474;463;463	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	C	463;463;476;433;207;474	ENSP00000302397:R463C;ENSP00000411503:R463C;ENSP00000444688:R476C;ENSP00000437577:R474C	ENSP00000302397:R463C	R	-	1	0	ATP1A3	47177544	0.309000	0.24518	0.966000	0.40874	0.990000	0.78478	2.548000	0.45794	2.449000	0.82847	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.552	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907275	12907275	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:12907275G>C	ENST00000317869.6	-	2	1093	c.868C>G	c.(868-870)Cag>Gag	p.Q290E		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	290						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						GAGTCATCCTGGCCATTGGTG	0.443																																					p.Q290E		Atlas-SNP	.											HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	1	0			c.C868G						scavenged	.						125.0	135.0	132.0					1																	12907275		2203	4299	6502	SO:0001583	missense	343069	exon2			CATCCTGGCCATT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.868C>G	1.37:g.12907275G>C	ENSP00000365370:p.Gln290Glu	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	104	2	0.0192308	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-4.135616	0.00001	.	.	ENSG00000179172	ENST00000317869	T	0.07216	3.21	1.09	-2.18	0.07037	.	0.420350	0.20880	N	0.084017	T	0.01353	0.0044	N	0.00583	-1.355	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	10	0.02654	T	1	.	2.6632	0.05032	0.0:0.3331:0.2756:0.3913	.	290	O60812	HNRCL_HUMAN	E	290	ENSP00000365370:Q290E	ENSP00000365370:Q290E	Q	-	1	0	HNRNPCL1	12829862	0.994000	0.37717	0.016000	0.15963	0.063000	0.16089	-0.019000	0.12546	-1.068000	0.03156	-0.786000	0.03341	CAG	.	.	none		0.443	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
OR6N1	128372	hgsc.bcm.edu	37	1	158735736	158735736	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:158735736G>A	ENST00000335094.2	-	1	756	c.737C>T	c.(736-738)aCt>aTt	p.T246I		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					GAGAACCACAGTGAAGTGGGA	0.532																																					p.T246I		Atlas-SNP	.											.	OR6N1	96	.	0			c.C737T						PASS	.						170.0	159.0	163.0					1																	158735736		2203	4300	6503	SO:0001583	missense	128372	exon1			ACCACAGTGAAGT	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.737C>T	1.37:g.158735736G>A	ENSP00000335535:p.Thr246Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	94	35	0.37234	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	.	.	.	.	.	.	.	.	.	.	G	7.489	0.650179	0.14516	.	.	ENSG00000197403	ENST00000335094	T	0.00350	7.98	4.74	3.8	0.43715	GPCR, rhodopsin-like superfamily (1);	0.159979	0.30227	N	0.010102	T	0.00073	0.0002	L	0.38692	1.165	0.26491	N	0.974945	B	0.22080	0.064	B	0.22152	0.038	T	0.27191	-1.0081	10	0.38643	T	0.18	-6.181	11.135	0.48368	0.0962:0.0:0.9038:0.0	.	246	Q8NGY5	OR6N1_HUMAN	I	246	ENSP00000335535:T246I	ENSP00000335535:T246I	T	-	2	0	OR6N1	157002360	0.000000	0.05858	0.998000	0.56505	0.513000	0.34164	0.272000	0.18644	1.129000	0.42072	0.655000	0.94253	ACT	.	.	none		0.532	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
GML	2765	hgsc.bcm.edu	37	8	143927837	143927837	+	Missense_Mutation	SNP	T	T	C	rs527963435		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:143927837T>C	ENST00000220940.1	+	4	298	c.208T>C	c.(208-210)Tat>Cat	p.Y70H		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	70	UPAR/Ly6.				apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACTACTTGTTTATAAGAACTG	0.358																																					p.Y70H		Atlas-SNP	.											.	GML	34	.	0			c.T208C						PASS	.						47.0	50.0	49.0					8																	143927837		2203	4300	6503	SO:0001583	missense	2765	exon4			CTTGTTTATAAGA	D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02						4375	protein-coding gene	gene with protein product		602370	"""GPI anchored molecule like protein"", ""glycosylphosphatidylinositol anchored molecule like protein"""			8934543, 9169150	Standard	NM_002066		Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.208T>C	8.37:g.143927837T>C	ENSP00000220940:p.Tyr70His	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	162	67	0.41358	NM_002066	A0AVF6|O00686|O00731	Missense_Mutation	SNP	ENST00000220940.1	37	CCDS6391.1	.	.	.	.	.	.	.	.	.	.	N	12.72	2.021959	0.35701	.	.	ENSG00000104499	ENST00000220940	T	0.22134	1.97	3.52	0.822	0.18806	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);	0.882556	0.09431	N	0.803024	T	0.31857	0.0810	L	0.56769	1.78	0.09310	N	1	D	0.64830	0.994	P	0.61477	0.889	T	0.15464	-1.0436	10	0.38643	T	0.18	-9.9934	2.9907	0.05982	0.2121:0.122:0.0:0.6659	.	70	Q99445	GML_HUMAN	H	70	ENSP00000220940:Y70H	ENSP00000220940:Y70H	Y	+	1	0	GML	143924839	0.415000	0.25416	0.010000	0.14722	0.004000	0.04260	0.819000	0.27308	0.158000	0.19367	0.455000	0.32223	TAT	.	.	none		0.358	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379659.1	NM_002066	
POLN	353497	hgsc.bcm.edu	37	4	2097647	2097647	+	Missense_Mutation	SNP	C	C	T	rs571169469		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:2097647C>T	ENST00000511885.2	-	20	2349	c.1996G>A	c.(1996-1998)Gtg>Atg	p.V666M	POLN_ENST00000382865.1_Missense_Mutation_p.V666M			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	666					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			ACCTGTTCCACGGGCACATCC	0.597								DNA polymerases (catalytic subunits)																													p.V666M		Atlas-SNP	.											.	POLN	82	.	0			c.G1996A						PASS	.						225.0	169.0	187.0					4																	2097647		2203	4300	6503	SO:0001583	missense	353497	exon18			GTTCCACGGGCAC	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.1996G>A	4.37:g.2097647C>T	ENSP00000435506:p.Val666Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	17	0.157407	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	.	.	.	.	.	.	.	.	.	.	C	5.125	0.208765	0.09757	.	.	ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313;ENST00000382857	D;D	0.96651	-4.08;-4.08	3.68	-6.39	0.01951	DNA-directed DNA polymerase, family A, palm domain (2);	1.857100	0.02434	N	0.083837	D	0.89574	0.6754	L	0.39085	1.19	0.09310	N	1	B;P;B	0.35807	0.025;0.522;0.007	B;B;B	0.18561	0.022;0.021;0.01	D	0.84221	0.0461	10	0.39692	T	0.17	0.6846	2.5723	0.04798	0.1033:0.4161:0.1645:0.3161	.	197;357;666	C9JDP8;E9PE06;Q7Z5Q5	.;.;DPOLN_HUMAN	M	666;666;357;197	ENSP00000435506:V666M;ENSP00000372316:V666M	ENSP00000253313:V357M	V	-	1	0	POLN	2067445	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.471000	0.00990	-1.765000	0.01303	-1.332000	0.01269	GTG	.	.	none		0.597	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
IGSF11	152404	hgsc.bcm.edu	37	3	118649074	118649074	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:118649074A>G	ENST00000393775.2	-	2	406	c.101T>C	c.(100-102)gTg>gCg	p.V34A	IGSF11_ENST00000441144.2_Missense_Mutation_p.V33A|IGSF11_ENST00000459718.1_5'UTR|IGSF11_ENST00000489689.1_Missense_Mutation_p.V34A|IGSF11_ENST00000491903.1_Missense_Mutation_p.V34A|IGSF11_ENST00000425327.2_Missense_Mutation_p.V33A|IGSF11_ENST00000354673.2_Missense_Mutation_p.V33A	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	34	Ig-like V-type.				cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						ACCCCGGGCCACCTGGATACT	0.557																																					p.V34A		Atlas-SNP	.											.	IGSF11	122	.	0			c.T101C						PASS	.						104.0	104.0	104.0					3																	118649074		2203	4300	6503	SO:0001583	missense	152404	exon2			CGGGCCACCTGGA	AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"""Immunoglobulin superfamily / I-set domain containing"""	16669	protein-coding gene	gene with protein product	"""cancer/testis antigen 119"""	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.101T>C	3.37:g.118649074A>G	ENSP00000377370:p.Val34Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	66	14	0.212121	NM_001015887	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Missense_Mutation	SNP	ENST00000393775.2	37	CCDS46891.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357979	0.82243	.	.	ENSG00000144847	ENST00000425327;ENST00000393775;ENST00000489689;ENST00000354673;ENST00000441144;ENST00000491903	T;T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36;-0.36	5.27	5.27	0.74061	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	L	0.37697	1.125	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;0.999	D;D;D;D;D	0.87578	0.998;0.99;0.997;0.998;0.994	T	0.69045	-0.5249	10	0.23891	T	0.37	.	14.5182	0.67833	1.0:0.0:0.0:0.0	.	34;33;33;34;34	C9JBA5;Q5DX21-3;Q5DX21-2;C9JMW0;Q5DX21	.;.;.;.;IGS11_HUMAN	A	33;34;34;33;33;34	ENSP00000406092:V33A;ENSP00000377370:V34A;ENSP00000420486:V34A;ENSP00000346700:V33A;ENSP00000401240:V33A;ENSP00000417413:V34A	ENSP00000346700:V33A	V	-	2	0	IGSF11	120131764	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.692000	0.91284	2.207000	0.71202	0.533000	0.62120	GTG	.	.	none		0.557	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2		
RPTN	126638	hgsc.bcm.edu	37	1	152128973	152128973	+	Missense_Mutation	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:152128973C>A	ENST00000316073.3	-	3	666	c.602G>T	c.(601-603)aGt>aTt	p.S201I		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	201	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GGAGTCTTGACTTTGTCTCTC	0.453																																					p.S201I		Atlas-SNP	.											.	RPTN	123	.	0			c.G602T						PASS	.						288.0	250.0	262.0					1																	152128973		1568	3582	5150	SO:0001583	missense	126638	exon3			TCTTGACTTTGTC	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.602G>T	1.37:g.152128973C>A	ENSP00000317895:p.Ser201Ile	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	270	124	0.459259	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.710731	0.30322	.	.	ENSG00000215853	ENST00000316073	T	0.14022	2.54	4.43	-0.543	0.11851	.	.	.	.	.	T	0.05135	0.0137	N	0.22421	0.69	0.09310	N	1	D	0.62365	0.991	P	0.53593	0.73	T	0.31280	-0.9949	9	0.35671	T	0.21	0.1604	6.4478	0.21885	0.0:0.4361:0.0:0.5639	.	201	Q6XPR3	RPTN_HUMAN	I	201	ENSP00000317895:S201I	ENSP00000317895:S201I	S	-	2	0	RPTN	150395597	0.048000	0.20356	0.000000	0.03702	0.024000	0.10985	0.878000	0.28126	0.008000	0.14787	0.442000	0.29010	AGT	.	.	none		0.453	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
PABPC1	26986	hgsc.bcm.edu	37	8	101730422	101730422	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:101730422G>C	ENST00000318607.5	-	2	1408	c.280C>G	c.(280-282)Cgc>Ggc	p.R94G	PABPC1_ENST00000519596.1_5'Flank|PABPC1_ENST00000519004.1_Missense_Mutation_p.R49G|PABPC1_ENST00000522387.1_Missense_Mutation_p.R94G	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	94					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CCACTTTTGCGAAGTGATGGA	0.413																																					p.R94G		Atlas-SNP	.											PABPC1,NS,carcinoma,+2,2	PABPC1	76	2	0			c.C280G						scavenged	.						94.0	88.0	90.0					8																	101730422		2203	4300	6503	SO:0001583	missense	26986	exon2			TTTTGCGAAGTGA	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.280C>G	8.37:g.101730422G>C	ENSP00000313007:p.Arg94Gly	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	107	38	0.35514	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	g	19.43	3.826868	0.71143	.	.	ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000518196;ENST00000521865;ENST00000520142	T;T;T;T;T;T	0.05786	3.39;3.39;3.39;3.39;3.39;3.39	5.37	4.5	0.54988	.	0.086607	0.49916	N	0.000131	T	0.37237	0.0996	H	0.96889	3.9	0.47994	D	0.99956	D;D;D	0.76494	0.999;0.998;0.998	D;P;P	0.63597	0.916;0.845;0.845	T	0.62412	-0.6860	10	0.87932	D	0	.	16.6119	0.84885	0.0:0.1303:0.8697:0.0	.	94;94;94	E7ERJ7;B3KT93;P11940	.;.;PABP1_HUMAN	G	94;94;49;94;49;94;94	ENSP00000313007:R94G;ENSP00000429594:R49G;ENSP00000429395:R94G;ENSP00000430159:R49G;ENSP00000429119:R94G;ENSP00000430012:R94G	ENSP00000313007:R94G	R	-	1	0	PABPC1	101799598	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.090000	0.57693	1.421000	0.47157	-0.127000	0.14921	CGC	.	.	none		0.413	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:203274867G>C	ENST00000290551.4	+	1	204	c.133G>C	c.(133-135)Gca>Cca	p.A45P	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					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)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45P		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133C						PASS	.						11.0	13.0	13.0					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		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.133G>C	1.37:g.203274867G>C	ENSP00000290551:p.Ala45Pro	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	53	14	0.264151	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163593	0.78226	.	.	ENSG00000159388	ENST00000290551	T	0.25085	1.82	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.52008	0.1708	M	0.82630	2.6	0.47374	D	0.999406	D	0.62365	0.991	D	0.64687	0.928	T	0.58222	-0.7674	10	0.51188	T	0.08	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	P	45	ENSP00000290551:A45P	ENSP00000290551:A45P	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
NFATC1	4772	hgsc.bcm.edu	37	18	77156301	77156301	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr18:77156301C>G	ENST00000427363.2	+	1	77	c.77C>G	c.(76-78)aCt>aGt	p.T26S	NFATC1_ENST00000397790.2_5'UTR|NFATC1_ENST00000587635.1_Missense_Mutation_p.T26S|NFATC1_ENST00000542384.1_Missense_Mutation_p.T26S|NFATC1_ENST00000591814.1_Missense_Mutation_p.T26S|NFATC1_ENST00000253506.5_Missense_Mutation_p.T26S			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	26					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	AGAGGAGAAACTTTggggccc	0.731																																					p.T26S	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C77G						PASS	.						6.0	6.0	6.0					18																	77156301		2092	4172	6264	SO:0001583	missense	4772	exon1			GAGAAACTTTGGG	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.77C>G	18.37:g.77156301C>G	ENSP00000389377:p.Thr26Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	96	23	0.239583	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		.	.	.	.	.	.	.	.	.	.	-	3.969	-0.008806	0.07727	.	.	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384	T;T	0.13538	3.0;2.58	2.46	-0.0619	0.13783	.	.	.	.	.	T	0.06050	0.0157	N	0.08118	0	0.80722	D	1	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.001	T	0.36432	-0.9748	9	0.22706	T	0.39	.	9.1199	0.36780	0.0:0.5714:0.4286:0.0	.	26;26;26;26	B5B2M6;O95644;B5B2M4;Q2M1S3	.;NFAC1_HUMAN;.;.	S	26	ENSP00000253506:T26S;ENSP00000442435:T26S	ENSP00000253506:T26S	T	+	2	0	NFATC1	75257289	0.998000	0.40836	1.000000	0.80357	0.974000	0.67602	0.909000	0.28558	0.139000	0.18822	0.437000	0.28790	ACT	.	.	none		0.731	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
IPO7	10527	hgsc.bcm.edu	37	11	9459505	9459505	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:9459505G>A	ENST00000379719.3	+	21	2615	c.2473G>A	c.(2473-2475)Gtt>Att	p.V825I		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	825					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		GCTTAATGATGTTGACTGTTT	0.313																																					p.V825I		Atlas-SNP	.											IPO7,NS,carcinoma,-1,1	IPO7	72	1	0			c.G2473A						PASS	.						79.0	76.0	77.0					11																	9459505		2201	4294	6495	SO:0001583	missense	10527	exon21			AATGATGTTGACT	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2473G>A	11.37:g.9459505G>A	ENSP00000369042:p.Val825Ile	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	218	23	0.105505	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978231	0.34942	.	.	ENSG00000205339	ENST00000379719	T	0.64260	-0.09	4.93	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.058434	0.64402	D	0.000002	T	0.34106	0.0886	N	0.01438	-0.865	0.48830	D	0.99971	B	0.09022	0.002	B	0.10450	0.005	T	0.37407	-0.9707	10	0.07325	T	0.83	.	18.1413	0.89641	0.0:0.0:1.0:0.0	.	825	O95373	IPO7_HUMAN	I	825	ENSP00000369042:V825I	ENSP00000369042:V825I	V	+	1	0	IPO7	9416081	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.085000	0.64468	2.270000	0.75569	0.460000	0.39030	GTT	.	.	none		0.313	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
DNASE1L2	1775	hgsc.bcm.edu	37	16	2287821	2287821	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:2287821G>A	ENST00000564065.1	+	5	1646	c.645G>A	c.(643-645)caG>caA	p.Q215Q	DNASE1L2_ENST00000567494.1_Silent_p.Q215Q|DNASE1L2_ENST00000382437.4_Silent_p.Q194Q|RP11-304L19.12_ENST00000564055.1_lincRNA|RP11-304L19.11_ENST00000565709.1_RNA|DNASE1L2_ENST00000320700.5_Silent_p.Q215Q			Q92874	DNSL2_HUMAN	deoxyribonuclease I-like 2	215					corneocyte development (GO:0003335)|DNA metabolic process (GO:0006259)|hair follicle development (GO:0001942)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			endometrium(1)|prostate(1)|skin(2)	4						TGCGGGCGCAGGACTGGGCCG	0.672																																					p.Q215Q		Atlas-SNP	.											.	DNASE1L2	14	.	0			c.G645A						PASS	.						19.0	24.0	22.0					16																	2287821		2092	4205	6297	SO:0001819	synonymous_variant	1775	exon6			GGCGCAGGACTGG	U62647	CCDS42105.1	16p13.3	2008-02-05				ENSG00000167968			2958	protein-coding gene	gene with protein product		602622				9205125, 1577479	Standard	NM_001374		Approved	DNAS1L2	uc002cpp.3	Q92874		ENST00000564065.1:c.645G>A	16.37:g.2287821G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_001374	E9PBY4|Q6JVM2|Q6JVM3	Silent	SNP	ENST00000564065.1	37	CCDS42105.1																																																																																			.	.	none		0.672	DNASE1L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435236.1	NM_001374	
ZNF285	26974	hgsc.bcm.edu	37	19	44891202	44891202	+	Missense_Mutation	SNP	C	C	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:44891202C>G	ENST00000330997.4	-	4	1269	c.1205G>C	c.(1204-1206)tGc>tCc	p.C402S	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.C402S|ZNF285_ENST00000591679.1_Missense_Mutation_p.C409S	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C402S(2)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						ACACTCACTGCATTTGTAGGG	0.478																																					p.C402S		Atlas-SNP	.											ZNF285,NS,carcinoma,0,2	ZNF285	86	2	2	Substitution - Missense(2)	prostate(2)	c.G1205C						scavenged	.						54.0	52.0	52.0					19																	44891202		2203	4300	6503	SO:0001583	missense	26974	exon4			TCACTGCATTTGT	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1205G>C	19.37:g.44891202C>G	ENSP00000333595:p.Cys402Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	3	0.0454545	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.689844	0.68271	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	D	0.85171	-1.95	3.36	3.36	0.38483	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93262	0.7853	M	0.91612	3.225	0.39148	D	0.962161	D;B	0.89917	1.0;0.007	D;B	0.97110	1.0;0.151	D	0.95026	0.8165	9	0.62326	D	0.03	.	13.918	0.63914	0.0:1.0:0.0:0.0	.	426;402	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	S	425;402	ENSP00000333595:C402S	ENSP00000333595:C402S	C	-	2	0	ZNF285	49583042	1.000000	0.71417	0.664000	0.29753	0.967000	0.64934	4.406000	0.59748	1.598000	0.50083	0.298000	0.19748	TGC	.	.	none		0.478	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
LCA5	167691	hgsc.bcm.edu	37	6	80223259	80223259	+	Silent	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:80223259T>G	ENST00000392959.1	-	4	1001	c.390A>C	c.(388-390)ctA>ctC	p.L130L	LCA5_ENST00000467898.3_Silent_p.L130L|LCA5_ENST00000369846.4_Silent_p.L130L	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	130					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TATTTTCTTTTAGCAGCTCAG	0.373																																					p.L130L		Atlas-SNP	.											.	LCA5	71	.	0			c.A390C						PASS	.						74.0	76.0	75.0					6																	80223259		2203	4299	6502	SO:0001819	synonymous_variant	167691	exon3			TTCTTTTAGCAGC		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.390A>C	6.37:g.80223259T>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	165	113	0.684848	NM_001122769	E1P542|Q9BWX7	Silent	SNP	ENST00000392959.1	37	CCDS4990.1																																																																																			.	.	none		0.373	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714	
FGG	2266	hgsc.bcm.edu	37	4	155526109	155526109	+	Silent	SNP	G	G	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:155526109G>T	ENST00000336098.3	-	9	1277	c.1239C>A	c.(1237-1239)atC>atA	p.I413I	FGG_ENST00000404648.3_Silent_p.I413I|FGG_ENST00000405164.1_Silent_p.I421I|FGG_ENST00000407946.1_Silent_p.I421I	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	413	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.|Gamma-chain polymerization, binding amino end of another fibrin alpha chain.				blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TGTTGAATGGGATTATCTTCA	0.458																																					p.I413I		Atlas-SNP	.											.	FGG	71	.	0			c.C1239A						PASS	.						202.0	184.0	190.0					4																	155526109		2203	4300	6503	SO:0001819	synonymous_variant	2266	exon9			GAATGGGATTATC		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3694	protein-coding gene	gene with protein product		134850	"""fibrinogen, gamma polypeptide"""				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.1239C>A	4.37:g.155526109G>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	164	34	0.207317	NM_000509	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Silent	SNP	ENST00000336098.3	37	CCDS3788.1																																																																																			.	.	none		0.458	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760492	186760492	+	Start_Codon_SNP	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:186760492A>G	ENST00000169298.3	+	4	675	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Start_Codon_SNP_p.M1V	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	1					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		CATCTTCATTATGATTCACAC	0.393																																					p.M1V		Atlas-SNP	.											ST6GAL1,NS,carcinoma,-2,1	ST6GAL1	36	1	0			c.A1G						scavenged	.						161.0	158.0	159.0					3																	186760492		2203	4299	6502	SO:0001582	initiator_codon_variant	6480	exon3			TTCATTATGATTC	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.1A>G	3.37:g.186760492A>G	ENSP00000169298:p.Met1Val	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.691248	0.68271	.	.	ENSG00000073849	ENST00000169298;ENST00000458216;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.25912	1.77;1.77	5.44	5.44	0.79542	.	0.101544	0.64402	D	0.000002	T	0.35799	0.0944	.	.	.	0.80722	D	1	D	0.58620	0.983	P	0.49752	0.621	T	0.20174	-1.0283	9	0.87932	D	0	-38.7341	12.2097	0.54373	1.0:0.0:0.0:0.0	.	1	P15907	SIAT1_HUMAN	V	1	ENSP00000169298:M1V;ENSP00000389337:M1V	ENSP00000169298:M1V	M	+	1	0	ST6GAL1	188243186	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.705000	0.68355	2.200000	0.70718	0.459000	0.35465	ATG	.	.	none		0.393	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	Missense_Mutation
CACNA1H	8912	hgsc.bcm.edu	37	16	1255246	1255246	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:1255246G>A	ENST00000348261.5	+	11	2832	c.2584G>A	c.(2584-2586)Ggc>Agc	p.G862S	CACNA1H_ENST00000358590.4_Missense_Mutation_p.G862S|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Missense_Mutation_p.G862S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	862					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CATCTTCGACGGCATCATCGT	0.602																																					p.G862S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G2584A						PASS	.						85.0	88.0	87.0					16																	1255246		2054	4196	6250	SO:0001583	missense	8912	exon11			TTCGACGGCATCA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2584G>A	16.37:g.1255246G>A	ENSP00000334198:p.Gly862Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.612304	0.28712	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98362	-4.89;-4.89	3.93	3.93	0.45458	Ion transport (1);	0.179382	0.49305	D	0.000150	D	0.97145	0.9067	L	0.47716	1.5	0.44302	D	0.997171	P;D	0.58268	0.808;0.982	B;P	0.50270	0.17;0.636	D	0.96334	0.9246	10	0.33940	T	0.23	.	15.1309	0.72523	0.0:0.0:1.0:0.0	.	862;862	O95180-2;O95180	.;CAC1H_HUMAN	S	862	ENSP00000334198:G862S;ENSP00000351401:G862S	ENSP00000334198:G862S	G	+	1	0	CACNA1H	1195247	0.999000	0.42202	0.721000	0.30653	0.300000	0.27592	2.892000	0.48625	2.034000	0.60081	0.655000	0.94253	GGC	.	.	none		0.602	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135239666	135239666	+	Missense_Mutation	SNP	T	T	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:135239666T>A	ENST00000265605.2	-	7	1419	c.1351A>T	c.(1351-1353)Agg>Tgg	p.R451W	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.R397W|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.R401W	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	451					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		TTCAGCTCCCTGATGAGCCAG	0.567																																					p.R451W		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A1351T						PASS	.						86.0	74.0	78.0					6																	135239666		2203	4300	6503	SO:0001583	missense	64577	exon7			GCTCCCTGATGAG	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.1351A>T	6.37:g.135239666T>A	ENSP00000265605:p.Arg451Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	51	39	0.764706	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.709287	0.89018	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.76709	-1.04;1.54;-1.04	6.07	4.88	0.63580	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.82051	0.4953	M	0.64404	1.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.84435	0.0579	10	0.66056	D	0.02	.	13.3589	0.60644	0.0:0.0:0.1316:0.8684	.	401;397;451	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	W	451;397;401	ENSP00000265605:R451W;ENSP00000356819:R397W;ENSP00000356821:R401W	ENSP00000265605:R451W	R	-	1	2	ALDH8A1	135281359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.074000	0.41529	1.081000	0.41110	0.533000	0.62120	AGG	.	.	none		0.567	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
CD97	976	hgsc.bcm.edu	37	19	14512523	14512523	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:14512523C>T	ENST00000242786.5	+	11	1214	c.1134C>T	c.(1132-1134)agC>agT	p.S378S	CD97_ENST00000358600.3_Silent_p.S285S|CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Silent_p.S329S	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	378					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GTCAGAGCAGCGCACGCATGA	0.622																																					p.S378S		Atlas-SNP	.											.	CD97	86	.	0			c.C1134T						PASS	.						66.0	54.0	58.0					19																	14512523		2203	4300	6503	SO:0001819	synonymous_variant	976	exon11			GAGCAGCGCACGC		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1134C>T	19.37:g.14512523C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	57	22	0.385965	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	37	CCDS32929.1																																																																																			.	.	none		0.622	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481	
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158526	26158526	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26158526C>T	ENST00000289316.2	+	1	153	c.129C>T	c.(127-129)taC>taT	p.Y43Y	HIST1H2BD_ENST00000377777.4_Silent_p.Y43Y	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	43					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						TGTATGTGTACAAGGTGCTGA	0.557																																					p.Y43Y		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C129T						PASS	.						203.0	188.0	193.0					6																	26158526		2203	4300	6503	SO:0001819	synonymous_variant	3017	exon1			TGTGTACAAGGTG	M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"""Histones / Replication-dependent"""	4747	protein-coding gene	gene with protein product		602799	"""H2B histone family, member B"", ""histone 1, H2bd"""	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.129C>T	6.37:g.26158526C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	20	0.165289	NM_021063		Silent	SNP	ENST00000289316.2	37	CCDS4587.1																																																																																			.	.	none		0.557	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063	
MUC4	4585	hgsc.bcm.edu	37	3	195505772	195505772	+	Missense_Mutation	SNP	C	C	G	rs556354486		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:195505772C>G	ENST00000463781.3	-	2	13138	c.12679G>C	c.(12679-12681)Gtc>Ctc	p.V4227L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V4227L|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	984					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.V4227L(1)		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)		AGGCTGGTGACAGGAAGAGGG	0.582													.|||	1	0.000199681	0.0	0.0	5008	,	,		15508	0.0		0.001	False		,,,				2504	0.0				p.V4227L		Atlas-SNP	.											MUC4_ENST00000463781,bladder,carcinoma,0,4	MUC4	1505	4	1	Substitution - Missense(1)	lung(1)	c.G12679C						scavenged	.																																			SO:0001583	missense	4585	exon2			TGGTGACAGGAAG	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.12679G>C	3.37:g.195505772C>G	ENSP00000417498:p.Val4227Leu	Somatic	111	5	0.045045		WXS	Illumina HiSeq	Phase_I	72	5	0.0694444	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	.	.	.	.	.	.	.	.	.	.	c	5.247	0.230981	0.09969	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.6	1.57	0.566	0.17317	.	.	.	.	.	T	0.14227	0.0344	N	0.14661	0.345	0.19300	N	0.999978	B	0.27765	0.188	B	0.22601	0.04	T	0.27640	-1.0068	8	.	.	.	.	5.595	0.17321	0.0:0.6491:0.3509:0.0	.	4099	E7ESK3	.	L	4227	ENSP00000417498:V4227L;ENSP00000420243:V4227L	.	V	-	1	0	MUC4	196990551	0.000000	0.05858	0.020000	0.16555	0.011000	0.07611	-0.070000	0.11523	0.201000	0.20466	0.484000	0.47621	GTC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NBPF10	100132406	hgsc.bcm.edu	37	1	145299906	145299906	+	Missense_Mutation	SNP	T	T	G	rs199863138		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:145299906T>G	ENST00000369338.1	+	2	332	c.142T>G	c.(142-144)Tcc>Gcc	p.S48A	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.S319A			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	319						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AACTCAACTGTCCGGCTTCCT	0.418																																					p.S319A		Atlas-SNP	.											NBPF10,NS,carcinoma,-2,1	NBPF10	221	1	0			c.T955G						scavenged	.						53.0	36.0	41.0					1																	145299906		692	1591	2283	SO:0001583	missense	100132406	exon6			CAACTGTCCGGCT	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.142T>G	1.37:g.145299906T>G	ENSP00000358344:p.Ser48Ala	Somatic	25	8	0.32		WXS	Illumina HiSeq	Phase_I	24	4	0.166667	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	0.007	-1.951406	0.00470	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.09255	3.0;4.33	1.05	-0.0548	0.13812	.	.	.	.	.	T	0.00784	0.0026	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.47045	-0.9147	6	0.02654	T	1	.	5.2063	0.15293	0.0:0.0:0.4021:0.5979	.	.	.	.	A	244;48;48;319	ENSP00000358344:S48A;ENSP00000345684:S319A	ENSP00000345684:S319A	S	+	1	0	NBPF10	144011263	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-0.175000	0.09825	-0.480000	0.06803	-0.807000	0.03187	TCC	.	.	weak		0.418	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
EIF3B	8662	hgsc.bcm.edu	37	7	2409105	2409105	+	Splice_Site	SNP	A	A	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:2409105A>C	ENST00000360876.4	+	10	1459		c.e10-1		EIF3B_ENST00000397011.2_Splice_Site	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B											breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		CCTGTTCTGCAGAGACTTTTC	0.423																																					.		Atlas-SNP	.											.	EIF3B	54	.	0			c.1404-2A>C						PASS	.						186.0	199.0	194.0					7																	2409105		2203	4300	6503	SO:0001630	splice_region_variant	8662	exon10			TTCTGCAGAGACT	U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"""RNA binding motif (RRM) containing"""	3280	protein-coding gene	gene with protein product		603917	"""eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"""	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1404-1A>C	7.37:g.2409105A>C		Somatic	484	0	0		WXS	Illumina HiSeq	Phase_I	366	128	0.349727	NM_003751		Splice_Site	SNP	ENST00000360876.4	37	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	A	16.26	3.071841	0.55646	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8091	0.78543	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF3B	2375631	1.000000	0.71417	0.958000	0.39756	0.625000	0.37756	9.048000	0.93830	2.192000	0.70111	0.459000	0.35465	.	.	.	none		0.423	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1		Intron
TRIOBP	11078	hgsc.bcm.edu	37	22	38119894	38119894	+	Missense_Mutation	SNP	G	G	A	rs35105846	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr22:38119894G>A	ENST00000406386.3	+	7	1586	c.1331G>A	c.(1330-1332)aGt>aAt	p.S444N		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	444					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.S444N(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCCTCTCCCAGTAGAGCTACA	0.587																																					p.S444N		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	1	Substitution - Missense(1)	prostate(1)	c.G1331A						scavenged	.						70.0	74.0	73.0					22																	38119894		1882	4104	5986	SO:0001583	missense	11078	exon7			CTCCCAGTAGAGC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1331G>A	22.37:g.38119894G>A	ENSP00000384312:p.Ser444Asn	Somatic	70	5	0.0714286		WXS	Illumina HiSeq	Phase_I	57	10	0.175439	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	3.506	-0.100772	0.06967	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19938	2.11	3.02	-0.653	0.11447	.	.	.	.	.	T	0.04003	0.0112	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33266	-0.9875	9	0.15952	T	0.53	.	0.3565	0.00358	0.3833:0.1916:0.2386:0.1864	rs35105846	444	Q9H2D6	TARA_HUMAN	N	444	ENSP00000384312:S444N	ENSP00000384312:S444N	S	+	2	0	TRIOBP	36449840	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.155000	0.03163	-0.991000	0.03476	-3.651000	0.00026	AGT	G|0.500;A|0.500	0.500	strong		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
OTULIN	90268	hgsc.bcm.edu	37	5	14681631	14681631	+	Missense_Mutation	SNP	A	A	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:14681631A>T	ENST00000284274.4	+	4	461	c.383A>T	c.(382-384)tAc>tTc	p.Y128F		NM_138348.4	NP_612357.4	Q96BN8	OTUL_HUMAN		128	OTU.				canonical Wnt signaling pathway (GO:0060070)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|protein linear deubiquitination (GO:1990108)|sprouting angiogenesis (GO:0002040)	cytoplasm (GO:0005737)|LUBAC complex (GO:0071797)	cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	14	Lung NSC(4;0.00696)					GGTGATAATTACTGTGCACTG	0.562																																					p.Y128F		Atlas-SNP	.											.	FAM105B	36	.	0			c.A383T						PASS	.						76.0	83.0	81.0					5																	14681631		2080	4218	6298	SO:0001583	missense	90268	exon4			ATAATTACTGTGC																												ENST00000284274.4:c.383A>T	5.37:g.14681631A>T	ENSP00000284274:p.Tyr128Phe	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	116	36	0.310345	NM_138348	D3DTD3|Q8NAS0|Q96IA3	Missense_Mutation	SNP	ENST00000284274.4	37	CCDS43302.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542953	0.86022	.	.	ENSG00000154124	ENST00000284274	T	0.19532	2.14	5.82	5.82	0.92795	.	0.061315	0.64402	D	0.000002	T	0.41143	0.1146	M	0.68317	2.08	0.50813	D	0.999894	D	0.71674	0.998	D	0.63488	0.915	T	0.31558	-0.9939	10	0.87932	D	0	-16.5211	11.3113	0.49366	0.9272:0.0:0.0728:0.0	.	128	Q96BN8	F105B_HUMAN	F	128	ENSP00000284274:Y128F	ENSP00000284274:Y128F	Y	+	2	0	FAM105B	14734631	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.027000	0.93706	2.225000	0.72522	0.460000	0.39030	TAC	.	.	none		0.562	FAM105B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366012.1		
DLGAP2	9228	hgsc.bcm.edu	37	8	1497114	1497114	+	Missense_Mutation	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:1497114C>A	ENST00000421627.2	+	2	389	c.255C>A	c.(253-255)caC>caA	p.H85Q		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	164					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CGCGGATGCACTACAGCTCGC	0.682																																					p.H85Q		Atlas-SNP	.											.	DLGAP2	292	.	0			c.C255A						PASS	.						18.0	20.0	19.0					8																	1497114		2176	4269	6445	SO:0001583	missense	9228	exon2			GATGCACTACAGC	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.255C>A	8.37:g.1497114C>A	ENSP00000400258:p.His85Gln	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	21	7	0.333333	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.604713|4.604713	0.87157|0.87157	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000356067;ENST00000421627|ENST00000520901	T|.	0.16743|.	2.32|.	5.43|5.43	4.56|4.56	0.56223|0.56223	.|.	0.101563|.	0.85682|.	D|.	0.000000|.	T|T	0.75339|0.75339	0.3836|0.3836	M|M	0.79926|0.79926	2.475|2.475	0.45806|0.45806	D|D	0.998684|0.998684	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.998;0.996|.	T|T	0.76889|0.76889	-0.2792|-0.2792	10|5	0.87932|.	D|.	0|.	-18.5305|-18.5305	14.0129|14.0129	0.64507|0.64507	0.0:0.9271:0.0:0.0729|0.0:0.9271:0.0:0.0729	.|.	164;164|.	Q9P1A6-2;Q9P1A6|.	.;DLGP2_HUMAN|.	Q|N	130;85|102	ENSP00000400258:H85Q|.	ENSP00000348366:H130Q|.	H|T	+|+	3|2	2|0	DLGAP2|DLGAP2	1484521|1484521	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	1.532000|1.532000	0.36029|0.36029	1.292000|1.292000	0.44672|0.44672	0.561000|0.561000	0.74099|0.74099	CAC|ACT	.	.	none		0.682	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
PIM1	5292	hgsc.bcm.edu	37	6	37138423	37138423	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138423G>C	ENST00000373509.5	+	1	445	c.72G>C	c.(70-72)aaG>aaC	p.K24N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	115					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.K24N(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)	ACGCCACCAAGCTGGCGCCCG	0.726			T	BCL6	NHL																																p.K115N		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.G345C						PASS	.						22.0	25.0	24.0					6																	37138423		2197	4289	6486	SO:0001583	missense	5292	exon1			CACCAAGCTGGCG		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.72G>C	6.37:g.37138423G>C	ENSP00000362608:p.Lys24Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	59	15	0.254237	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	9.145	1.014762	0.19355	.	.	ENSG00000137193	ENST00000373509	T	0.69685	-0.42	4.2	2.33	0.28932	Protein kinase-like domain (1);	0.226724	0.29775	N	0.011236	T	0.17280	0.0415	N	0.08118	0	0.26025	N	0.981812	B	0.33266	0.404	B	0.25759	0.063	T	0.21552	-1.0242	10	0.18276	T	0.48	.	8.2558	0.31756	0.2022:0.0:0.7978:0.0	.	115	P11309	PIM1_HUMAN	N	24	ENSP00000362608:K24N	ENSP00000362608:K24N	K	+	3	2	PIM1	37246401	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	1.199000	0.32235	0.461000	0.27071	-0.284000	0.09977	AAG	.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
DKK2	27123	hgsc.bcm.edu	37	4	107845787	107845787	+	Silent	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:107845787T>C	ENST00000285311.3	-	3	1149	c.444A>G	c.(442-444)agA>agG	p.R148R	DKK2_ENST00000510463.1_Silent_p.R102R|DKK2_ENST00000513208.1_Silent_p.R48R	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	148					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		GGTTTCGATCTCTGTGCCGAG	0.443																																					p.R148R		Atlas-SNP	.											.	DKK2	96	.	0			c.A444G						PASS	.						236.0	214.0	222.0					4																	107845787		2203	4300	6503	SO:0001819	synonymous_variant	27123	exon3			TCGATCTCTGTGC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.444A>G	4.37:g.107845787T>C		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	224	152	0.678571	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Silent	SNP	ENST00000285311.3	37	CCDS3675.1																																																																																			.	.	none		0.443	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33041314	33041314	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:33041314C>T	ENST00000419277.1	-	2	163	c.34G>A	c.(34-36)Gct>Act	p.A12T	HLA-DPB1_ENST00000418931.2_5'Flank|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.A12T|HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPB1_ENST00000535465.1_5'Flank	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	12					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						AAGATCACAGCTCTGATATGG	0.557																																					p.A12T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G34A						PASS	.						190.0	174.0	180.0					6																	33041314		1511	2709	4220	SO:0001583	missense	3113	exon1			TCACAGCTCTGAT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.34G>A	6.37:g.33041314C>T	ENSP00000393566:p.Ala12Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392417	0.42410	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337;ENST00000417724	T;T;T	0.02552	4.6;4.6;4.25	4.1	-1.87	0.07737	.	0.640274	0.14756	N	0.300279	T	0.00998	0.0033	L	0.59436	1.845	0.09310	N	1	B	0.32717	0.381	B	0.32624	0.149	T	0.44483	-0.9325	10	0.87932	D	0	.	1.319	0.02112	0.1483:0.409:0.146:0.2967	.	12	P20036	DPA1_HUMAN	T	12	ENSP00000393566:A12T;ENSP00000402872:A12T;ENSP00000390929:A12T	ENSP00000398134:A12T	A	-	1	0	HLA-DPA1	33149292	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	0.524000	0.22940	-0.286000	0.09076	0.643000	0.83706	GCT	.	.	none		0.557	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
PIGF	5281	hgsc.bcm.edu	37	2	46839367	46839367	+	Splice_Site	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:46839367C>T	ENST00000281382.6	-	4	607	c.437G>A	c.(436-438)gGa>gAa	p.G146E	PIGF_ENST00000306465.4_Splice_Site_p.G146E|PIGF_ENST00000495933.1_5'UTR	NM_002643.3	NP_002634.1	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class F	146					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ethanolaminephosphotransferase activity (GO:0004307)			breast(1)|endometrium(1)|lung(1)|stomach(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			taaaaCTTACCCATTTCTACT	0.284																																					p.G146E		Atlas-SNP	.											.	PIGF	9	.	0			c.G437A						PASS	.						15.0	13.0	14.0					2																	46839367		2052	4024	6076	SO:0001630	splice_region_variant	5281	exon4			ACTTACCCATTTC		CCDS1827.1, CCDS1828.1	2p21-p16	2013-02-26	2006-06-28		ENSG00000151665	ENSG00000151665		"""Phosphatidylinositol glycan anchor biosynthesis"""	8962	protein-coding gene	gene with protein product		600153	"""phosphatidylinositol glycan, class F"""			8575782, 8463218	Standard	NM_173074		Approved		uc002rvd.3	Q07326	OTTHUMG00000128816	ENST00000281382.6:c.437+1G>A	2.37:g.46839367C>T		Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	206	81	0.393204	NM_002643	Q8WW20	Missense_Mutation	SNP	ENST00000281382.6	37	CCDS1827.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693759	0.88735	.	.	ENSG00000151665	ENST00000281382;ENST00000306465	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.79323	0.4426	M	0.70595	2.14	0.80722	D	1	D;D	0.76494	0.999;0.991	D;P	0.72982	0.979;0.895	T	0.76892	-0.2791	8	.	.	.	-9.518	19.9893	0.97361	0.0:1.0:0.0:0.0	.	146;146	Q07326;Q07326-2	PIGF_HUMAN;.	E	146	.	.	G	-	2	0	PIGF	46692871	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.336000	0.72954	2.826000	0.97356	0.563000	0.77884	GGA	.	.	none		0.284	PIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250749.2	NM_173074	Missense_Mutation
POU3F3	5455	hgsc.bcm.edu	37	2	105473228	105473228	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:105473228G>A	ENST00000361360.2	+	1	1260	c.1260G>A	c.(1258-1260)gcG>gcA	p.A420A	RP11-13J10.1_ENST00000598623.1_RNA	NM_006236.1	NP_006227.1	P20264	PO3F3_HUMAN	POU class 3 homeobox 3	420					central nervous system development (GO:0007417)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain ventricular zone progenitor cell division (GO:0021869)|metanephric ascending thin limb development (GO:0072218)|metanephric DCT cell differentiation (GO:0072240)|metanephric loop of Henle development (GO:0072236)|metanephric macula densa development (GO:0072227)|metanephric thick ascending limb development (GO:0072233)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TCAAGGGCGCGCTGGAGAGCC	0.657																																					p.A420A		Atlas-SNP	.											.	POU3F3	43	.	0			c.G1260A						PASS	.						36.0	37.0	37.0					2																	105473228		2203	4300	6503	SO:0001819	synonymous_variant	5455	exon1			GGGCGCGCTGGAG		CCDS33265.1	2q12.1	2011-06-20	2007-07-13		ENSG00000198914	ENSG00000198914		"""Homeoboxes / POU class"""	9216	protein-coding gene	gene with protein product		602480	"""POU domain class 3, transcription factor 3"""				Standard	NM_006236		Approved	BRN1, OTF8	uc010ywg.2	P20264	OTTHUMG00000153067	ENST00000361360.2:c.1260G>A	2.37:g.105473228G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_006236	P78379|Q4ZG25	Silent	SNP	ENST00000361360.2	37	CCDS33265.1																																																																																			.	.	none		0.657	POU3F3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329335.2		
SPATA20	64847	hgsc.bcm.edu	37	17	48631644	48631644	+	Missense_Mutation	SNP	G	G	A	rs200274697		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:48631644G>A	ENST00000356488.4	+	14	2025	c.1942G>A	c.(1942-1944)Gtg>Atg	p.V648M	CACNA1G-AS1_ENST00000505495.1_RNA|SPATA20_ENST00000393244.3_Missense_Mutation_p.V604M|SPATA20_ENST00000511937.1_3'UTR|CACNA1G-AS1_ENST00000508920.1_RNA|SPATA20_ENST00000006658.6_Missense_Mutation_p.V664M|CACNA1G-AS1_ENST00000505793.1_RNA	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	648					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CGCCAATTCCGTGTCAGCCCA	0.627																																					p.V664M		Atlas-SNP	.											.	SPATA20	59	.	0			c.G1990A						PASS	.						109.0	77.0	88.0					17																	48631644		2203	4300	6503	SO:0001583	missense	64847	exon15			AATTCCGTGTCAG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1942G>A	17.37:g.48631644G>A	ENSP00000348878:p.Val648Met	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	26.5	4.744792	0.89663	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.64085	-0.08;-0.08;-0.08	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.77485	0.4137	M	0.83774	2.66	0.80722	D	1	D;D	0.65815	0.995;0.972	P;P	0.55713	0.781;0.782	T	0.80865	-0.1191	10	0.56958	D	0.05	-22.9431	18.4943	0.90858	0.0:0.0:1.0:0.0	.	648;664	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	M	664;648;604	ENSP00000006658:V664M;ENSP00000348878:V648M;ENSP00000376935:V604M	ENSP00000006658:V664M	V	+	1	0	SPATA20	45986643	1.000000	0.71417	0.853000	0.33588	0.785000	0.44390	7.586000	0.82596	2.467000	0.83353	0.561000	0.74099	GTG	G|1.000;A|0.000	0.000	strong		0.627	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
RGPD8	727851	hgsc.bcm.edu	37	2	113127775	113127775	+	Missense_Mutation	SNP	G	G	C	rs370761877		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:113127775G>C	ENST00000302558.3	-	23	5469	c.5278C>G	c.(5278-5280)Cct>Gct	p.P1760A	RGPD8_ENST00000409750.1_Missense_Mutation_p.P1620A	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	1760				P -> A (in Ref. 3; CAI56757). {ECO:0000305}.	protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)	p.P1760A(12)		endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						GAACGGGAAGGATTTTCTTCC	0.308																																					p.P1760A		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,0,18	RGPD8	81	18	12	Substitution - Missense(12)	prostate(6)|urinary_tract(2)|endometrium(2)|kidney(2)	c.C5278G						scavenged	.						235.0	168.0	189.0					2																	113127775		686	1558	2244	SO:0001583	missense	727851	exon23			GGGAAGGATTTTC	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.5278C>G	2.37:g.113127775G>C	ENSP00000306637:p.Pro1760Ala	Somatic	602	6	0.00996678		WXS	Illumina HiSeq	Phase_I	562	7	0.0124555	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	g	0.008	-1.892319	0.00522	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.36520	1.25;1.25	0.719	0.719	0.18208	.	.	.	.	.	T	0.11239	0.0274	N	0.02011	-0.69	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.18650	-1.0330	9	0.10902	T	0.67	-6.3628	6.3935	0.21599	0.0:0.6881:0.3119:0.0	.	1760	O14715	RGPD8_HUMAN	A	1760;1620	ENSP00000306637:P1760A;ENSP00000386511:P1620A	ENSP00000306637:P1760A	P	-	1	0	RGPD8	112844246	0.746000	0.28272	0.842000	0.33263	0.015000	0.08874	0.243000	0.18106	-0.105000	0.12132	-1.123000	0.02005	CCT	.	.	weak		0.308	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
PCDHA4	56144	hgsc.bcm.edu	37	5	140186856	140186856	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:140186856C>T	ENST00000530339.1	+	1	84	c.84C>T	c.(82-84)aaC>aaT	p.N28N	PCDHA4_ENST00000512229.2_Silent_p.N28N|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.N28N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	28					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.N28N(1)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCAGGGAACGGTCAGCTCC	0.627																																					p.N28N		Atlas-SNP	.											PCDHA4_ENST00000530339,colon,carcinoma,+1,5	PCDHA4	419	5	1	Substitution - coding silent(1)	ovary(1)	c.C84T						scavenged	.						64.0	71.0	69.0					5																	140186856		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			AGGGAACGGTCAG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.84C>T	5.37:g.140186856C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	92	30	0.326087	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.627	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
SCNN1A	6337	hgsc.bcm.edu	37	12	6457289	6457289	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:6457289C>T	ENST00000228916.2	-	13	1858	c.1760G>A	c.(1759-1761)aGg>aAg	p.R587K	SCNN1A_ENST00000358945.3_Missense_Mutation_p.R609K|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R610K|SCNN1A_ENST00000540037.1_Missense_Mutation_p.R287K|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R646K|SCNN1A_ENST00000396966.2_3'UTR	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	587					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GCTTCGGAACCTTCGGAGCAG	0.622																																					p.R646K		Atlas-SNP	.											.	SCNN1A	54	.	0			c.G1937A						PASS	.						53.0	53.0	53.0					12																	6457289		2203	4300	6503	SO:0001583	missense	6337	exon12			CGGAACCTTCGGA	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1760G>A	12.37:g.6457289C>T	ENSP00000228916:p.Arg587Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.810468	0.50421	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000540037;ENST00000228916;ENST00000543768	T;T;T;T;T	0.71817	-0.54;-0.6;-0.33;-0.5;-0.53	4.54	3.63	0.41609	.	0.092333	0.44688	D	0.000423	T	0.64789	0.2630	M	0.74881	2.28	0.25856	N	0.983882	B;B;B	0.28512	0.214;0.214;0.208	B;B;B	0.22152	0.031;0.018;0.038	T	0.58662	-0.7597	10	0.40728	T	0.16	-30.2911	7.5852	0.27989	0.0:0.7999:0.0:0.2001	.	610;587;646	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	K	646;609;287;587;610	ENSP00000353292:R646K;ENSP00000351825:R609K;ENSP00000440876:R287K;ENSP00000228916:R587K;ENSP00000438739:R610K	ENSP00000228916:R587K	R	-	2	0	SCNN1A	6327550	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	2.385000	0.44371	2.090000	0.63153	0.561000	0.74099	AGG	.	.	none		0.622	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
RPUSD4	84881	hgsc.bcm.edu	37	11	126081386	126081386	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:126081386G>A	ENST00000298317.4	-	1	201	c.148C>T	c.(148-150)Ctc>Ttc	p.L50F	FAM118B_ENST00000533050.1_5'UTR|RP11-50B3.4_ENST00000532866.1_RNA|FAM118B_ENST00000360194.4_5'Flank|RNU4-86P_ENST00000410135.1_RNA|FAM118B_ENST00000529731.1_5'Flank|RPUSD4_ENST00000534393.1_5'Flank|RPUSD4_ENST00000533628.1_Missense_Mutation_p.L50F	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	50					pseudouridine synthesis (GO:0001522)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0761)		TGGGCTCGGAGCTTCTCCGCT	0.572																																					p.L50F		Atlas-SNP	.											.	RPUSD4	36	.	0			c.C148T						PASS	.						147.0	156.0	153.0					11																	126081386		2201	4299	6500	SO:0001583	missense	84881	exon1			CTCGGAGCTTCTC	BC014131	CCDS8469.1, CCDS53721.1	11q24.2	2013-02-11			ENSG00000165526	ENSG00000165526		"""RNA pseudouridylate synthase domain containing"""	25898	protein-coding gene	gene with protein product							Standard	NM_032795		Approved	FLJ14494	uc001qde.3	Q96CM3	OTTHUMG00000165815	ENST00000298317.4:c.148C>T	11.37:g.126081386G>A	ENSP00000298317:p.Leu50Phe	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_001144827	E9PML2|Q96K56	Missense_Mutation	SNP	ENST00000298317.4	37	CCDS8469.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493570	0.44352	.	.	ENSG00000165526	ENST00000298317;ENST00000533628;ENST00000532674	T;T;T	0.43688	2.69;2.49;0.94	5.31	3.44	0.39384	.	0.671765	0.14801	N	0.297611	T	0.60090	0.2242	M	0.77616	2.38	0.80722	D	1	D;D	0.76494	0.99;0.999	P;D	0.68943	0.866;0.961	T	0.56390	-0.7987	10	0.45353	T	0.12	-22.2246	7.8321	0.29349	0.1845:0.0:0.8155:0.0	.	50;50	E9PML2;Q96CM3	.;RUSD4_HUMAN	F	50	ENSP00000298317:L50F;ENSP00000433065:L50F;ENSP00000433709:L50F	ENSP00000298317:L50F	L	-	1	0	RPUSD4	125586596	0.960000	0.32886	0.643000	0.29450	0.026000	0.11368	1.570000	0.36439	0.809000	0.34255	0.650000	0.86243	CTC	.	.	none		0.572	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795	
FZD1	8321	hgsc.bcm.edu	37	7	90894950	90894950	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:90894950A>G	ENST00000287934.2	+	1	1168	c.755A>G	c.(754-756)cAg>cGg	p.Q252R		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	252					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			AGCAACCCTCAGCACGGCGGC	0.736																																					p.Q252R		Atlas-SNP	.											.	FZD1	64	.	0			c.A755G						PASS	.						8.0	9.0	8.0					7																	90894950		2150	4250	6400	SO:0001583	missense	8321	exon1			ACCCTCAGCACGG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"""GPCR / Class F : Frizzled receptors"""	4038	protein-coding gene	gene with protein product	"""Wnt receptor"", ""frizzled, Drosophila, homolog of, 1"""	603408	"""frizzled (Drosophila) homolog 1"", ""frizzled homolog 1 (Drosophila)"", ""frizzled 1, seven transmembrane spanning receptor"", ""frizzled family receptor 1"""			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.755A>G	7.37:g.90894950A>G	ENSP00000287934:p.Gln252Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	60	13	0.216667	NM_003505	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	37	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.866343	0.32977	.	.	ENSG00000157240	ENST00000287934	T	0.76316	-1.01	4.73	4.73	0.59995	.	0.781766	0.10486	N	0.668960	T	0.55721	0.1938	N	0.02539	-0.55	0.41784	D	0.989832	B	0.02656	0.0	B	0.04013	0.001	T	0.47394	-0.9121	10	0.17369	T	0.5	.	14.0288	0.64601	1.0:0.0:0.0:0.0	.	252	Q9UP38	FZD1_HUMAN	R	252	ENSP00000287934:Q252R	ENSP00000287934:Q252R	Q	+	2	0	FZD1	90732886	0.733000	0.28132	1.000000	0.80357	0.985000	0.73830	0.944000	0.29043	1.985000	0.57927	0.418000	0.28097	CAG	.	.	none		0.736	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505	
PLCH2	9651	hgsc.bcm.edu	37	1	2422698	2422698	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:2422698C>T	ENST00000419816.2	+	11	1857	c.1583C>T	c.(1582-1584)tCg>tTg	p.S528L	RP3-395M20.2_ENST00000424657.1_RNA|RP3-395M20.3_ENST00000442305.1_RNA|PLCH2_ENST00000288766.5_Intron|PLCH2_ENST00000378488.3_Missense_Mutation_p.S528L|PLCH2_ENST00000378486.3_Missense_Mutation_p.S528L|PLCH2_ENST00000449969.1_Missense_Mutation_p.S501L			O75038	PLCH2_HUMAN	phospholipase C, eta 2	528					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		ATCAAAGAGTCGAAGATTCGG	0.542																																					p.S528L		Atlas-SNP	.											.	PLCH2	131	.	0			c.C1583T						PASS	.						83.0	91.0	88.0					1																	2422698		1982	4152	6134	SO:0001583	missense	9651	exon11			AAGAGTCGAAGAT	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"""EF-hand domain containing"""	29037	protein-coding gene	gene with protein product		612836	"""phospholipase C-like 4"""	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.1583C>T	1.37:g.2422698C>T	ENSP00000389803:p.Ser528Leu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	7	0.179487	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	37		.	.	.	.	.	.	.	.	.	.	C	18.90	3.722431	0.68959	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488;ENST00000343889;ENST00000278878	T;T;T	0.46451	0.87;0.87;0.87	5.03	4.1	0.47936	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.329188	0.28871	N	0.013871	T	0.63177	0.2489	M	0.81341	2.54	0.80722	D	1	D;P;D;P	0.71674	0.998;0.949;0.996;0.865	P;B;P;B	0.62184	0.899;0.275;0.819;0.233	T	0.69139	-0.5224	10	0.66056	D	0.02	.	14.474	0.67535	0.0:0.8518:0.1482:0.0	.	375;316;501;528	B9DI81;B9DI82;O75038-2;O75038	.;.;.;PLCH2_HUMAN	L	501;528;528;375;316	ENSP00000397289:S501L;ENSP00000367747:S528L;ENSP00000367749:S528L	ENSP00000278878:S316L	S	+	2	0	PLCH2	2412558	1.000000	0.71417	0.958000	0.39756	0.901000	0.52897	5.514000	0.67043	1.083000	0.41159	0.561000	0.74099	TCG	.	.	none		0.542	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638	
PDLIM5	10611	hgsc.bcm.edu	37	4	95575792	95575792	+	Splice_Site	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:95575792G>A	ENST00000317968.4	+	10	1600		c.e10+1		PDLIM5_ENST00000437932.1_Splice_Site|PDLIM5_ENST00000514743.1_Splice_Site|PDLIM5_ENST00000542407.1_Splice_Site|PDLIM5_ENST00000380176.3_Splice_Site	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5						regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		GATCCTTGGAGTAAGTATTGG	0.348																																					.		Atlas-SNP	.											.	PDLIM5	76	.	0			c.1464+1G>A						PASS	.						110.0	112.0	111.0					4																	95575792		2203	4300	6503	SO:0001630	splice_region_variant	10611	exon10			CTTGGAGTAAGTA	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.1464+1G>A	4.37:g.95575792G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	200	45	0.225	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Splice_Site	SNP	ENST00000317968.4	37	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.666750	0.88251	.	.	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.452	0.99131	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDLIM5	95794815	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.832000	0.99423	2.838000	0.97847	0.591000	0.81541	.	.	.	none		0.348	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		Intron
DEPDC5	9681	hgsc.bcm.edu	37	22	32257381	32257381	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr22:32257381C>T	ENST00000382112.3	+	32	3335	c.3265C>T	c.(3265-3267)Cgc>Tgc	p.R1089C	DEPDC5_ENST00000266091.3_Intron|DEPDC5_ENST00000400249.2_Intron|DEPDC5_ENST00000535622.1_Intron|DEPDC5_ENST00000539165.1_Intron|DEPDC5_ENST00000400248.2_Intron|DEPDC5_ENST00000382105.2_Missense_Mutation_p.R1020C|DEPDC5_ENST00000382111.2_Missense_Mutation_p.R1098C|DEPDC5_ENST00000494060.1_Intron|DEPDC5_ENST00000400246.1_Missense_Mutation_p.R1098C	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1098					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GGAGTTTGTCCGCAGCCCACG	0.577																																					p.R1098C		Atlas-SNP	.											.	DEPDC5	266	.	0			c.C3292T						PASS	.						80.0	71.0	73.0					22																	32257381		692	1591	2283	SO:0001583	missense	9681	exon33			TTTGTCCGCAGCC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3265C>T	22.37:g.32257381C>T	ENSP00000371546:p.Arg1089Cys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	115	38	0.330435	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671763	0.88348	.	.	ENSG00000100150	ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111	T;T;T;T	0.35973	1.73;1.28;1.77;1.73	5.51	5.51	0.81932	.	0.000000	0.37437	U	0.002098	T	0.44456	0.1294	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.71674	0.994;0.993;0.998;0.993	P;B;P;B	0.56700	0.731;0.446;0.804;0.348	T	0.36939	-0.9727	10	0.59425	D	0.04	.	17.9698	0.89110	0.0:1.0:0.0:0.0	.	419;1098;484;1089	B4DSS1;B9EGN9;O75140-7;A8MPX9	.;.;.;.	C	1098;1020;1089;1098	ENSP00000383105:R1098C;ENSP00000371539:R1020C;ENSP00000371546:R1089C;ENSP00000371545:R1098C	ENSP00000371539:R1020C	R	+	1	0	DEPDC5	30587381	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.620000	0.61226	2.598000	0.87819	0.650000	0.86243	CGC	.	.	none		0.577	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
TGFBR3	7049	hgsc.bcm.edu	37	1	92262875	92262875	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:92262875G>A	ENST00000525962.1	-	2	276	c.215C>T	c.(214-216)gCa>gTa	p.A72V	TGFBR3_ENST00000370399.2_Missense_Mutation_p.A72V|TGFBR3_ENST00000212355.4_Missense_Mutation_p.A72V			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	72					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		CCCCTGGCCTGCAGTGCGGAG	0.582																																					p.A72V		Atlas-SNP	.											.	TGFBR3	103	.	0			c.C215T						PASS	.						129.0	135.0	133.0					1																	92262875		2203	4300	6503	SO:0001583	missense	7049	exon4			TGGCCTGCAGTGC	L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"""Proteoglycans / Cell surface : Other"""	11774	protein-coding gene	gene with protein product	"""betaglycan proteoglycan"""	600742	"""transforming growth factor, beta receptor III (betaglycan, 300kDa)"""			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.215C>T	1.37:g.92262875G>A	ENSP00000436127:p.Ala72Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	147	63	0.428571	NM_001195684	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Missense_Mutation	SNP	ENST00000525962.1	37	CCDS30770.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.973422	0.34848	.	.	ENSG00000069702	ENST00000212355;ENST00000370399;ENST00000525962;ENST00000465892	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.57	0.33	0.15929	.	1.116350	0.06529	N	0.741131	T	0.09730	0.0239	L	0.36672	1.1	0.09310	N	1	B;B	0.23249	0.082;0.037	B;B	0.28011	0.085;0.025	T	0.43475	-0.9389	10	0.59425	D	0.04	0.0	4.6991	0.12818	0.0674:0.2453:0.4336:0.2537	.	72;72	Q03167-2;Q03167	.;TGBR3_HUMAN	V	72	ENSP00000212355:A72V;ENSP00000359426:A72V;ENSP00000436127:A72V;ENSP00000432638:A72V	ENSP00000212355:A72V	A	-	2	0	TGFBR3	92035463	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.743000	0.26231	-0.177000	0.10690	-0.182000	0.12963	GCA	.	.	none		0.582	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243	
MFSD6	54842	hgsc.bcm.edu	37	2	191301341	191301341	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:191301341C>T	ENST00000392328.1	+	3	910	c.586C>T	c.(586-588)Cgt>Tgt	p.R196C	MFSD6_ENST00000281416.7_Missense_Mutation_p.R196C	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	196					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						ACCAAAAATGCGTGAGAAAAG	0.458																																					p.R196C		Atlas-SNP	.											MFSD6,caecum,carcinoma,0,1	MFSD6	58	1	0			c.C586T						PASS	.						76.0	83.0	81.0					2																	191301341		2203	4300	6503	SO:0001583	missense	54842	exon3			AAAATGCGTGAGA		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.586C>T	2.37:g.191301341C>T	ENSP00000376141:p.Arg196Cys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	99	63	0.636364	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	C	9.956	1.221465	0.22457	.	.	ENSG00000151690	ENST00000392328;ENST00000281416	T;T	0.35048	1.33;1.33	5.39	3.57	0.40892	Major facilitator superfamily domain, general substrate transporter (1);	0.219617	0.41605	D	0.000844	T	0.37758	0.1015	L	0.48642	1.525	0.41426	D	0.987836	D	0.71674	0.998	P	0.49528	0.614	T	0.18272	-1.0342	10	0.54805	T	0.06	-5.0941	10.2208	0.43196	0.154:0.6982:0.1478:0.0	.	196	Q6ZSS7	MFSD6_HUMAN	C	196	ENSP00000376141:R196C;ENSP00000281416:R196C	ENSP00000281416:R196C	R	+	1	0	MFSD6	191009586	0.045000	0.20229	0.002000	0.10522	0.075000	0.17131	1.907000	0.39897	0.823000	0.34589	-0.133000	0.14855	CGT	.	.	none		0.458	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
PRB2	653247	hgsc.bcm.edu	37	12	11545937	11545937	+	Missense_Mutation	SNP	C	C	G	rs367874175	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:11545937C>G	ENST00000389362.4	-	3	1110	c.1075G>C	c.(1075-1077)Gcc>Ccc	p.A359P	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	359	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGAGATCGGGCACTTCGGGAC	0.602																																					p.A359P		Atlas-SNP	.											PRB2_ENST00000389362,brain,glioma,0,2	PRB2	168	2	0			c.G1075C						scavenged	.						206.0	230.0	222.0					12																	11545937		2203	4300	6503	SO:0001583	missense	653247	exon3			ATCGGGCACTTCG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.1075G>C	12.37:g.11545937C>G	ENSP00000374013:p.Ala359Pro	Somatic	830	10	0.0120482		WXS	Illumina HiSeq	Phase_I	985	30	0.0304569	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	0.008	-1.864195	0.00552	.	.	ENSG00000121335	ENST00000389362	T	0.03358	3.96	0.862	-1.72	0.08107	.	.	.	.	.	T	0.01387	0.0045	N	0.01705	-0.755	0.09310	N	1	B	0.20780	0.048	B	0.19391	0.025	T	0.46048	-0.9219	9	0.27785	T	0.31	.	4.4192	0.11472	0.3727:0.6273:0.0:0.0	.	359	P02812	PRB2_HUMAN	P	359	ENSP00000374013:A359P	ENSP00000374013:A359P	A	-	1	0	PRB2	11437204	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-2.967000	0.00669	-1.539000	0.01732	-1.549000	0.00901	GCC	.	.	weak		0.602	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
VANGL1	81839	hgsc.bcm.edu	37	1	116206843	116206843	+	Missense_Mutation	SNP	C	C	T	rs199932833		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:116206843C>T	ENST00000355485.2	+	4	1037	c.766C>T	c.(766-768)Cgc>Tgc	p.R256C	VANGL1_ENST00000369509.1_Missense_Mutation_p.R256C|VANGL1_ENST00000310260.3_Missense_Mutation_p.R256C|VANGL1_ENST00000369510.4_Missense_Mutation_p.R254C	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	256					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GCAGGTGGTCCGCTCCACCGA	0.597																																					p.R256C		Atlas-SNP	.											.	VANGL1	65	.	0			c.C766T						PASS	.						53.0	50.0	51.0					1																	116206843		2203	4300	6503	SO:0001583	missense	81839	exon4			GTGGTCCGCTCCA	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"""vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)"", ""vang-like 1 (van gogh, Drosophila)"""			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.766C>T	1.37:g.116206843C>T	ENSP00000347672:p.Arg256Cys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	96	34	0.354167	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631358	0.87660	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.93969	0.8069	M	0.90198	3.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94379	0.7603	10	0.87932	D	0	-0.3431	15.0586	0.71933	0.1419:0.8581:0.0:0.0	.	254;256	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	C	256;254;256;256	ENSP00000347672:R256C;ENSP00000358523:R254C;ENSP00000310800:R256C;ENSP00000358522:R256C	ENSP00000310800:R256C	R	+	1	0	VANGL1	116008366	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.621000	0.67743	2.879000	0.98667	0.650000	0.86243	CGC	.	.	weak		0.597	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1		
SLC25A44	9673	hgsc.bcm.edu	37	1	156182902	156182902	+	IGR	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:156182902T>C	ENST00000359511.4	+	0	3482				PMF1_ENST00000368279.3_Silent_p.I32I|PMF1_ENST00000368277.3_Silent_p.I32I|PMF1-BGLAP_ENST00000490491.1_Silent_p.I32I|PMF1-BGLAP_ENST00000320139.5_Silent_p.I32I|PMF1_ENST00000368273.4_Silent_p.I32I|PMF1-BGLAP_ENST00000368276.4_Silent_p.I32I|PMF1_ENST00000567140.1_Silent_p.I32I|PMF1_ENST00000565805.1_Silent_p.I32I	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN	solute carrier family 25, member 44						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Hepatocellular(266;0.158)					GCACTACCATTTCGAGGGTGA	0.572																																					p.I32I		Atlas-SNP	.											.	.	.	.	0			c.T96C						PASS	.						91.0	84.0	86.0					1																	156182902		2203	4300	6503	SO:0001628	intergenic_variant	100527963	exon1			TACCATTTCGAGG	AB007915	CCDS1133.1, CCDS72943.1	1q22	2013-05-22			ENSG00000160785	ENSG00000160785		"""Solute carriers"""	29036	protein-coding gene	gene with protein product		610824				16949250	Standard	NM_001286184		Approved	FLJ90431, KIAA0446	uc001fnp.3	Q96H78	OTTHUMG00000014816		1.37:g.156182902T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_001199664	O75034	Silent	SNP	ENST00000359511.4	37	CCDS1133.1																																																																																			.	.	none		0.572	SLC25A44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040856.1	NM_014655	
MUC2	4583	hgsc.bcm.edu	37	11	1092800	1092800	+	Missense_Mutation	SNP	T	T	G	rs200412404	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:1092800T>G	ENST00000441003.2	+	30	4646	c.4619T>G	c.(4618-4620)aTc>aGc	p.I1540S	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.I1541S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accactcccatcaccaccacc	0.632													t|||	1837	0.366813	0.3714	0.3804	5008	,	,		6221	0.3532		0.332	False		,,,				2504	0.4008				p.I1540S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,4	MUC2	614	4	0			c.T4619G						scavenged	.						46.0	100.0	81.0					11																	1092800		1619	2882	4501	SO:0001583	missense	4583	exon30			CTCCCATCACCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4619T>G	11.37:g.1092800T>G	ENSP00000415183:p.Ile1540Ser	Somatic	25	18	0.72		WXS	Illumina HiSeq	Phase_I	30	21	0.7	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	t	3.637	-0.074328	0.07184	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13778	2.6;2.56	1.6	-1.26	0.09376	.	0.514693	0.14353	U	0.324963	T	0.04543	0.0124	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43114	-0.9411	9	0.06494	T	0.89	.	5.8358	0.18607	0.0:0.509:0.3489:0.1421	.	1540	E7EUV1	.	S	1540;1541	ENSP00000415183:I1540S;ENSP00000351956:I1541S	ENSP00000351956:I1541S	I	+	2	0	MUC2	1082800	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.045000	0.14013	-0.383000	0.07858	0.000000	0.15137	ATC	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TAPT1	202018	hgsc.bcm.edu	37	4	16165117	16165117	+	Silent	SNP	T	T	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:16165117T>C	ENST00000405303.2	-	14	1601	c.1518A>G	c.(1516-1518)caA>caG	p.Q506Q	TAPT1_ENST00000304584.8_3'UTR|TAPT1_ENST00000399920.3_Silent_p.Q395Q	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	506					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)			NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						GATGAATAGGTTGTTTGGTGA	0.363																																					p.Q506Q		Atlas-SNP	.											.	TAPT1	31	.	0			c.A1518G						PASS	.						92.0	87.0	88.0					4																	16165117		1875	4124	5999	SO:0001819	synonymous_variant	202018	exon14			AATAGGTTGTTTG	AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.1518A>G	4.37:g.16165117T>C		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	209	45	0.215311	NM_153365	Q8N2S3|Q9NZK9	Silent	SNP	ENST00000405303.2	37	CCDS47030.1																																																																																			.	.	none		0.363	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365	
RAB22A	57403	hgsc.bcm.edu	37	20	56928537	56928537	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:56928537G>A	ENST00000244040.3	+	5	601	c.320G>A	c.(319-321)gGc>gAc	p.G107D		NM_020673.2	NP_065724.1	Q9UL26	RB22A_HUMAN	RAB22A, member RAS oncogene family	107					endocytosis (GO:0006897)|endosome organization (GO:0007032)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(1)|large_intestine(2)|pancreas(1)	6	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)			CGACAGCATGGCCCACCTAAT	0.368																																					p.G107D		Atlas-SNP	.											.	RAB22A	15	.	0			c.G320A						PASS	.						116.0	110.0	112.0					20																	56928537		2203	4300	6503	SO:0001583	missense	57403	exon5			AGCATGGCCCACC	AF091034	CCDS33497.1	20q13	2008-07-03			ENSG00000124209	ENSG00000124209		"""RAB, member RAS oncogene"""	9764	protein-coding gene	gene with protein product		612966					Standard	NM_020673		Approved		uc002xyz.3	Q9UL26	OTTHUMG00000032844	ENST00000244040.3:c.320G>A	20.37:g.56928537G>A	ENSP00000244040:p.Gly107Asp	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	207	84	0.405797	NM_020673	B3KR86|E1P605|Q8TF12|Q9H4E6	Missense_Mutation	SNP	ENST00000244040.3	37	CCDS33497.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970755	0.92919	.	.	ENSG00000124209	ENST00000244040	T	0.76448	-1.02	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84665	0.5522	L	0.37466	1.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85299	0.1072	10	0.87932	D	0	-23.3447	20.3081	0.98638	0.0:0.0:1.0:0.0	.	107	Q9UL26	RB22A_HUMAN	D	107	ENSP00000244040:G107D	ENSP00000244040:G107D	G	+	2	0	RAB22A	56361943	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.795000	0.96236	0.655000	0.94253	GGC	.	.	none		0.368	RAB22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079880.2		
AIM1	202	hgsc.bcm.edu	37	6	106968969	106968969	+	Missense_Mutation	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:106968969T>G	ENST00000369066.3	+	2	3149	c.2662T>G	c.(2662-2664)Ttg>Gtg	p.L888V		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GCCCTGTGGTTTGAACAAAGA	0.478																																					p.L888V		Atlas-SNP	.											.	AIM1	161	.	0			c.T2662G						PASS	.						79.0	84.0	83.0					6																	106968969		2203	4300	6503	SO:0001583	missense	202	exon2			TGTGGTTTGAACA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2662T>G	6.37:g.106968969T>G	ENSP00000358062:p.Leu888Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	65	56	0.861538	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	0.856	-0.736842	0.03111	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71341	-0.56	5.99	0.485	0.16830	.	1.843970	0.02402	N	0.080812	T	0.33089	0.0851	N	0.22421	0.69	0.09310	N	0.99999	B	0.17667	0.023	B	0.14023	0.01	T	0.08146	-1.0736	10	0.32370	T	0.25	.	5.9215	0.19084	0.2723:0.0:0.2831:0.4446	.	888	Q9Y4K1	AIM1_HUMAN	V	1296;888	ENSP00000358062:L888V	ENSP00000285105:L1296V	L	+	1	2	AIM1	107075662	0.951000	0.32395	0.000000	0.03702	0.986000	0.74619	0.678000	0.25277	-0.127000	0.11661	0.533000	0.62120	TTG	.	.	none		0.478	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
MAGI1	9223	hgsc.bcm.edu	37	3	65415776	65415776	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:65415776C>T	ENST00000497477.2	-	12	1585	c.1586G>A	c.(1585-1587)gGa>gAa	p.G529E	MAGI1_ENST00000483466.1_Missense_Mutation_p.G529E|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000402939.2_Missense_Mutation_p.G529E|MAGI1_ENST00000330909.8_Missense_Mutation_p.G529E			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	529	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		ATGTGTGTGTCCCAAAACACA	0.468																																					p.G529E		Atlas-SNP	.											.	MAGI1	481	.	0			c.G1586A						PASS	.						87.0	72.0	77.0					3																	65415776		2203	4300	6503	SO:0001583	missense	9223	exon12			GTGTGTCCCAAAA	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1586G>A	3.37:g.65415776C>T	ENSP00000424369:p.Gly529Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.210525|5.210525	0.95069|0.95069	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477;ENST00000472257	.|T;T;T;T;T;T	.|0.54479	.|0.57;0.57;0.57;0.57;0.57;0.57	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78375|0.78375	0.4273|0.4273	M|M	0.87038|0.87038	2.855|2.855	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|1.0;0.999;1.0;1.0;1.0	T|T	0.80271|0.80271	-0.1452|-0.1452	5|10	.|0.66056	.|D	.|0.02	-12.8008|-12.8008	20.3065|20.3065	0.98633|0.98633	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|529;529;529;529;529	.|Q96QZ7-6;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;.;.;.;.	N|E	410|529;529;425;404;529;529;315	.|ENSP00000385450:G529E;ENSP00000331157:G529E;ENSP00000418177:G404E;ENSP00000420323:G529E;ENSP00000424369:G529E;ENSP00000420796:G315E	.|ENSP00000331157:G529E	D|G	-|-	1|2	0|0	MAGI1|MAGI1	65390816|65390816	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.818000|7.818000	0.86416|0.86416	2.809000|2.809000	0.96659|0.96659	0.650000|0.650000	0.86243|0.86243	GAC|GGA	.	.	none		0.468	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:1643066A>G	ENST00000399682.1	-	1	302	c.258T>C	c.(256-258)ggT>ggC	p.G86G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G86G(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCTTGGAACCCCCACAAG	0.667																																					p.G86G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,3	KRTAP5-4	78	3	1	Substitution - coding silent(1)	endometrium(1)	c.T258C						scavenged	.						9.0	15.0	13.0					11																	1643066		683	1577	2260	SO:0001819	synonymous_variant	387267	exon1			CTTGGAACCCCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.258T>C	11.37:g.1643066A>G		Somatic	98	4	0.0408163		WXS	Illumina HiSeq	Phase_I	87	10	0.114943	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
PIM1	5292	hgsc.bcm.edu	37	6	37138242	37138242	+	5'UTR	SNP	G	G	C	rs146002992		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138242G>C	ENST00000373509.5	+	0	264					NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase						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)			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)	gccacccgcagccacagccac	0.746			T	BCL6	NHL																																p.S55T		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G164C						PASS	.																																			SO:0001623	5_prime_UTR_variant	5292	exon1			CCCGCAGCCACAG		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.-110G>C	6.37:g.37138242G>C		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.746	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
CACNA2D3	55799	hgsc.bcm.edu	37	3	54798316	54798316	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:54798316C>T	ENST00000474759.1	+	13	1366	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	CACNA2D3_ENST00000288197.5_Missense_Mutation_p.R440W|CACNA2D3_ENST00000490478.1_Missense_Mutation_p.R346W|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.R440W	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	440						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CGTGCTTAGCCGGCCCAAAGT	0.517																																					p.R440W		Atlas-SNP	.											CACNA2D3,caecum,carcinoma,-2,1	CACNA2D3	159	1	0			c.C1318T						PASS	.						136.0	132.0	133.0					3																	54798316		2065	4199	6264	SO:0001583	missense	55799	exon13			CTTAGCCGGCCCA	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1318C>T	3.37:g.54798316C>T	ENSP00000419101:p.Arg440Trp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	46	12	0.26087	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857144	0.91433	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	T;T;T;T	0.14391	2.51;2.51;2.51;2.56	5.95	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.28034	0.0691	L	0.32530	0.975	0.58432	D	0.999998	D	0.89917	1.0	D	0.75020	0.985	T	0.03296	-1.1051	10	0.87932	D	0	.	16.492	0.84203	0.1322:0.8678:0.0:0.0	.	440	Q8IZS8	CA2D3_HUMAN	W	440;440;440;346;346;345	ENSP00000389506:R440W;ENSP00000419101:R440W;ENSP00000288197:R440W;ENSP00000417279:R346W	ENSP00000288197:R440W	R	+	1	2	CACNA2D3	54773356	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.348000	0.59379	1.502000	0.48669	0.650000	0.86243	CGG	.	.	none		0.517	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
ETFDH	2110	hgsc.bcm.edu	37	4	159601621	159601621	+	Missense_Mutation	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:159601621T>G	ENST00000511912.1	+	2	369	c.37T>G	c.(37-39)Tat>Gat	p.Y13D	ETFDH_ENST00000307738.5_Intron	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	13					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		TTGTGCAGCATATCAGTGCTT	0.308																																					p.Y13D		Atlas-SNP	.											.	ETFDH	57	.	0			c.T37G						PASS	.						69.0	65.0	66.0					4																	159601621		2203	4300	6503	SO:0001583	missense	2110	exon2			GCAGCATATCAGT	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.37T>G	4.37:g.159601621T>G	ENSP00000426638:p.Tyr13Asp	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	339	209	0.616519	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	37	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990778	0.35131	.	.	ENSG00000171503	ENST00000511912	D	0.97186	-4.28	5.63	1.57	0.23409	.	0.343116	0.34435	N	0.003961	D	0.92237	0.7538	L	0.29908	0.895	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	D	0.85706	0.1316	10	0.36615	T	0.2	0.1782	7.7593	0.28942	0.0:0.403:0.0:0.597	.	13	Q16134	ETFD_HUMAN	D	13	ENSP00000426638:Y13D	ENSP00000426638:Y13D	Y	+	1	0	ETFDH	159821071	0.697000	0.27767	0.728000	0.30774	0.906000	0.53458	0.223000	0.17719	0.503000	0.28060	-0.376000	0.06991	TAT	.	.	none		0.308	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
SACS	26278	hgsc.bcm.edu	37	13	23913163	23913163	+	Missense_Mutation	SNP	A	A	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr13:23913163A>G	ENST00000382292.3	-	9	5125	c.4852T>C	c.(4852-4854)Ttc>Ctc	p.F1618L	SACS_ENST00000382298.3_Missense_Mutation_p.F1618L|SACS_ENST00000402364.1_Missense_Mutation_p.F868L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1618					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AATGGTTTGAACTGATTAGGA	0.338																																					p.F1618L		Atlas-SNP	.											.	SACS	871	.	0			c.T4852C						PASS	.						91.0	88.0	89.0					13																	23913163		2203	4299	6502	SO:0001583	missense	26278	exon10			GTTTGAACTGATT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.4852T>C	13.37:g.23913163A>G	ENSP00000371729:p.Phe1618Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	20.8	4.058297	0.76074	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.94793	-3.52;-3.52;-3.52	5.84	5.84	0.93424	ATPase-like, ATP-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.94804	0.8322	L	0.55481	1.735	0.53688	D	0.999977	P	0.39717	0.684	P	0.48334	0.574	D	0.94681	0.7865	10	0.52906	T	0.07	.	16.2302	0.82332	1.0:0.0:0.0:0.0	.	1618	Q9NZJ4	SACS_HUMAN	L	1618;868;1618	ENSP00000371729:F1618L;ENSP00000385844:F868L;ENSP00000371735:F1618L	ENSP00000371729:F1618L	F	-	1	0	SACS	22811163	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	8.962000	0.93254	2.228000	0.72767	0.533000	0.62120	TTC	.	.	none		0.338	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
SLC1A6	6511	hgsc.bcm.edu	37	19	15073065	15073065	+	Missense_Mutation	SNP	G	G	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:15073065G>T	ENST00000221742.3	-	5	691	c.684C>A	c.(682-684)ttC>ttA	p.F228L	SLC1A6_ENST00000598504.1_Missense_Mutation_p.F228L|SLC1A6_ENST00000430939.2_Missense_Mutation_p.F164L|SLC1A6_ENST00000544886.2_Missense_Mutation_p.F228L|SLC1A6_ENST00000600144.1_Missense_Mutation_p.F228L	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	228					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						TCTCCACTGAGAATGGAGGAG	0.567																																					p.F228L		Atlas-SNP	.											.	SLC1A6	111	.	0			c.C684A						PASS	.						111.0	105.0	107.0					19																	15073065		2203	4300	6503	SO:0001583	missense	6511	exon8			CACTGAGAATGGA		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.684C>A	19.37:g.15073065G>T	ENSP00000221742:p.Phe228Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_001272087	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	g	3.890	-0.024160	0.07634	.	.	ENSG00000105143	ENST00000430939;ENST00000221742;ENST00000544886	T;T;T	0.69306	-0.39;0.67;1.4	4.42	0.947	0.19555	.	0.359970	0.28332	N	0.015725	T	0.31009	0.0783	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.17098	0.017;0.0;0.0	T	0.25012	-1.0144	10	0.08179	T	0.78	-12.7775	5.5234	0.16945	0.3711:0.0:0.6289:0.0	.	164;228;228	E7EV13;Q8N753;P48664	.;.;EAA4_HUMAN	L	164;228;228	ENSP00000409386:F164L;ENSP00000221742:F228L;ENSP00000446175:F228L	ENSP00000221742:F228L	F	-	3	2	SLC1A6	14934065	0.812000	0.29077	0.300000	0.25030	0.783000	0.44284	0.099000	0.15210	0.513000	0.28278	0.454000	0.30748	TTC	.	.	none		0.567	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
NGLY1	55768	hgsc.bcm.edu	37	3	25781094	25781094	+	Silent	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:25781094G>A	ENST00000280700.5	-	5	1015	c.855C>T	c.(853-855)gcC>gcT	p.A285A	NGLY1_ENST00000417874.2_Silent_p.A243A|NGLY1_ENST00000422724.2_Intron|NGLY1_ENST00000428257.1_Silent_p.A285A|NGLY1_ENST00000396649.3_Silent_p.A285A	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	285					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						TGAACTGGCAGGCATCACAGT	0.423																																					p.A285A		Atlas-SNP	.											.	NGLY1	57	.	0			c.C855T						PASS	.						154.0	121.0	132.0					3																	25781094		2203	4300	6503	SO:0001819	synonymous_variant	55768	exon5			CTGGCAGGCATCA	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.855C>T	3.37:g.25781094G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	155	14	0.0903226	NM_018297	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Silent	SNP	ENST00000280700.5	37	CCDS33719.1																																																																																			.	.	none		0.423	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2		
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296201	39296201	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:39296201C>T	ENST00000345847.4	-	1	538	c.539G>A	c.(538-540)tGc>tAc	p.C180Y		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	180						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						AGTGGTGTGGCAGGAGACTCG	0.632																																					p.C180Y		Atlas-SNP	.											.	KRTAP4-6	46	.	0			c.G539A						PASS	.																																			SO:0001583	missense	81871	exon1			GTGTGGCAGGAGA	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.539G>A	17.37:g.39296201C>T	ENSP00000328270:p.Cys180Tyr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	.	.	.	.	.	.	.	.	.	.	.	10.68	1.418268	0.25552	.	.	ENSG00000198090	ENST00000345847	T	0.00628	6.11	3.66	3.66	0.41972	.	0.000000	0.39909	U	0.001229	T	0.02888	0.0086	M	0.83312	2.635	0.42816	D	0.993973	.	.	.	.	.	.	T	0.49322	-0.8952	8	0.52906	T	0.07	.	13.7444	0.62865	0.0:1.0:0.0:0.0	.	.	.	.	Y	180	ENSP00000328270:C180Y	ENSP00000328270:C180Y	C	-	2	0	KRTAP4-6	36549727	0.000000	0.05858	1.000000	0.80357	0.051000	0.14879	-0.647000	0.05397	2.344000	0.79699	0.558000	0.71614	TGC	.	.	none		0.632	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
CEP112	201134	hgsc.bcm.edu	37	17	64125942	64125942	+	Splice_Site	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:64125942C>A	ENST00000392769.2	-	6	783		c.e6-1		CEP112_ENST00000537949.1_Splice_Site|CEP112_ENST00000535342.2_Splice_Site	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa						receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						AATAAACTTCCTGAAATACAa	0.333																																					.		Atlas-SNP	.											.	CEP112	192	.	0			c.565-1G>T						PASS	.						59.0	60.0	60.0					17																	64125942		2202	4299	6501	SO:0001630	splice_region_variant	201134	exon7			AACTTCCTGAAAT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.565-1G>T	17.37:g.64125942C>A		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	290	141	0.486207	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Splice_Site	SNP	ENST00000392769.2	37	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843859	0.32606	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000537949	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5104	0.67784	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CEP112	61556404	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	4.453000	0.60061	2.493000	0.84123	0.650000	0.86243	.	.	.	none		0.333	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	Intron
LTB	4050	hgsc.bcm.edu	37	6	31549597	31549597	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:31549597C>T	ENST00000429299.2	-	2	209	c.202G>A	c.(202-204)Gga>Aga	p.G68R	LTB_ENST00000483972.1_Intron|LTB_ENST00000446745.2_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	68				DPGAQAQQGL -> GLSAPGSGRT (in Ref. 2; AAB37342). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						TTACCCAGTCCTTGCTGGGCC	0.622																																					p.G68R		Atlas-SNP	.											LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	0			c.G202A						PASS	.						93.0	102.0	99.0					6																	31549597		1510	2708	4218	SO:0001583	missense	4050	exon2			CCAGTCCTTGCTG	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.202G>A	6.37:g.31549597C>T	ENSP00000410481:p.Gly68Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.398347	0.25205	.	.	ENSG00000227507	ENST00000429299	T	0.20200	2.09	5.45	2.51	0.30379	.	1.717780	0.03086	N	0.159154	T	0.02230	0.0069	N	0.01668	-0.77	0.09310	N	0.999994	B	0.06786	0.001	B	0.08055	0.003	T	0.34725	-0.9817	10	0.15952	T	0.53	1.0706	8.1037	0.30872	0.0:0.5863:0.2923:0.1214	.	68	Q06643	TNFC_HUMAN	R	68	ENSP00000410481:G68R	ENSP00000410481:G68R	G	-	1	0	LTB	31657576	0.038000	0.19896	0.101000	0.21167	0.840000	0.47671	0.893000	0.28336	0.656000	0.30886	0.655000	0.94253	GGA	.	.	none		0.622	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
APMAP	57136	hgsc.bcm.edu	37	20	24959519	24959519	+	Splice_Site	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:24959519C>T	ENST00000217456.2	-	3	503		c.e3-1		APMAP_ENST00000447138.1_Splice_Site	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein						biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										TTCTTTGAAGCTGCAAAATAA	0.438																																					.		Atlas-SNP	.											.	APMAP	3	.	0			c.213-1G>A						PASS	.						45.0	48.0	47.0					20																	24959519		2203	4300	6503	SO:0001630	splice_region_variant	57136	exon4			TTGAAGCTGCAAA	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.213-1G>A	20.37:g.24959519C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Splice_Site	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116208	0.77323	.	.	ENSG00000101474	ENST00000451442;ENST00000217456;ENST00000447138	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0204	0.80478	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C20orf3	24907519	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.018000	0.76406	2.642000	0.89623	0.561000	0.74099	.	.	.	none		0.438	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	Intron
FOXD4	2298	hgsc.bcm.edu	37	9	117303	117303	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:117303C>T	ENST00000382500.2	-	1	1114	c.817G>A	c.(817-819)Gcc>Acc	p.A273T		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	273	Pro-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CCGGCATAGGCGGGGGCCGAG	0.701																																					p.A273T		Atlas-SNP	.											.	FOXD4	75	.	0			c.G817A						PASS	.						21.0	29.0	26.0					9																	117303		1510	3118	4628	SO:0001583	missense	2298	exon1			CATAGGCGGGGGC	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.817G>A	9.37:g.117303C>T	ENSP00000371940:p.Ala273Thr	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	16	5	0.3125	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	9.647	1.140578	0.21205	.	.	ENSG00000170122	ENST00000382500	D	0.95035	-3.59	2.41	0.42	0.16444	.	0.439500	0.16007	U	0.234007	D	0.86372	0.5917	N	0.20986	0.625	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.75025	-0.3463	10	0.45353	T	0.12	.	3.4329	0.07434	0.0:0.5061:0.2126:0.2813	.	273	Q12950	FOXD4_HUMAN	T	273	ENSP00000371940:A273T	ENSP00000371940:A273T	A	-	1	0	FOXD4	107303	0.006000	0.16342	0.009000	0.14445	0.007000	0.05969	-0.062000	0.11674	-0.061000	0.13110	-0.751000	0.03497	GCC	.	.	none		0.701	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
GRID1	2894	hgsc.bcm.edu	37	10	87614258	87614258	+	Missense_Mutation	SNP	G	G	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr10:87614258G>A	ENST00000327946.7	-	8	1313	c.1228C>T	c.(1228-1230)Cgc>Tgc	p.R410C		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	410					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.R410S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CTTACCTTGCGCATGTCTTTG	0.512										Multiple Myeloma(13;0.14)																											p.R410C		Atlas-SNP	.											GRID1,right_upper_lobe,carcinoma,0,2	GRID1	204	2	1	Substitution - Missense(1)	lung(1)	c.C1228T						PASS	.						129.0	112.0	118.0					10																	87614258		2203	4300	6503	SO:0001583	missense	2894	exon8			CCTTGCGCATGTC	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1228C>T	10.37:g.87614258G>A	ENSP00000330148:p.Arg410Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055667	0.75960	.	.	ENSG00000182771	ENST00000327946	D	0.86694	-2.16	5.79	3.93	0.45458	.	0.558823	0.17213	N	0.182625	T	0.78786	0.4338	N	0.24115	0.695	0.80722	D	1	B	0.15719	0.014	B	0.06405	0.002	T	0.72769	-0.4193	10	0.87932	D	0	.	10.416	0.44322	0.0696:0.0:0.7963:0.1341	.	410	Q9ULK0	GRID1_HUMAN	C	410	ENSP00000330148:R410C	ENSP00000330148:R410C	R	-	1	0	GRID1	87604238	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.806000	0.62569	0.782000	0.33613	0.563000	0.77884	CGC	.	.	none		0.512	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
KIF6	221458	hgsc.bcm.edu	37	6	39607449	39607449	+	Silent	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:39607449C>T	ENST00000287152.7	-	4	430	c.336G>A	c.(334-336)gaG>gaA	p.E112E	KIF6_ENST00000538893.1_Silent_p.E112E|KIF6_ENST00000373215.3_Silent_p.E112E|KIF6_ENST00000373216.3_Silent_p.E112E	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	112	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						CACTGTAACGCTCTGCACCCC	0.413																																					p.E112E		Atlas-SNP	.											.	KIF6	233	.	0			c.G336A						PASS	.						184.0	137.0	153.0					6																	39607449		2203	4300	6503	SO:0001819	synonymous_variant	221458	exon4			GTAACGCTCTGCA	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.336G>A	6.37:g.39607449C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	126	48	0.380952	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Silent	SNP	ENST00000287152.7	37	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	C	9.295	1.051571	0.19827	.	.	ENSG00000164627	ENST00000458470	.	.	.	5.67	-0.341	0.12639	.	.	.	.	.	T	0.43612	0.1255	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41980	-0.9478	4	.	.	.	.	10.5753	0.45223	0.0:0.4399:0.0:0.5601	.	.	.	.	N	4	.	.	S	-	2	0	KIF6	39715427	0.985000	0.35326	0.989000	0.46669	0.921000	0.55340	0.304000	0.19228	-0.138000	0.11434	-0.736000	0.03550	AGC	.	.	none		0.413	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
TENM3	55714	hgsc.bcm.edu	37	4	183650276	183650276	+	Missense_Mutation	SNP	T	T	G			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:183650276T>G	ENST00000511685.1	+	14	2650	c.2527T>G	c.(2527-2529)Ttc>Gtc	p.F843V	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.F843V			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	843					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TCGAATCAGTTTCCTTATAGG	0.418																																					p.F843V		Atlas-SNP	.											.	.	.	.	0			c.T2527G						PASS	.						113.0	110.0	111.0					4																	183650276		1918	4133	6051	SO:0001583	missense	55714	exon13			ATCAGTTTCCTTA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.2527T>G	4.37:g.183650276T>G	ENSP00000424226:p.Phe843Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	136	17	0.125	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.367200	0.41902	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.89810	-2.57;-2.57	4.84	4.84	0.62591	.	.	.	.	.	D	0.94291	0.8166	M	0.85710	2.77	0.80722	D	1	D	0.57899	0.981	D	0.65140	0.932	D	0.95185	0.8303	9	0.87932	D	0	.	14.8669	0.70422	0.0:0.0:0.0:1.0	.	843	Q9P273	TEN3_HUMAN	V	843	ENSP00000424226:F843V;ENSP00000385276:F843V	ENSP00000385276:F843V	F	+	1	0	ODZ3	183887270	1.000000	0.71417	0.946000	0.38457	0.603000	0.37013	5.991000	0.70602	2.154000	0.67381	0.460000	0.39030	TTC	.	.	none		0.418	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
SLITRK1	114798	hgsc.bcm.edu	37	13	84454425	84454425	+	Silent	SNP	C	C	A			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr13:84454425C>A	ENST00000377084.2	-	1	2103	c.1218G>T	c.(1216-1218)ctG>ctT	p.L406L		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	406					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		TATTGTTGCCCAGATCCAACA	0.453																																					p.L406L		Atlas-SNP	.											.	SLITRK1	196	.	0			c.G1218T						PASS	.						235.0	228.0	231.0					13																	84454425		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			GTTGCCCAGATCC	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1218G>T	13.37:g.84454425C>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	33	0.311321	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	37	CCDS9464.1																																																																																			.	.	none		0.453	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
OR52R1	119695	hgsc.bcm.edu	37	11	4825232	4825232	+	Missense_Mutation	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:4825232C>T	ENST00000356069.2	-	1	378	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.V206M	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGATAGCCACGTAGCAGTCC	0.557																																					p.V127M		Atlas-SNP	.											.	OR52R1	81	.	0			c.G379A						PASS	.						127.0	113.0	118.0					11																	4825232		2201	4298	6499	SO:0001583	missense	119695	exon1			TAGCCACGTAGCA	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.379G>A	11.37:g.4825232C>T	ENSP00000348368:p.Val127Met	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	C	14.11	2.438113	0.43326	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00366	7.79;7.79	5.42	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.182661	0.26731	N	0.022798	T	0.00936	0.0031	M	0.84773	2.715	0.29270	N	0.870731	D	0.89917	1.0	D	0.72338	0.977	T	0.15292	-1.0442	10	0.72032	D	0.01	.	9.1316	0.36848	0.1468:0.7743:0.0:0.079	.	127	Q8NGF1	O52R1_HUMAN	M	127;206	ENSP00000348368:V127M;ENSP00000369742:V206M	ENSP00000348368:V127M	V	-	1	0	OR52R1	4781808	0.001000	0.12720	0.999000	0.59377	0.167000	0.22549	0.028000	0.13644	2.826000	0.97356	0.650000	0.86243	GTG	.	.	none		0.557	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
FAM66D	100132923	hgsc.bcm.edu	37	8	11990866	11990866	+	RNA	SNP	T	T	A	rs183048633	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:11990866T>A	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		CAGGTAAGGGTCAAAGGTGTC	0.498													t|||	49	0.00978435	0.0	0.0202	5008	,	,		25451	0.0		0.0219	False		,,,				2504	0.0133				p.D218V		Atlas-SNP	.											.	.	.	.	0			c.A653T						PASS	.																																					392197	exon1			TAAGGGTCAAAGG			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990866T>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				T|0.993;A|0.007	0.007	strong		0.498	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
DLG2	1740	hgsc.bcm.edu	37	11	83770527	83770527	+	Splice_Site	SNP	C	C	T			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:83770527C>T	ENST00000532653.1	-	6	737	c.435G>A	c.(433-435)agG>agA	p.R145R	DLG2_ENST00000398309.2_Splice_Site_p.R145R|DLG2_ENST00000280241.8_Splice_Site_p.R184R|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000537455.1_5'UTR|DLG2_ENST00000418306.2_Splice_Site_p.R94R|DLG2_ENST00000543673.1_Splice_Site_p.R250R|DLG2_ENST00000524982.1_Splice_Site_p.R145R|DLG2_ENST00000398301.2_Splice_Site_p.R184R|DLG2_ENST00000376104.2_Splice_Site_p.R250R|DLG2_ENST00000330014.6_Splice_Site_p.R84R|DLG2_ENST00000531015.1_Splice_Site_p.R112R			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				AATCATTGACCCTGCAAGGAA	0.433																																					p.R250R		Atlas-SNP	.											.	DLG2	448	.	0			c.G750A						PASS	.						54.0	48.0	50.0					11																	83770527		1878	4117	5995	SO:0001630	splice_region_variant	1740	exon11			ATTGACCCTGCAA	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.435-1G>A	11.37:g.83770527C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	20	0.238095	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000532653.1	37																																																																																				.	.	none		0.433	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	Silent
MAN2B2	23324	hgsc.bcm.edu	37	4	6612851	6612851	+	Missense_Mutation	SNP	G	G	C			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:6612851G>C	ENST00000285599.3	+	15	2445	c.2409G>C	c.(2407-2409)tgG>tgC	p.W803C	MAN2B2_ENST00000504248.1_Missense_Mutation_p.W752C	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	803					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						ACTTCGACTGGGACCTGGGCT	0.652																																					p.W803C		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G2409C						PASS	.						58.0	58.0	58.0					4																	6612851		2203	4300	6503	SO:0001583	missense	23324	exon15			CGACTGGGACCTG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.2409G>C	4.37:g.6612851G>C	ENSP00000285599:p.Trp803Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	61	40	0.655738	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.50|14.50	2.554295|2.554295	0.45487|0.45487	.|.	.|.	ENSG00000013288|ENSG00000013288	ENST00000505907|ENST00000285599;ENST00000504248	.|D;D	.|0.83591	.|-1.74;-1.74	4.87|4.87	4.87|4.87	0.63330|0.63330	.|Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	.|0.126763	.|0.56097	.|D	.|0.000023	D|D	0.90164|0.90164	0.6926|0.6926	M|M	0.78801|0.78801	2.425|2.425	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.996	.|D;D;D	.|0.74348	.|0.974;0.983;0.917	D|D	0.90939|0.90939	0.4796|0.4796	5|10	.|0.59425	.|D	.|0.04	-9.7275|-9.7275	13.6149|13.6149	0.62101|0.62101	0.0:0.0:0.8445:0.1555|0.0:0.0:0.8445:0.1555	.|.	.|752;803;803	.|E9PCD7;Q9Y2E5;Q9Y2E5-2	.|.;MA2B2_HUMAN;.	A|C	802|803;752	.|ENSP00000285599:W803C;ENSP00000423129:W752C	.|ENSP00000285599:W803C	G|W	+|+	2|3	0|0	MAN2B2|MAN2B2	6663752|6663752	1.000000|1.000000	0.71417|0.71417	0.019000|0.019000	0.16419|0.16419	0.679000|0.679000	0.39708|0.39708	6.770000|6.770000	0.74990|0.74990	2.260000|2.260000	0.74910|0.74910	0.555000|0.555000	0.69702|0.69702	GGG|TGG	.	.	none		0.652	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
